Contacts of the strand formed by residues 151 - 156 (chain B) in PDB entry 2G8N
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 VAL 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.4 12.3 - - + +
99B MET* 3.8 36.1 - - + -
113B TRP* 5.9 0.4 - - + -
114B LEU* 4.1 32.7 - - + +
147B LEU* 3.0 37.4 + - + +
148B ARG 3.8 9.2 + - - +
149B ALA 3.5 1.8 - - - +
150B ARG* 1.3 74.6 - - - +
152B LYS* 1.3 60.8 + - - +
153B ARG 4.0 18.6 - - - +
154B VAL* 4.1 2.9 - - + -
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Residues in contact with LYS 152 (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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95B GLU 3.5 19.9 + - - -
96B ASP* 3.4 23.8 - - - +
97B ILE 2.8 9.3 + - - +
149B ALA 2.8 26.7 + - - +
150B ARG* 3.5 8.8 - - - +
151B VAL* 1.3 72.6 - - - +
153B ARG* 1.3 87.0 + - - +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP* 2.8 38.6 + - - -
97B ILE 3.8 1.2 + - - -
98B THR* 2.7 43.5 + - + +
99B MET 3.0 24.3 + - - -
151B VAL* 3.5 6.2 + - - +
152B LYS* 1.3 98.2 + - - +
154B VAL* 1.3 67.1 + - - +
155B LEU* 3.9 27.6 - - + -
170B PRO* 4.0 21.1 + - + +
171B ALA 4.1 3.8 - - - +
172B PRO* 3.4 19.8 - - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET* 3.3 15.7 - - + +
100B THR* 5.1 0.9 - - - +
107B ARG* 3.9 42.3 - - + +
110B LEU* 4.0 22.2 - - + -
111B GLY* 6.1 0.2 - - - -
114B LEU* 3.8 28.3 - - + -
151B VAL* 4.1 8.1 - - + -
153B ARG* 1.3 78.9 - - - +
155B LEU* 1.3 64.3 + - - +
156B PRO* 4.5 1.2 - - - +
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Residues in contact with LEU 155 (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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98B THR* 3.7 21.5 - - + -
99B MET 2.9 12.2 + - - +
100B THR* 3.0 9.0 - - + -
101B ASP 2.9 25.5 + - - +
107B ARG* 3.7 5.9 - - - -
153B ARG* 3.9 28.3 - - + -
154B VAL* 1.3 80.6 - - - +
156B PRO* 1.3 80.1 - - + +
165B LEU* 4.4 10.8 - - + -
169B SER* 5.1 0.9 - - - -
170B PRO* 4.0 27.4 - - + -
171B ALA* 4.0 20.0 - - + +
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Residues in contact with PRO 156 (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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101B ASP 3.2 10.5 - - - +
102B PHE 5.4 0.9 - - - +
107B ARG* 3.4 26.2 - - - +
154B VAL 4.5 1.8 - - - +
155B LEU* 1.3 98.1 - - + +
157B ILE* 1.3 61.6 + - - +
165B LEU* 3.8 19.4 - - - +
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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