Contacts of the strand formed by residues 172 - 176 (chain B) in PDB entry 5H15
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 ILE 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ALA* 4.5 4.5 - - + -
165B VAL 3.6 7.6 - - - +
166B ALA* 4.2 0.9 - - + -
171B ILE* 1.3 71.4 - - - +
173B ARG* 1.3 63.7 + - - +
174B ILE* 4.2 10.1 - - + -
184B LYS 4.0 0.2 - - - +
185B HIS* 2.9 7.3 - - - +
186B TYR* 2.8 53.3 + - + +
193B ILE* 3.6 20.6 - - + -
196B LEU* 4.1 9.2 - - + -
206B LEU* 3.7 26.7 - - + -
208B SER* 3.9 13.2 - - - -
218B TRP* 3.3 45.5 - - + +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.5 19.5 + - - -
140B ASP* 3.0 33.4 + - - -
142B ASP* 6.0 1.6 - - - +
145B GLU* 4.9 4.2 + - - -
147B PHE* 4.6 5.3 - - + -
163B LEU 3.6 1.9 - - - +
164B ALA* 3.3 4.9 - - - +
165B VAL* 2.9 45.9 + - + +
171B ILE* 3.8 39.0 - - + +
172B ILE* 1.3 76.2 - - - +
174B ILE* 1.3 61.1 + - - +
175B ILE* 3.8 6.2 + - + -
182B CYS* 3.9 18.8 - - - +
184B LYS 3.6 4.0 - - - -
185B HIS* 3.6 29.9 + - - +
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Residues in contact with ILE 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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153B THR* 5.8 0.2 - - + -
162B LEU* 4.2 37.9 - - + -
163B LEU 3.6 4.0 - - - +
164B ALA* 3.7 25.4 - - + -
172B ILE* 4.2 11.2 - - + -
173B ARG* 1.3 70.4 - - - +
175B ILE* 1.3 54.2 + - - +
182B CYS* 3.5 2.8 - - - -
183B ILE* 2.8 36.4 + - + +
184B LYS* 2.7 45.8 + - + +
186B TYR* 3.9 12.6 - - + -
198B PHE* 4.6 1.1 - - + -
206B LEU* 4.3 2.9 - - + -
220B ILE* 4.0 31.4 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.4 8.3 - - + -
138B TYR* 3.8 40.8 - - + -
162B LEU* 3.7 5.9 - - - +
163B LEU* 2.8 41.2 + - + +
165B VAL* 3.8 31.0 - - + -
173B ARG* 4.4 6.5 - - + -
174B ILE* 1.3 77.5 - - - +
176B ASN* 1.3 75.5 + - - +
177B PRO* 3.3 4.2 - - + +
180B MET* 3.8 30.1 - - + +
181B GLN 3.4 7.6 - - - +
182B CYS* 4.2 5.6 - - - -
183B ILE* 4.6 2.7 - - - -
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Residues in contact with ASN 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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160B HIS* 2.8 37.3 + - - -
162B LEU* 4.7 1.6 - - - -
175B ILE* 1.3 72.0 - - - +
177B PRO* 1.4 60.8 - - - +
178B ILE* 3.1 13.2 + - - +
179B THR* 3.4 29.8 + - - +
180B MET* 2.8 30.5 + - - -
181B GLN* 2.9 16.6 + - + +
183B ILE* 3.7 23.7 - - + +
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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