Contacts of the strand formed by residues 156 - 159 (chain A) in PDB entry 3W31
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 4.5 2.1 - - - +
42A ASP* 4.3 0.5 - - - +
119A ARG* 3.4 20.7 + - - -
123A ALA* 3.8 21.1 - - + +
126A ILE* 3.1 32.5 - - + -
127A LEU* 3.6 17.5 - - + +
150A PHE 3.3 12.6 - - - +
151A ASN* 3.1 37.7 - - - +
155A LYS* 1.3 88.7 - - - +
157A MET* 1.3 77.7 + - - +
158A PHE* 4.1 21.3 - - + -
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Residues in contact with MET 157 (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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28A LEU* 5.0 7.9 - - + -
31A LEU 5.0 2.5 - - - +
32A ASN* 5.8 0.9 - - + -
41A LYS* 3.7 43.7 - - + +
42A ASP* 3.4 11.4 - - - +
45A LEU* 4.0 29.2 - - + -
73A MET* 5.3 0.2 - - - -
148A ALA 3.6 2.6 - - - +
150A PHE* 2.8 61.7 + - + +
152A ASP* 5.0 4.9 - - - +
155A LYS* 3.8 23.1 - - + +
156A ILE* 1.3 79.0 - - - +
158A PHE* 1.3 62.7 + - - +
159A LEU* 3.7 10.8 - - + +
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Residues in contact with PHE 158 (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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42A ASP* 3.4 14.1 + - - +
119A ARG* 3.4 59.5 - - + -
122A ILE* 4.3 11.9 - - + -
123A ALA* 4.3 6.5 - - + -
126A ILE* 3.7 21.3 - - + -
138A ILE* 3.4 34.8 - - + -
147A ILE* 4.7 5.6 - - + -
148A ALA 3.4 3.4 - - - +
149A GLY* 4.7 0.7 - - - -
156A ILE* 4.1 13.2 - - + -
157A MET* 1.3 76.3 - - - +
159A LEU* 1.3 62.4 + - - +
166A GLY* 3.5 18.4 - - - -
167A PHE* 3.5 38.5 + + + +
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Residues in contact with LEU 159 (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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42A ASP* 5.0 2.0 - - - +
45A LEU* 3.6 39.7 - - + -
46A ALA* 3.8 16.8 - - + +
49A LEU* 4.2 9.6 - - + -
69A ALA* 5.0 2.2 - - + -
73A MET* 4.6 15.0 - - + -
147A ILE* 3.8 3.8 - - - -
148A ALA* 2.8 54.5 + - + +
150A PHE* 4.3 14.6 - - + -
157A MET* 3.7 22.7 - - + +
158A PHE* 1.3 77.4 - - - +
160A ASP* 1.3 63.2 + - - +
161A VAL* 3.8 14.9 - - + +
165A LYS 4.0 2.9 - - - -
166A GLY 5.3 0.2 - - - -
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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