Contacts of the strand formed by residues 182 - 190 (chain B) in PDB entry 4HXG
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 SER 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TRP* 3.2 14.4 - - - -
179B HIS* 2.6 37.9 + - - -
181B ASP* 1.3 75.0 - - - +
183B ILE* 1.3 64.0 + - - +
204B LEU* 3.5 31.8 - - - +
205B TRP 3.5 9.0 - - - -
206B LYS* 4.0 17.3 + - - +
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Residues in contact with ILE 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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119B LEU* 3.9 30.7 - - + -
154B PHE* 5.2 2.0 - - + -
156B VAL* 4.5 13.5 - - + -
168B PHE* 4.2 22.0 - - + -
176B GLY* 4.4 1.8 - - - -
177B ILE 3.4 15.0 - - - +
178B TRP* 4.0 16.8 - - + -
182B SER* 1.3 80.7 - - - +
184B VAL* 1.3 69.7 + - - +
185B VAL* 3.6 21.3 - - + -
203B TYR 3.5 0.5 - - - +
204B LEU* 3.5 4.3 - - - -
205B TRP* 2.7 58.0 + - + +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER 3.9 0.2 - - - +
176B GLY* 3.1 5.4 - - - -
177B ILE* 2.9 46.3 + - + +
179B HIS* 3.4 29.4 - - + -
183B ILE* 1.3 71.0 - - - +
185B VAL* 1.3 60.7 + - - +
186B SER* 4.0 2.1 + - - +
202B ILE* 3.7 19.1 - - + -
203B TYR 3.4 4.3 - - - +
204B LEU* 4.3 5.6 - - + -
213B LEU* 5.0 3.1 - - + -
221B ALA* 3.4 27.7 - - + +
229B ILE* 3.6 27.1 - - + -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 4.2 8.5 - - + -
168B PHE* 4.2 20.4 - - + -
170B LYS* 4.0 22.0 - - + -
174B SER* 4.8 0.9 - - - -
175B SER 3.4 11.4 - - - +
183B ILE* 3.6 28.9 - - + +
184B VAL* 1.3 69.6 - - - +
186B SER* 1.3 63.0 + - - +
187B VAL* 3.7 21.6 + - + -
201B ASP 3.7 1.4 - - - +
202B ILE* 3.4 3.8 - - - -
203B TYR* 2.7 49.4 + - + +
205B TRP* 4.3 8.7 - - + -
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Residues in contact with SER 186 (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 PHE 4.4 0.9 - - - +
174B SER* 3.4 4.2 - - - -
175B SER* 2.9 45.4 + - - -
184B VAL 4.8 1.0 + - - -
185B VAL* 1.3 72.0 - - - +
187B VAL* 1.3 61.3 + - - +
188B PRO* 4.3 0.7 - - - +
200B TRP* 4.3 6.5 - - - -
201B ASP 3.7 4.5 - - - -
202B ILE* 4.2 7.1 - - - +
220B TYR* 3.6 23.5 - - - -
221B ALA* 3.1 33.8 + - - +
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Residues in contact with VAL 187 (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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170B LYS* 4.4 10.1 - - + -
171B PRO* 3.7 22.4 - - + -
174B SER* 3.6 16.8 - - - +
185B VAL* 3.7 20.0 - - + -
186B SER* 1.3 78.7 - - - +
188B PRO* 1.3 84.2 - - + +
200B TRP* 3.2 8.0 - - - -
201B ASP* 2.8 42.7 + - + +
203B TYR* 4.1 23.6 - - + -
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Residues in contact with PRO 188 (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 PRO* 5.1 3.4 - - + +
172B ARG 3.5 20.0 - - - +
173B PHE* 3.6 23.3 - - + +
174B SER* 3.8 6.5 - - - +
186B SER 4.3 0.4 - - - +
187B VAL* 1.3 103.5 - - + +
189B HIS* 1.3 63.1 + - - +
190B ARG* 3.7 3.3 + - - +
194B PRO* 4.4 10.0 - - + +
195B ARG 4.3 7.0 - - - +
196B TYR* 4.0 26.5 - - + -
199B TYR 3.8 7.4 - - - +
200B TRP* 3.9 9.6 - - + +
201B ASP* 4.6 1.7 - - - +
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Residues in contact with HIS 189 (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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187B VAL 3.3 1.6 + - - -
188B PRO* 1.3 71.0 - - - +
190B ARG* 1.3 80.1 + - - +
191B ASP* 3.4 18.7 + - - -
194B PRO* 3.6 0.8 - - - +
195B ARG* 2.8 34.4 + - + +
199B TYR* 3.1 30.2 + - + +
200B TRP 4.4 0.2 - - - +
201B ASP* 2.9 39.4 + - - +
215B GLU* 3.5 22.0 - - - -
216B LYS* 3.7 31.8 + - + +
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Residues in contact with ARG 190 (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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136B ASP* 2.8 32.1 + - - -
171B PRO* 5.4 10.1 - - - +
188B PRO 3.7 3.7 + - - +
189B HIS* 1.3 92.5 + - - +
191B ASP* 1.3 73.2 + - - +
192B VAL 3.9 14.0 + - - +
194B PRO* 3.3 37.6 - - + +
201B ASP* 4.9 1.0 + - - -
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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