Contacts of the helix formed by residues 123 - 145 (chain B) in PDB entry 3CJD
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 PRO 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.9 19.1 - - + -
116B MSE 3.9 21.3 - - + -
121B PRO 3.9 5.4 - - - +
122B VAL* 1.4 81.9 - - + +
124B GLN* 1.3 65.5 + - - +
125B TRP* 3.3 25.1 - - + +
126B TYR* 3.0 17.8 + - + +
127B GLY 3.1 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL 3.4 5.7 + - - +
123B PRO* 1.3 70.9 - - - +
125B TRP* 1.3 57.1 + - - +
127B GLY* 3.5 1.6 + - - -
128B HIS* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 5.7 0.2 - - - -
60B LEU* 3.4 35.4 - - + +
61B GLU* 3.9 32.0 + - - -
64B GLY* 3.9 20.2 - - - -
123B PRO* 3.2 21.5 + - + +
124B GLN* 1.3 76.8 - - - +
126B TYR* 1.3 79.7 + + + +
128B HIS* 3.8 8.0 - - - +
129B ALA* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 3.8 25.6 - - + -
201A STE 5.1 2.7 + - - +
60B LEU* 3.5 51.6 - - + +
63B ASN* 3.1 30.2 + - + +
64B GLY 4.4 0.7 - - - -
67B PHE* 3.5 29.9 - + - -
111B LEU* 4.5 5.5 + - - +
114B VAL* 4.2 4.7 - - - +
116B MSE 4.0 19.1 - - + -
122B VAL* 4.6 1.1 - - + -
123B PRO* 3.0 18.5 + - + +
125B TRP* 1.3 102.1 - + + +
127B GLY* 1.3 64.0 + - - +
129B ALA* 3.3 4.7 + - - +
130B MSE 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.5 9.0 - - - -
122B VAL* 4.1 15.6 - - - +
123B PRO 3.1 11.9 + - - -
124B GLN* 4.0 2.5 - - - -
126B TYR* 1.3 74.9 - - - +
128B HIS* 1.3 55.9 + - - +
130B MSE 3.4 3.1 + - - +
131B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
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 GLN 3.0 20.3 + - - +
125B TRP* 3.8 7.4 - - - +
127B GLY* 1.3 72.9 - - - +
129B ALA* 1.3 61.4 + - - +
131B ALA* 3.4 8.1 + - - +
132B GLN* 3.0 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 5.9 0.9 - - - +
67B PHE* 3.8 23.4 - - + +
125B TRP* 3.0 26.1 + - + +
126B TYR* 3.3 7.4 + - - +
128B HIS* 1.3 74.0 - - - +
130B MSE 1.3 63.6 + - - +
132B GLN* 3.4 18.6 - - - +
133B LEU* 3.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 3.4 52.3 - - + +
177A SER* 3.8 10.5 - - - -
201A STE 4.1 17.9 - - + -
67B PHE* 4.0 21.7 - - + -
126B TYR 3.1 16.0 + - - +
127B GLY 3.8 3.8 - - - +
129B ALA* 1.3 75.3 - - - +
131B ALA* 1.3 68.3 + - + +
133B LEU* 3.1 20.1 + - - +
134B PHE* 3.2 47.0 + - + -
158B ARG* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY 2.9 19.2 + - - +
128B HIS* 3.6 11.7 - - - +
129B ALA 3.4 0.2 - - - -
130B MSE 1.3 85.9 - - + +
132B GLN* 1.3 55.6 + - - +
134B PHE* 3.3 7.1 + - - +
135B SER* 3.1 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 3.0 33.8 + - + +
129B ALA* 3.4 20.4 - - - +
131B ALA* 1.3 74.3 - - - +
133B LEU* 1.3 62.0 - - + +
135B SER* 2.6 26.4 + - - +
136B TYR* 3.3 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A STE 3.5 49.5 - - + +
67B PHE* 3.7 41.3 - - + +
70B LEU* 4.2 7.4 - - + -
71B GLY* 3.5 36.3 - - - +
74B VAL* 5.8 0.2 - - + -
129B ALA 3.4 11.0 + - - +
130B MSE 3.1 9.9 + - - +
132B GLN* 1.3 78.7 - - + +
134B PHE* 1.3 62.0 + - - +
136B TYR* 3.2 32.3 + - + +
137B ILE* 3.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 3.4 39.9 - - - -
201A STE 4.1 21.8 - - + -
130B MSE 3.2 38.2 + - + +
131B ALA* 3.3 11.4 + - - +
133B LEU* 1.3 74.8 - - - +
135B SER* 1.3 59.3 + - - +
136B TYR 3.2 0.2 - - - -
137B ILE* 3.1 12.3 + - + +
138B THR* 3.0 31.7 + - - +
154B ASP* 5.1 5.2 - - - +
157B THR* 3.6 16.8 - - + +
158B ARG* 3.7 30.5 - - + -
161B PHE* 3.9 29.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 3.1 11.7 + - - -
132B GLN* 2.6 26.0 + - - +
134B PHE* 1.3 75.4 - - - +
136B TYR* 1.3 69.4 + - - +
138B THR* 3.9 8.7 - - - -
139B THR* 3.0 31.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
201A STE 5.2 0.4 - - + -
71B GLY* 4.6 14.2 + - - -
74B VAL* 4.0 17.0 - - + -
75B GLY* 5.7 7.0 - - - -
93B MSE 3.4 27.1 - - - +
132B GLN* 3.3 37.1 + - + +
133B LEU* 3.4 38.4 - - + +
134B PHE 3.2 0.8 - - - -
135B SER* 1.3 83.3 + - - +
137B ILE* 1.3 55.8 + - - +
139B THR* 4.4 2.9 - - - -
140B PRO* 3.1 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A STE 3.9 70.0 - - + -
90B LEU* 4.0 12.6 - - + -
93B MSE 3.8 8.1 - - + -
133B LEU 4.3 2.2 - - - +
134B PHE* 3.1 13.4 + - + +
136B TYR* 1.3 75.8 - - - +
138B THR* 1.3 64.4 + - - +
139B THR 3.3 0.4 - - - -
140B PRO* 3.3 15.4 - - - +
141B LEU* 3.4 24.8 + - + +
157B THR* 3.7 24.2 - - + +
160B LEU* 5.5 0.2 - - + -
161B PHE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.0 17.8 + - - +
135B SER* 3.5 8.9 + - - -
137B ILE* 1.3 74.5 - - - +
139B THR* 1.3 58.7 + - - +
141B LEU* 3.3 2.9 + - - +
142B ALA* 2.8 30.3 + - + +
153B LEU* 4.1 28.0 - - + +
154B ASP* 5.2 3.6 + - - +
157B THR* 2.7 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.0 18.7 + - - -
136B TYR* 4.4 3.4 - - - -
138B THR* 1.3 76.6 - - - +
140B PRO* 1.4 69.1 - - + +
142B ALA* 3.3 14.1 + - - +
143B LYS* 3.4 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.5 34.7 - - + +
89B ARG* 4.5 9.4 - - + -
90B LEU* 3.8 16.4 - - + -
93B MSE 4.0 6.3 - - + -
136B TYR 3.1 24.0 - - - +
137B ILE 3.3 13.7 - - - +
139B THR* 1.4 86.7 - - + +
141B LEU* 1.3 57.8 + - - +
143B LYS* 3.1 11.1 + - + +
144B ILE* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.8 17.5 - - + -
137B ILE* 3.4 20.5 + - + +
138B THR* 3.3 9.9 + - - +
140B PRO* 1.3 77.0 - - - +
142B ALA* 1.3 52.8 + - - +
144B ILE* 3.3 3.0 + - + -
145B PHE* 2.8 59.7 + - + +
153B LEU* 3.8 11.7 - - + +
156B MSE 3.8 11.7 - - + +
157B THR* 3.4 43.7 - - - +
160B LEU* 3.5 25.1 - - + -
195B VAL* 4.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 2.8 17.8 + - + +
139B THR* 3.3 11.8 + - - +
141B LEU* 1.3 72.1 - - - +
143B LYS* 1.3 61.0 + - + +
145B PHE 3.5 0.7 - - - -
146B PRO* 3.4 24.6 - - - +
153B LEU* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 4.5 21.6 + - + +
86B PRO* 4.1 27.4 - - + -
139B THR* 3.4 23.7 + - - +
140B PRO* 3.1 11.0 + - + +
142B ALA* 1.3 76.5 - - + +
144B ILE* 1.3 61.9 + - - +
146B PRO* 3.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.7 16.4 - - + -
87B ASN* 3.4 29.2 - - - +
90B LEU* 3.5 32.1 - - + -
140B PRO 3.0 18.1 + - - +
141B LEU* 3.7 10.8 - - + +
143B LYS* 1.3 77.8 - - - +
145B PHE* 1.3 73.4 + - + +
146B PRO* 3.3 8.3 - - - +
195B VAL* 4.1 3.8 - - + +
196B GLY* 3.5 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLN* 3.5 35.2 - - - -
141B LEU* 2.8 35.5 + - + +
142B ALA* 3.5 8.0 - - - +
144B ILE* 1.3 88.6 - - + +
146B PRO* 1.4 64.7 - - - +
147B GLU 3.2 2.7 - - - +
148B SER* 3.2 34.7 + - - +
153B LEU* 4.1 8.9 - - + +
156B MSE 4.1 19.7 - - + -
195B VAL* 3.6 15.3 - - + -
196B GLY* 3.5 19.7 - - - -
197B ARG* 4.7 7.4 - - - -
----------------------------------------------------------
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