Contacts of the helix formed by residues 112 - 133 (chain B) in PDB entry 1YRP
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 THR 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER 5.6 1.1 - - - +
111B LEU* 1.3 75.6 - - - +
113B GLU* 1.3 54.9 + - - +
114B ASP* 3.9 6.4 + - - +
115B GLU* 2.9 37.6 + - - +
116B ALA* 2.6 34.3 + - - +
211B LEU* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU 4.1 0.4 + - - -
112B THR* 1.3 72.5 - - - +
114B ASP* 1.3 61.1 + - - +
116B ALA* 3.6 7.3 - - - +
117B THR* 2.9 35.7 + - - +
211B LEU* 4.3 15.5 - - + -
243B ASN 4.1 4.2 - - - +
244B THR* 3.5 11.7 - - + +
245B SER* 2.7 50.0 + - - -
248B ALA* 3.9 7.6 - - + -
274B TRP* 3.2 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 3.2 7.0 + - - +
113B GLU* 1.3 75.7 - - - +
115B GLU* 1.3 64.2 + - + +
117B THR* 2.9 17.7 + - - -
118B GLN* 3.1 19.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
108B LYS* 3.4 26.7 + - - -
110B SER 4.9 0.7 - - - +
111B LEU* 3.6 17.2 - - + +
112B THR* 2.9 41.8 + - - +
114B ASP* 1.3 75.8 - - + +
116B ALA* 1.3 66.0 + - - +
118B GLN* 2.9 17.7 + - - +
119B PHE* 3.2 18.1 + - + -
153B PRO 5.3 3.4 - - - +
154B ASN* 4.0 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.3 16.3 - - + +
112B THR 2.6 17.8 + - - +
113B GLU 3.6 4.5 - - - +
115B GLU* 1.3 72.6 - - - +
117B THR* 1.3 57.0 + - - +
119B PHE* 3.5 4.4 + - - +
120B LEU* 3.0 31.4 + - - +
210B LEU* 3.8 14.9 - - + +
211B LEU* 3.4 33.2 - - + -
274B TRP* 4.7 5.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
113B GLU 2.9 22.3 + - - +
114B ASP* 2.9 19.1 + - - -
116B ALA* 1.3 73.6 - - - +
118B GLN* 1.3 59.9 + - - +
120B LEU* 3.6 6.7 - - - -
121B LYS* 2.9 31.0 + - - +
274B TRP* 3.6 48.7 - - + +
275B ILE* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.1 20.2 + - + +
115B GLU 2.9 9.9 + - - +
117B THR* 1.3 78.1 - - - +
119B PHE* 1.3 63.0 + - + +
121B LYS* 4.2 4.9 - - - +
122B GLN* 3.5 14.9 + - - +
154B ASN* 3.6 39.5 + - + +
156B ARG* 3.4 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.6 33.9 - - + -
104B PHE* 3.8 20.9 - + - -
111B LEU* 4.4 18.8 - - + -
115B GLU* 3.2 28.7 + - + -
116B ALA 3.7 6.1 - - - +
118B GLN* 1.3 79.6 - - + +
120B LEU* 1.3 64.6 + - - +
122B GLN* 3.3 19.8 + - - +
123B ILE* 3.3 12.5 + - + +
147B LEU* 4.3 10.8 - - + -
153B PRO 5.7 0.4 - - - -
154B ASN* 5.3 3.8 - - - -
155B PRO* 3.5 46.0 - - + -
157B ILE* 3.5 23.6 - - + +
210B LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 3.0 22.3 + - + +
117B THR* 3.8 8.3 - - - +
118B GLN 3.4 0.2 - - - -
119B PHE* 1.3 73.7 - - - +
121B LYS* 1.3 67.2 + - - +
123B ILE* 3.0 15.3 + - + +
124B LEU* 2.9 36.3 + - + +
203B ILE* 3.7 30.1 - - + -
206B ILE* 5.5 4.7 - - + -
207B THR* 3.4 31.4 - - + +
210B LEU* 3.7 19.7 - - + -
251B PHE* 4.6 3.4 - - + -
274B TRP* 4.2 9.6 - - + -
275B ILE* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR 2.9 18.1 + - - +
118B GLN* 4.2 7.4 - - - +
119B PHE 3.4 0.2 - - - -
120B LEU* 1.3 76.4 - - - +
122B GLN* 1.3 58.2 + - + +
124B LEU* 3.3 8.6 + - - +
125B ASP* 2.7 64.3 + - - +
270B LEU* 4.1 15.7 - - + +
275B ILE* 4.2 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.3 33.5 + - - +
118B GLN 3.5 13.8 + - - +
119B PHE* 3.3 8.4 + - - +
120B LEU 3.2 0.8 - - - -
121B LYS* 1.3 78.6 - - + +
123B ILE* 1.3 60.9 + - - +
125B ASP* 3.4 9.2 + - - +
126B GLY* 3.1 17.3 + - - -
155B PRO 3.1 24.2 + - - -
156B ARG* 3.0 48.6 + - - +
157B ILE* 3.4 26.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
101B LEU* 6.0 1.6 - - + -
119B PHE* 3.3 15.5 + - + +
120B LEU* 3.0 20.1 + - + +
122B GLN* 1.3 77.6 - - - +
124B LEU* 1.3 53.7 + - - +
126B GLY* 3.0 3.9 + - - -
127B VAL* 2.7 49.4 + - + +
140B LEU* 5.2 3.6 - - + -
145B ILE* 3.7 30.1 - - + -
157B ILE* 3.3 21.1 - - + -
159B LEU* 3.7 22.5 - - + +
203B ILE* 4.1 20.2 - - + -
206B ILE* 5.5 8.7 - - + -
210B LEU* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 2.9 23.8 + - + +
121B LYS* 3.7 2.2 - - - +
123B ILE* 1.3 77.4 - - - +
125B ASP* 1.3 57.8 + - - +
128B HIS* 2.8 31.4 + - - +
200B MET* 4.7 0.4 - - + -
203B ILE* 4.0 29.4 - - + -
251B PHE* 4.3 6.3 - - + -
266B ILE* 3.7 18.9 - - + +
269B SER* 3.5 27.4 - - - +
270B LEU* 3.5 21.2 - - + +
275B ILE* 3.8 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.8 20.2 + - + +
75B ASN* 4.5 4.9 + - - +
121B LYS* 2.7 55.9 + - - +
122B GLN* 3.5 11.5 - - - +
123B ILE 3.1 0.2 - - - -
124B LEU* 1.3 74.9 - - - +
126B GLY* 1.3 59.1 + - - +
128B HIS* 3.3 7.5 + - - +
129B TYR* 3.0 28.9 + - - +
270B LEU* 3.7 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.7 19.5 + - - -
75B ASN* 4.6 2.2 - - - -
76B ILE* 3.9 3.5 - - - +
122B GLN 3.1 7.7 + - - -
123B ILE 3.0 6.2 + - - -
125B ASP* 1.3 79.4 - - - +
127B VAL* 1.3 62.1 + - - +
129B TYR* 3.4 5.0 + - - +
130B LEU* 3.3 25.6 + - - +
159B LEU* 4.0 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 2.7 36.5 + - + +
126B GLY* 1.3 71.5 - - - +
128B HIS* 1.3 64.0 + - - +
130B LEU* 3.5 8.9 + - + +
131B HIS* 3.0 50.0 + - + +
137B HIS* 6.0 0.4 - - + -
140B LEU* 3.8 29.8 - - + -
159B LEU* 4.5 5.6 - - + -
199B ASP* 4.5 5.2 - - + +
200B MET* 4.5 0.2 - - - -
203B ILE* 4.1 9.9 - - + -
266B ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 2.8 22.1 + - - +
125B ASP* 3.5 6.7 - - - +
127B VAL* 1.3 73.4 - - - +
129B TYR* 1.3 60.3 + - - +
131B HIS* 3.3 2.4 + - - +
132B SER* 2.5 43.4 + - - -
266B ILE* 3.6 27.2 - - + +
267B ALA* 4.4 17.5 - - + -
270B LEU* 3.8 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU 3.7 1.9 + - - -
71B ILE* 4.3 7.6 - - + -
72B ARG* 3.3 44.3 + - - +
73B HIS* 3.8 30.3 - - + +
76B ILE* 4.4 3.1 - - + -
125B ASP 3.0 12.9 + - - +
126B GLY 3.6 7.6 - - - +
127B VAL 3.4 0.2 - - - -
128B HIS* 1.3 82.1 - - - +
130B LEU* 1.3 72.3 + - + +
132B SER* 3.2 21.5 + - - -
133B LYS* 2.8 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.6 28.5 - - + -
76B ILE* 3.6 28.3 - - + -
126B GLY 3.3 14.6 + - - +
127B VAL* 3.8 14.4 - - + +
128B HIS 3.3 0.2 - - - -
129B TYR* 1.3 84.0 - - + +
131B HIS* 1.3 55.6 + - + +
133B LYS* 3.1 15.7 + - - -
134B ARG 3.1 0.2 + - - -
135B ILE* 2.8 58.5 + - + +
137B HIS* 4.5 18.6 - - + +
159B LEU* 4.8 4.0 - - + -
162B PHE* 4.0 15.9 - - + -
199B ASP* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.0 42.8 + - + +
128B HIS 3.8 4.3 - - - +
130B LEU* 1.3 74.7 - - + +
132B SER* 1.3 65.8 + - - +
134B ARG* 3.1 15.1 + - - +
135B ILE 3.3 16.8 - - - +
196B LEU* 3.2 59.3 + - + +
199B ASP* 3.3 24.9 + - + -
200B MET* 4.0 11.9 - - + +
266B ILE* 3.9 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 2.5 40.0 + - - -
129B TYR* 3.2 14.0 + - - -
131B HIS* 1.3 78.5 - - - +
133B LYS* 1.3 60.7 + - - +
134B ARG* 3.4 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 2.8 53.4 + - - +
71B ILE* 3.4 5.3 - - - +
129B TYR* 2.8 54.4 + - + +
130B LEU* 3.1 8.5 + - - +
132B SER* 1.3 76.3 - - - +
134B ARG* 1.3 69.0 + - - +
135B ILE* 3.3 13.7 + - + +
167B LYS* 3.4 20.9 - - - -
169B GLU* 4.2 0.7 - - - +
----------------------------------------------------------
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