Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 2IQ6
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 ASN 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP* 3.3 21.2 + - + +
90A GLU* 3.6 23.5 - - - +
91A TRP* 2.7 32.2 + - - -
169A GLY 3.4 4.1 + - - +
170A LYS* 1.3 70.0 - - - +
172A VAL* 1.3 64.6 + - - +
173A VAL* 3.3 10.5 + - - +
238A TYR* 5.1 1.9 - - - -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 3.5 11.9 - - + +
93A VAL* 4.2 11.0 - - + -
165A TYR* 3.7 32.1 - - + -
170A LYS* 3.4 5.7 + - + -
171A ASN* 1.3 74.2 + - - +
173A VAL* 1.3 63.4 + - - +
174A SER 3.7 25.4 - - - +
175A ALA* 4.4 5.6 - - + -
233A TRP* 3.8 14.6 - - + -
238A TYR* 3.6 43.4 - - + -
239A PRO* 3.6 8.8 - - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.5 11.8 - - + +
2A PRO* 6.0 0.7 - - + -
90A GLU* 3.9 28.0 - - + -
91A TRP 2.8 16.0 + - - +
92A ILE* 3.9 7.2 - - + -
141A ARG* 4.0 22.0 - - - +
171A ASN* 4.0 13.2 - - - +
172A VAL* 1.3 71.9 - - - +
174A SER* 1.3 61.5 + - - +
239A PRO* 3.4 19.9 - - - +
286A MET* 3.5 26.0 - - + -
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.4 0.9 - - - -
91A TRP 3.8 0.6 + - - -
92A ILE* 3.8 5.7 - - - +
93A VAL* 2.9 27.7 + - - +
172A VAL* 3.3 8.4 - - - +
173A VAL* 1.3 82.1 - - - +
175A ALA* 1.3 60.7 + - - +
201A PHE* 3.7 26.7 - - - -
239A PRO* 3.4 9.6 - - - -
282A TYR* 2.8 29.1 + - - -
286A MET* 3.7 16.8 - - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.4 19.1 - - + -
172A VAL* 4.4 4.9 - - + -
174A SER* 1.3 75.7 - - - +
176A LEU* 1.3 61.9 + - - +
177A GLN 3.9 0.2 + - - -
201A PHE* 3.8 2.7 - - - -
230A HIS* 5.2 1.2 - - - +
233A TRP* 3.6 42.4 - - + -
239A PRO 2.9 11.9 + - - +
240A ALA* 3.3 5.4 - - + +
241A ALA 3.2 23.0 + - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 2.8 10.2 + - - +
94A ILE* 3.3 20.6 - - + +
95A GLY 3.0 26.5 + - - +
148A TYR* 5.3 1.2 + - - -
175A ALA* 1.3 73.5 - - - +
177A GLN* 1.3 61.9 + - - +
178A LEU* 4.8 9.2 - - + -
201A PHE* 4.2 2.9 - - + -
205A LEU* 3.5 26.9 - - + -
241A ALA* 3.7 5.6 - - + +
243A PRO* 3.4 33.9 - - + -
278A LEU* 5.2 2.7 - - + +
279A GLY* 4.0 13.2 - - - +
282A TYR* 3.7 42.3 + - + -
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Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 3.3 5.6 - - - +
96A GLY* 3.9 11.5 - - - -
97A HIS 4.2 1.6 - - - +
118A ASP* 4.6 0.2 + - - -
148A TYR* 3.3 25.6 + - - -
176A LEU* 1.3 74.6 - - - +
178A LEU* 1.3 66.6 + - - +
179A ASP* 4.0 7.9 + - - +
228A SER* 3.0 14.3 + - - +
229A ASP* 2.9 31.8 + - - +
230A HIS* 3.7 33.4 + - + +
233A TRP* 5.9 0.8 - - + -
241A ALA 2.9 9.3 + - - +
242A MET* 3.4 29.1 - - + +
243A PRO* 3.3 23.1 - - - +
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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