Contacts of the helix formed by residues 166 - 176 (chain B) in PDB entry 4S0H
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B SER* 3.2 12.6 - - - +
165B ALA* 1.4 92.1 - - + +
167B GLU* 1.3 58.5 + - + +
168B ARG 3.1 2.0 - - - -
169B ASP* 2.8 32.3 + - + +
170B GLN* 3.0 14.6 + - - +
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Residues in contact with GLU 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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156B ARG* 3.2 5.6 + - - +
160B GLN* 3.1 38.1 + - - +
162B TYR 4.4 1.0 - - - +
163B LEU* 3.7 12.4 - - + +
164B SER* 2.9 44.0 + - - +
166B PRO* 1.3 78.5 - - + +
168B ARG* 1.3 60.0 + - - +
170B GLN* 3.0 41.0 + - - +
171B LEU* 3.4 11.1 + - - +
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Residues in contact with ARG 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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163B LEU* 3.5 45.6 + - + +
164B SER 3.1 16.3 + - - +
165B ALA* 3.8 24.2 + - - +
166B PRO 3.1 0.8 - - - -
167B GLU* 1.3 75.8 - - - +
169B ASP* 1.3 63.0 + - - +
171B LEU* 4.2 1.8 - - - +
172B ALA* 3.1 26.4 + - - +
179B SER* 3.8 12.6 + - - +
182B VAL* 4.2 6.9 - - + +
183B LYS* 3.4 60.0 - - - +
186B PHE* 6.0 1.1 - - + -
190B ARG* 5.7 4.2 - - - +
1D C 5.9 1.2 - - - -
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Residues in contact with ASP 169 (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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165B ALA 3.4 17.8 - - - +
166B PRO* 2.8 16.3 + - + +
168B ARG* 1.3 77.0 - - - +
170B GLN* 1.3 64.8 + - - +
171B LEU 3.1 1.1 - - - -
172B ALA* 3.2 4.6 + - - +
173B SER* 3.1 25.8 + - - -
179B SER* 3.2 24.2 + - - -
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Residues in contact with GLN 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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156B ARG* 3.4 35.1 - - - +
166B PRO 3.0 7.2 + - - +
167B GLU* 3.0 34.0 + - - +
169B ASP* 1.3 74.4 - - - +
171B LEU* 1.3 70.1 + - - +
173B SER* 2.8 21.7 + - - -
174B VAL* 3.1 19.4 - - + +
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Residues in contact with LEU 171 (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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152B GLU* 4.6 11.4 - - + +
153B LEU* 4.9 3.4 - - + -
156B ARG* 3.7 45.3 - - + +
163B LEU* 3.9 16.2 - - + -
167B GLU 3.4 13.0 + - - +
168B ARG 4.2 2.9 - - - +
169B ASP 3.1 0.6 - - - -
170B GLN* 1.3 82.0 - - + +
172B ALA* 1.3 65.3 + - - +
174B VAL* 3.4 7.5 + - + +
175B LEU* 3.2 48.4 + - + +
182B VAL* 4.3 9.9 - - + -
186B PHE* 4.3 9.2 - - + -
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Residues in contact with ALA 172 (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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168B ARG 3.1 21.0 + - - +
169B ASP* 3.5 6.1 - - - +
171B LEU* 1.3 78.2 - - - +
173B SER* 1.3 51.8 + - - +
175B LEU* 3.3 1.7 + - - +
176B LYS 2.8 30.5 + - - -
177B LEU* 3.0 29.0 + - - +
179B SER* 3.6 22.2 - - - +
182B VAL* 3.8 11.6 - - + +
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Residues in contact with SER 173 (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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169B ASP 3.1 8.1 + - - -
170B GLN* 2.8 17.2 + - - -
172B ALA* 1.3 77.4 - - - +
174B VAL* 1.3 67.0 + - - +
176B LYS* 2.7 34.4 + - - +
177B LEU 5.0 0.7 - - - -
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Residues in contact with VAL 174 (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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152B GLU* 4.8 8.7 - - - +
170B GLN* 3.1 24.5 + - + +
171B LEU* 3.6 10.8 - - + +
172B ALA 3.3 0.2 - - - -
173B SER* 1.3 83.7 + - - +
175B LEU* 1.3 75.6 + - + +
176B LYS* 3.8 18.4 + - - -
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Residues in contact with LEU 175 (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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148B ALA 5.9 0.2 - - - -
149B GLN* 3.0 55.2 + - + +
152B GLU* 3.4 31.9 - - + +
153B LEU* 3.9 29.4 - - + +
171B LEU* 3.2 34.8 + - + +
172B ALA* 4.1 2.2 - - - +
173B SER 3.2 0.4 - - - -
174B VAL* 1.3 87.6 - - + +
176B LYS* 1.3 67.4 + - - +
177B LEU* 4.0 8.9 - - + +
182B VAL* 5.9 2.2 - - + -
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Residues in contact with LYS 176 (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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149B GLN* 4.1 4.1 + - - +
172B ALA 2.8 4.3 + - - -
173B SER* 2.7 21.2 + - - +
174B VAL 3.8 16.2 + - - -
175B LEU* 1.3 82.7 + - - +
177B LEU* 1.3 63.3 + - - +
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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