Contacts of the helix formed by residues 158 - 170 (chain B) in PDB entry 3N1Q
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 LYS 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B TRP* 3.4 59.9 - - + +
121B VAL* 4.9 2.2 - - + -
151B THR* 4.0 16.4 - - + -
153B ASP* 2.8 28.7 + - - +
155B ASP* 2.8 46.7 + - + +
157B ASN* 1.3 77.8 - - - +
159B TYR* 1.3 60.5 + - - +
160B GLY 3.4 1.8 - - - -
161B LEU* 3.4 10.5 + - + +
162B LEU* 2.8 27.1 + - - +
92E ASN* 2.9 15.2 + - - +
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B THR* 3.3 21.7 - - - -
151B THR* 3.4 27.1 - - + -
154B ARG* 3.4 14.9 - - - +
155B ASP 3.4 16.8 - - - -
156B ARG* 3.2 50.2 + - - +
157B ASN 3.4 0.2 - - - -
158B LYS* 1.3 78.7 - - - +
160B GLY* 1.3 60.7 + - - +
162B LEU* 3.3 16.9 - - + +
163B ALA* 2.8 31.0 + - - +
176B TYR* 3.4 22.2 - + + +
179B ARG 3.6 17.9 - - - -
180B ASN 3.8 15.7 - - - -
181B HIS* 4.4 3.1 - - - -
182B VAL* 3.7 12.2 - - + +
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.3 13.1 - - - +
43B LEU 3.1 37.5 + - - -
156B ARG 4.9 0.6 + - - -
157B ASN 4.8 3.0 + - - -
158B LYS 3.4 0.8 - - - -
159B TYR* 1.3 77.5 - - - +
161B LEU* 1.3 60.3 + - - +
163B ALA* 3.5 2.0 + - - +
164B ARG 3.3 10.9 + - - -
176B TYR* 3.8 14.2 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.6 13.9 - - + +
42B PRO* 3.7 33.0 - - + -
117B MET* 4.4 19.1 - - + -
118B TRP* 3.8 26.0 - - + +
157B ASN 4.8 13.4 + - - +
158B LYS* 3.4 8.6 + - + +
159B TYR 3.2 0.2 - - - -
160B GLY* 1.3 74.7 - - - +
162B LEU* 1.3 66.6 + - - +
164B ARG* 3.3 5.0 + - + +
165B LEU* 3.0 28.5 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.2 4.0 - - + +
114B VAL* 3.7 30.5 - - + -
118B TRP* 3.9 10.0 - - + -
123B LEU* 4.1 5.4 - - + -
149B ILE* 3.7 32.1 - - + +
150B THR* 3.7 34.5 - - - +
151B THR* 4.1 11.7 - - + +
158B LYS 2.8 18.6 + - - +
159B TYR* 3.2 15.2 + - + +
161B LEU* 1.3 76.5 - - - +
163B ALA* 1.3 63.5 + - - +
165B LEU* 3.0 8.3 + - + +
166B ALA* 3.0 20.5 + - - +
182B VAL* 4.5 3.6 - - + -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.6 26.9 - - + -
159B TYR 2.8 16.5 + - - +
160B GLY* 3.6 7.0 - - - +
161B LEU 3.3 0.2 - - - -
162B LEU* 1.3 76.9 - - - +
164B ARG* 1.3 61.9 + - - +
166B ALA* 3.0 19.2 + - - +
167B VAL* 3.2 6.4 + - - +
174B VAL* 3.3 20.1 - - + +
176B TYR* 5.2 4.5 - - + -
182B VAL* 3.9 19.5 - - + +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.2 21.5 - - + -
41B VAL* 2.7 52.4 + - - +
42B PRO* 4.3 1.7 + - + -
43B LEU* 3.0 29.4 - - - +
47B GLN* 4.5 5.3 - - - +
49B VAL* 4.5 11.1 - - - +
160B GLY 3.3 8.4 + - - +
161B LEU* 3.3 9.8 + - + +
162B LEU 3.2 0.4 - - - -
163B ALA* 1.3 78.2 - - - +
165B LEU* 1.3 58.8 + - + +
167B VAL* 3.0 40.9 + - - +
168B GLU* 3.1 28.7 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.8 27.6 - - + -
110B LEU* 3.7 14.2 - - + +
113B ALA* 4.0 35.9 - - + +
114B VAL* 4.4 3.4 - - + -
117B MET* 4.0 15.7 - - + -
118B TRP* 3.7 35.7 - - + -
161B LEU 3.0 14.9 + - - +
162B LEU* 3.0 9.6 + - - +
164B ARG* 1.3 76.6 - - - +
166B ALA* 1.3 56.4 + - - +
168B GLU* 3.6 7.3 + - + +
169B ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.8 12.5 - - + +
149B ILE* 4.6 1.1 - - + -
162B LEU 3.0 11.0 + - - +
163B ALA* 3.0 14.3 + - - +
165B LEU* 1.3 78.6 - - - +
167B VAL* 1.3 59.4 + - - +
169B ALA* 3.4 6.2 - - - +
170B GLY 3.3 3.5 + - - -
171B PHE* 3.2 31.4 + - + +
174B VAL* 3.7 7.9 - - + -
184B VAL* 3.6 31.2 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.8 2.5 - - + -
49B VAL* 4.0 28.5 - - + +
163B ALA 3.2 9.1 + - - +
164B ARG* 3.0 34.1 + - - +
166B ALA* 1.3 73.8 - - - +
168B GLU* 1.3 66.6 + - - +
169B ALA 3.0 3.8 - - - -
170B GLY* 2.9 21.8 + - - -
171B PHE 4.6 5.7 - - - +
174B VAL* 3.6 25.1 - - + -
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.1 26.6 - - + +
164B ARG* 3.1 35.8 + - + +
165B LEU* 4.1 9.0 - - + +
167B VAL* 1.3 82.2 - - - +
169B ALA* 1.3 61.3 + - - +
170B GLY* 3.2 1.5 + - - -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.5 20.7 + - - +
109B ALA* 4.1 16.4 - - - +
110B LEU* 3.7 34.8 - - + +
113B ALA* 5.7 1.3 - - + -
165B LEU 2.9 20.1 + - - +
166B ALA* 3.4 9.4 - - - +
167B VAL 3.0 0.2 - - - -
168B GLU* 1.3 79.9 - - - +
170B GLY* 1.3 56.2 + - - +
171B PHE* 3.7 3.6 - - + -
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 4.7 1.9 + - - -
106B ARG* 3.1 21.0 + - - -
167B VAL 2.9 11.5 + - - -
168B GLU 3.2 2.0 - - - -
169B ALA* 1.3 80.2 - - - +
171B PHE* 1.3 68.3 + - - +
172B ASP* 3.2 12.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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