Contacts of the helix formed by residues 175 - 185 (chain B) in PDB entry 2J3W
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 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PRO* 3.2 36.6 + - - +
158B ALA* 4.2 6.2 + - - -
159B LYS* 5.1 0.9 + - - +
173B LYS 4.6 1.4 - - - +
174B PHE* 1.3 78.2 - - - +
176B GLU* 1.3 66.5 + - - +
177B SER* 3.7 17.4 + - - +
178B VAL* 3.0 18.6 + - + +
179B ILE* 3.6 3.8 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 5.8 0.9 - - - +
113B LYS* 3.3 37.8 + - + +
174B PHE 3.7 1.6 + - - -
175B ASP* 1.3 72.9 - - - +
177B SER* 1.3 57.3 + - - +
179B ILE* 3.1 10.3 + - - +
180B ALA* 2.8 45.0 + - + +
183B LYS* 5.3 3.3 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PRO* 4.6 5.4 - - - +
175B ASP* 3.7 15.8 + - - +
176B GLU* 1.3 78.3 - - - +
178B VAL* 1.3 63.1 + - - +
180B ALA* 3.5 6.6 + - - +
181B ARG* 3.0 31.7 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.7 24.5 - - + -
156B PHE* 3.8 19.5 - - + -
157B PRO* 3.7 50.7 - - + +
174B PHE* 4.1 16.8 - - + -
175B ASP 3.0 11.0 + - - +
177B SER* 1.3 84.4 + - - +
179B ILE* 1.3 57.5 + - - +
181B ARG* 3.4 18.6 + - - +
182B ASP* 2.9 27.0 + - - +
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Residues in contact with ILE 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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82B VAL* 4.3 17.0 - - + -
112B ASP* 3.6 28.0 - - + +
113B LYS* 3.6 32.1 - - + -
115B TYR* 4.7 5.6 - - + +
174B PHE* 4.3 16.6 - - + -
175B ASP 3.6 5.4 + - - +
176B GLU* 3.1 15.5 + - - +
178B VAL* 1.3 73.7 - - - +
180B ALA* 1.3 65.4 + - - +
182B ASP* 3.3 4.9 + - + +
183B LYS* 3.1 54.4 + - + +
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Residues in contact with ALA 180 (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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176B GLU* 2.8 28.3 + - + +
177B SER* 3.9 7.9 - - - +
179B ILE* 1.3 77.2 - - - +
181B ARG* 1.3 63.5 + - - +
183B LYS* 3.6 8.9 + - - +
184B ALA* 3.2 22.2 + - - +
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Residues in contact with ARG 181 (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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54A TRP* 3.0 63.5 - - + +
80B THR 4.8 0.6 + - - -
155B GLY 2.6 25.7 + - - -
156B PHE* 3.7 17.6 - - - -
157B PRO* 4.5 3.2 - - - +
177B SER* 3.0 20.5 + - - +
178B VAL* 3.6 24.6 + - - +
180B ALA* 1.3 74.6 - - - +
182B ASP* 1.3 65.6 + - - +
184B ALA* 3.2 8.3 + - - +
185B LEU* 3.1 37.9 + - + +
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Residues in contact with ASP 182 (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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80B THR 4.0 3.8 - - - +
81B LYS* 3.4 17.5 - - - +
82B VAL* 2.8 48.9 + - + +
83B LEU 5.0 0.9 + - - -
156B PHE* 4.8 0.7 - - - -
178B VAL 2.9 18.4 + - - +
179B ILE* 3.5 8.5 - - + +
181B ARG* 1.3 79.1 + - - +
183B LYS* 1.3 59.3 + - + +
185B LEU* 3.0 26.2 + - - +
186B ASP* 3.4 17.2 + - - +
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Residues in contact with LYS 183 (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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112B ASP* 2.6 32.2 + - - +
176B GLU* 5.3 4.0 + - - +
179B ILE* 3.1 34.7 + - + +
180B ALA* 3.9 7.2 - - - +
182B ASP* 1.3 71.7 - - + +
184B ALA* 1.3 63.7 + - - +
185B LEU 3.0 6.1 + - - -
186B ASP* 3.2 31.4 + - - +
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Residues in contact with ALA 184 (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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180B ALA 3.2 12.1 + - - +
181B ARG* 3.2 10.7 + - - +
183B LYS* 1.3 79.0 - - - +
185B LEU* 1.3 61.7 + - + +
186B ASP 3.5 3.6 - - - +
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Residues in contact with LEU 185 (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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54A TRP* 3.8 33.7 - - + +
55A LEU* 3.9 20.9 - - + -
80B THR* 3.7 24.2 - - - +
81B LYS* 3.7 22.5 + - + -
181B ARG* 3.1 39.7 + - + +
182B ASP* 3.0 13.0 + - - +
183B LYS 3.0 1.4 - - - -
184B ALA* 1.3 80.6 - - + +
186B ASP* 1.3 66.0 + - - +
187B GLY 3.5 6.2 + - - +
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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