Contacts of the helix formed by residues 114 - 138 (chain B) in PDB entry 1Q90
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY 3.3 27.6 - - - +
110B PHE* 3.8 3.2 - - - +
111B LYS 3.9 9.8 + - - +
113B PRO* 1.3 84.8 - - + +
115B GLU* 1.3 58.2 + - - +
116B LEU 3.1 3.6 - - - +
117B THR* 2.8 30.9 + - - +
118B TRP* 3.0 12.3 + - - +
206B ILE* 6.0 1.0 - - - +
209B GLN* 3.3 43.4 + - - +
210B GLY 2.5 25.1 + - - -
211B ILE 3.2 15.0 + - - -
212B SER* 3.3 19.5 - - - +
901B HEC 3.0 20.0 + - + +
21D GLY 2.7 28.7 + - - -
22D MET* 4.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE 3.7 13.9 - - - +
112B ARG* 3.0 31.7 - - - +
113B PRO* 2.7 44.5 + - - +
114B ARG* 1.3 73.0 - - - +
116B LEU* 1.3 60.1 + - + +
118B TRP* 3.2 5.4 + - - +
119B VAL* 2.9 31.2 + - - +
112D PRO* 4.0 26.3 - - + +
113D PHE* 4.3 24.0 - - + -
116D SER* 6.1 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG 3.1 0.8 - - - -
115B GLU* 1.3 77.7 - - + +
117B THR* 1.3 58.7 + - - +
119B VAL* 4.1 15.9 - - + -
120B THR* 2.7 41.6 + - + +
205B MET* 3.7 21.1 - - + -
113D PHE* 5.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 2.8 18.7 + - + +
116B LEU* 1.3 79.1 - - - +
118B TRP* 1.3 57.5 + - - +
120B THR* 2.8 19.8 + - - -
121B GLY 3.1 0.5 + - - -
202B HIS* 3.0 31.5 - - + +
205B MET* 3.6 25.6 - - - +
206B ILE* 3.8 18.3 + - + -
209B GLN* 3.6 14.4 + - - -
901B HEC 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.0 14.4 - - + -
104B VAL* 3.7 23.6 - - + -
105B TYR* 4.4 19.3 - + + -
110B PHE* 3.3 35.9 - + + -
114B ARG 3.0 9.9 + - - +
115B GLU* 3.5 9.0 - - - +
116B LEU 3.1 0.2 - - - -
117B THR* 1.3 76.2 - - - +
119B VAL* 1.3 68.1 + - - +
121B GLY* 3.0 3.5 + - - -
122B VAL* 2.9 32.9 + - + +
901B HEC 3.5 40.4 - - + +
108D LEU* 3.2 50.8 + - + -
109D ILE* 4.4 4.3 - - - -
111D VAL* 4.0 8.1 - - + -
112D PRO* 3.4 24.0 - - + +
910D CLA 4.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 2.9 21.7 + - - +
116B LEU* 3.1 18.6 + - + +
118B TRP* 1.3 78.6 - - + +
120B THR* 1.3 66.0 + - + +
122B VAL* 3.1 5.4 + - - +
123B ILE* 3.1 30.6 + - + +
109D ILE* 3.5 38.1 - - + +
113D PHE* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 2.7 22.6 + - + +
117B THR* 2.8 25.3 + - - -
119B VAL* 1.3 74.1 - - + +
121B GLY* 1.3 64.8 + - - +
123B ILE* 3.0 15.9 + - + +
124B MET* 2.9 26.3 + - - +
198B PHE* 4.4 23.5 - - + +
201B MET* 4.2 13.9 - - + -
202B HIS* 3.1 11.4 + - - -
205B MET* 3.2 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR 3.1 1.4 + - - -
118B TRP 3.0 8.5 + - - -
120B THR* 1.3 84.0 + - - +
122B VAL* 1.3 57.4 + - - +
124B MET* 2.9 8.7 + - - +
125B ALA 2.8 24.8 + - - -
202B HIS* 3.7 9.2 - - - -
901B HEC 2.9 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TRP* 2.9 43.1 + - + +
119B VAL 3.1 6.0 + - - +
121B GLY* 1.3 71.0 - - - +
123B ILE* 1.3 64.1 + - + +
125B ALA* 3.1 8.5 - - + +
126B VAL* 3.0 22.8 + - + +
901B HEC 3.6 19.3 - - + +
105D PRO* 4.0 34.8 - - + +
108D LEU* 4.6 11.4 - - + -
109D ILE* 4.2 21.8 - - + +
910D CLA 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.1 24.3 + - + +
120B THR* 3.0 12.8 + - + +
122B VAL* 1.3 75.5 - - - +
124B MET* 1.3 55.9 + - - +
126B VAL* 2.7 32.0 + - + +
127B CYS* 2.9 19.8 + - - -
198B PHE* 3.2 55.2 - - + -
109D ILE* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR 2.9 16.7 + - - +
121B GLY* 2.9 10.9 + - - +
123B ILE* 1.3 76.3 - - - +
125B ALA* 1.3 57.8 + - - +
127B CYS* 3.1 11.1 + - - +
128B THR* 2.8 36.6 + - - -
195B THR* 4.8 6.2 - - + +
198B PHE* 3.8 18.8 - - + +
199B MET* 3.1 65.5 - - + +
202B HIS* 3.8 27.4 - - + -
203B PHE* 5.2 0.2 - - + -
901B HEC 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.4 27.1 - - + +
121B GLY 2.8 5.9 + - - -
122B VAL* 3.1 16.6 - - + +
124B MET* 1.3 75.3 - - - +
126B VAL* 1.3 60.8 + - - +
128B THR* 3.5 1.7 + - - -
129B VAL* 3.0 28.8 + - - +
901B HEC 3.6 15.2 - - + +
108D LEU* 6.2 0.2 - - + -
910D CLA 3.1 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.0 17.5 + - + +
123B ILE* 2.7 18.3 + - + +
125B ALA* 1.3 70.7 - - + +
127B CYS* 1.3 56.1 + - - +
129B VAL* 3.3 6.5 + - - +
130B SER* 2.7 45.0 + - - +
105D PRO* 4.5 14.6 - - + -
910D CLA 3.8 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 2.9 31.5 + - - -
124B MET* 3.1 11.2 + - - +
126B VAL* 1.3 76.8 - - - +
128B THR* 1.3 52.7 + - - +
130B SER* 2.9 11.4 + - - -
131B PHE* 2.7 38.9 + - - -
191B LEU* 3.9 10.5 - - + +
194B LEU* 4.5 15.5 - - - -
195B THR* 3.2 36.8 - - + +
198B PHE* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MET* 3.1 43.3 - - + +
94B VAL* 4.0 29.1 - - + +
97B MET* 4.4 7.3 - - - -
124B MET 2.8 22.7 + - - -
125B ALA* 3.6 7.1 - - - -
127B CYS* 1.3 72.5 - - - +
129B VAL* 1.3 64.7 + - + +
131B PHE* 2.9 30.3 + - - +
132B GLY* 3.1 4.5 + - - -
195B THR* 4.8 2.1 + - - +
901B HEC 3.8 7.6 - - - +
902B HEC 4.3 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.9 13.5 - - + -
97B MET* 5.6 3.1 - - + -
125B ALA 3.0 16.2 + - - +
126B VAL* 3.7 5.4 - - - +
128B THR* 1.3 79.6 - - + +
130B SER* 1.3 63.6 + - - +
132B GLY* 3.3 10.5 + - - +
133B VAL* 3.3 14.3 + - + +
80D TYR* 4.2 21.9 + - + -
81D PHE* 3.2 32.1 - - + -
910D CLA 3.9 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 2.7 25.4 + - - +
127B CYS* 2.9 12.0 + - - -
129B VAL* 1.3 73.7 - - - +
131B PHE* 1.3 63.3 + - - +
133B VAL* 3.2 4.2 + - - +
134B THR* 3.0 26.2 + - - +
191B LEU* 3.6 22.5 - - - +
910D CLA 3.7 47.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.9 13.2 - + - -
93B MET* 5.8 0.7 - - + -
127B CYS 2.7 23.9 + - - -
128B THR* 3.1 15.9 - - - +
130B SER* 1.3 71.5 - - - +
132B GLY* 1.3 65.5 + - - +
134B THR* 3.1 2.0 + - - -
135B GLY* 2.8 20.8 + - - -
187B HIS* 3.2 38.0 + - - -
191B LEU* 3.3 19.4 - - + +
192B PRO* 3.3 33.4 - - + -
195B THR* 3.2 23.3 - - + -
902B HEC 3.6 55.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 6.0 0.4 - - - -
128B THR 3.1 8.6 + - - -
129B VAL 3.3 4.9 + - - -
130B SER 3.2 0.4 - - - -
131B PHE* 1.3 81.9 - - - +
133B VAL* 1.3 61.9 + - - +
135B GLY* 3.7 0.7 - - - -
136B TYR* 3.2 30.1 + - - -
902B HEC 4.0 19.0 - - - +
80D TYR* 3.7 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL 3.3 4.8 + - - +
130B SER 3.2 2.2 + - - -
132B GLY* 1.3 74.0 - - - +
134B THR* 1.3 68.6 + - - +
135B GLY 3.2 0.3 + - - -
136B TYR* 3.4 11.3 + - - +
137B SER* 3.6 9.9 + - - -
147B ALA* 5.5 7.3 - - + +
148B VAL* 5.2 4.5 - - + +
151B VAL* 4.2 28.0 - - + -
183B PHE* 4.5 13.6 - - + -
78D GLU* 4.1 9.0 - - - +
81D PHE* 3.6 30.5 - - + -
910D CLA 3.5 34.5 - - + -
920D TDS 5.1 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER 3.0 17.0 + - - +
131B PHE 3.1 7.3 + - - -
133B VAL* 1.3 79.0 - - + +
135B GLY* 1.3 60.6 + - - +
137B SER* 2.6 23.0 + - - -
138B LEU* 3.6 7.8 - - - +
183B PHE* 3.5 37.9 - - + +
186B LEU* 4.1 26.9 - - + -
187B HIS* 3.2 21.3 + - - +
191B LEU* 3.5 11.1 - - + +
910D CLA 5.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE 2.8 12.7 + - - -
132B GLY 3.7 1.1 - - - -
133B VAL 3.1 0.2 - - - -
134B THR* 1.3 77.8 + - - +
136B TYR* 1.3 62.1 + - - +
137B SER 3.0 1.4 + - - -
138B LEU* 3.1 20.0 + - - +
139B PRO* 3.7 0.5 - - - +
187B HIS* 3.4 25.8 - - - -
902B HEC 3.3 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.1 48.6 + - - +
90B ALA* 5.7 0.9 - - - +
91B SER* 4.3 13.2 + - - -
132B GLY* 3.2 23.3 + - - +
133B VAL* 3.4 5.8 + - - +
135B GLY* 1.3 73.7 - - - +
137B SER* 1.3 58.8 + - - +
139B PRO* 3.5 10.6 - - - +
141B ASP* 3.6 6.1 - - - +
143B VAL* 5.8 6.3 - - + -
144B GLY* 3.1 24.4 - - - +
902B HEC 3.5 36.1 - - + +
78D GLU* 3.5 39.9 - - + +
80D TYR* 4.5 5.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL 3.6 4.4 + - - -
134B THR 2.6 20.6 + - - -
135B GLY 3.0 0.6 + - - -
136B TYR* 1.3 77.9 - - - +
138B LEU* 1.3 62.1 + - - +
139B PRO 3.4 0.2 - - - -
140B TRP* 2.9 39.5 + - - -
144B GLY* 4.0 10.0 + - - -
148B VAL* 3.2 33.9 - - - -
180B LEU* 4.0 2.0 - - - +
183B PHE* 3.4 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.5 41.9 + - + +
65B ALA* 3.4 6.1 - - - +
134B THR 3.6 6.3 - - - +
135B GLY 3.1 13.8 + - - +
137B SER* 1.3 85.1 + - - +
139B PRO* 1.3 63.4 - - + +
140B TRP* 3.1 1.7 + - - +
180B LEU* 4.1 10.5 - - + +
183B PHE 4.7 0.7 - - - -
184B TYR* 3.8 39.3 - - + +
187B HIS* 3.8 21.3 - - + -
902B HEC 3.5 42.6 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il