Contacts of the helix formed by residues 172 - 179 (chain B) in PDB entry 3W7F
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 ASP 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ASN* 3.0 16.2 + - - +
169B ILE 3.3 2.3 + - - -
171B ARG* 1.3 108.4 + - - +
173B VAL* 1.3 65.5 + - - +
174B GLY 3.1 3.3 + - - -
175B GLU* 3.2 25.1 + - - +
176B ASP* 2.7 44.6 + - - +
265B ARG* 4.4 4.3 + - - +
301B FPS 2.7 6.8 + - - -
303B MG 1.9 32.4 - - - -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 3.4 17.4 + - + +
170B LEU* 4.0 11.4 - - - +
171B ARG 3.5 2.6 + - - -
172B ASP* 1.3 72.0 - - - +
174B GLY* 1.3 65.0 + - - +
176B ASP* 3.8 5.2 - - - +
177B PHE* 2.9 23.0 + - - +
181B ARG 4.8 0.2 - - - +
182B ILE* 6.4 0.4 - - + -
184B PHE* 3.7 34.5 - - + -
196B ILE* 4.2 20.2 - - + -
208B TYR* 3.4 27.1 - - - +
212B TRP* 4.5 0.4 - - + -
262B LEU* 4.2 14.1 - - + -
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Residues in contact with GLY 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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171B ARG 5.1 1.2 + - - -
172B ASP 3.2 0.6 - - - -
173B VAL* 1.3 77.4 - - - +
175B GLU* 1.3 62.0 + - - +
177B PHE* 3.0 6.3 + - - +
178B GLU* 3.0 29.6 + - - +
200B TYR* 4.2 4.8 - - - -
261B THR 5.3 0.4 + - - -
262B LEU* 3.0 43.2 - - - +
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Residues in contact with GLU 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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17A LYS* 2.7 39.5 + - - +
172B ASP* 3.2 24.6 + - + +
174B GLY* 1.3 74.6 - - - +
176B ASP* 1.3 66.4 + - - +
178B GLU* 3.5 16.5 + - - +
179B ASN* 3.2 37.4 + - - +
262B LEU 4.3 1.0 + - - -
265B ARG* 3.9 22.4 + - + +
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Residues in contact with ASP 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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169B ILE* 4.6 6.9 - - - +
172B ASP* 2.7 44.0 + - - +
173B VAL* 3.8 4.1 + - - +
175B GLU* 1.3 74.4 - - - +
177B PHE* 1.3 66.2 + - - +
179B ASN* 3.0 15.9 + - - +
180B GLU 3.0 0.3 + - - -
181B ARG* 2.8 38.7 + - + +
182B ILE* 5.5 0.2 - - - -
183B TYR* 3.3 35.9 - - + -
301B FPS 5.4 1.7 + - - -
303B MG 4.3 3.5 - - - -
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Residues in contact with PHE 177 (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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173B VAL 2.9 14.6 + - - +
174B GLY* 3.0 9.8 + - - +
176B ASP* 1.3 77.2 - - - +
178B GLU* 1.3 58.4 + - - +
180B GLU* 2.6 29.5 + - - +
181B ARG 3.4 8.5 + - - +
182B ILE* 4.2 17.9 - - + -
196B ILE* 3.5 25.4 - - + -
197B ALA* 3.3 40.8 - - + -
200B TYR* 3.7 38.6 - + + -
262B LEU* 5.7 0.2 - - + -
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Residues in contact with GLU 178 (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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9A LYS* 3.9 23.8 + - - +
16A LYS* 3.0 35.8 + - + +
174B GLY 3.0 16.0 + - - +
175B GLU* 3.7 18.0 - - - +
176B ASP 3.3 0.2 - - - -
177B PHE* 1.3 78.3 - - - +
179B ASN* 1.3 67.2 + - - +
180B GLU* 3.4 4.4 + - - +
200B TYR* 2.6 41.2 + - + +
262B LEU 4.6 3.5 - - - +
263B HIS* 4.6 5.0 - - - -
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Residues in contact with ASN 179 (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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13A LYS* 3.0 45.4 - - + +
175B GLU* 3.2 34.9 + - - +
176B ASP* 3.0 12.3 + - - +
178B GLU* 1.3 82.7 - - - +
180B GLU* 1.3 70.9 + - - +
181B ARG* 3.2 24.0 + - + +
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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