Contacts of the strand formed by residues 115 - 122 (chain A) in PDB entry 2V62
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.9 4.0 - - - +
65A GLN* 3.1 45.0 + - - +
108A LEU* 4.9 10.2 - - - +
109A THR 3.5 7.1 + - - -
110A GLU* 4.6 5.1 - - - +
113A GLY 3.9 3.2 + - - -
114A ARG* 1.3 74.5 - - - +
116A TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 116 (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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15A PHE* 4.1 8.5 - + - -
62A VAL* 3.8 20.0 - - + -
63A GLU* 3.4 7.4 - - - +
64A TYR* 3.5 31.6 - - + +
65A GLN* 4.8 0.4 - - - -
108A LEU* 3.1 9.7 - - - +
109A THR* 2.8 46.1 + - + +
111A PHE* 3.3 32.4 - - + +
114A ARG* 3.6 29.8 - - + +
115A SER* 1.3 77.4 - - - +
117A ARG* 1.3 60.1 + - - +
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Residues in contact with ARG 117 (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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62A VAL* 3.5 2.3 - - - +
63A GLU 2.7 34.8 + - - +
64A TYR 4.1 8.8 + - - +
65A GLN* 3.6 50.1 + - + +
66A GLU 5.3 1.2 + - - -
68A GLY 5.4 1.2 - - - +
70A LEU* 3.5 14.1 - - + +
71A PHE* 3.6 45.4 - - - +
74A LEU* 3.8 24.2 - - + -
107A GLY 3.5 9.4 - - - +
108A LEU* 3.8 7.6 - - + +
116A TYR* 1.3 74.5 - - - +
118A PHE* 1.3 66.7 + - - +
1332A SIN 2.7 35.1 + - - +
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.7 34.8 - - + -
22A ASP 3.5 28.7 - - - -
23A ASP* 3.8 5.8 - - + -
29A TRP* 4.5 1.6 - + - -
60A VAL* 3.7 21.5 - - + -
61A LYS 3.1 10.5 - - - +
62A VAL* 4.1 10.3 - - + -
70A LEU* 4.4 1.1 - - - -
74A LEU* 5.2 0.4 - - - +
106A SER* 3.1 11.2 - - - -
107A GLY 2.9 67.5 + - - +
108A LEU* 3.7 15.7 - - - -
109A THR* 4.2 7.4 - - + -
117A ARG* 1.3 81.4 - - - +
119A MET* 1.3 63.7 + - - +
120A VAL* 3.8 21.5 - - + -
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.3 3.0 - - - -
61A LYS* 2.8 56.4 + - + +
70A LEU* 3.7 26.0 - - + -
73A GLU* 4.1 4.9 - - + +
74A LEU* 3.8 31.0 - - + -
77A TYR* 3.7 38.4 - - + -
103A PHE* 3.6 25.4 - - + -
105A GLY 3.5 3.6 - - - -
118A PHE* 1.3 77.4 - - - +
120A VAL* 1.3 63.9 + - - +
121A MET* 3.8 13.0 + - + +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TRP* 3.7 63.7 - - + +
46A ALA* 4.5 3.4 - - + -
58A HIS* 4.0 11.9 - - + -
59A VAL 3.5 11.7 - - - +
60A VAL* 4.5 7.2 - - + -
103A PHE* 3.8 5.2 - - - -
104A TYR* 2.8 35.2 + - + -
105A GLY 2.7 19.4 + - - +
118A PHE* 3.8 18.2 - - + -
119A MET* 1.3 73.5 - - - +
121A MET* 1.3 64.6 + - - +
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.9 7.4 - - + -
58A HIS* 3.4 5.5 - - - +
59A VAL* 2.8 54.9 + - + +
61A LYS* 4.6 24.0 - - + -
77A TYR* 4.5 16.2 - - + +
101A PRO* 4.0 25.1 - - + -
102A LEU 3.4 11.4 - - - +
103A PHE* 5.0 2.2 - - + -
104A TYR* 3.7 6.5 - - - -
119A MET* 4.6 18.8 - - + +
120A VAL* 1.3 74.0 - - - +
122A GLU* 1.3 75.4 - - - +
124A LEU* 4.4 10.1 - - + +
173A LEU* 5.9 2.5 - - + -
185A ALA* 5.5 5.8 - - + -
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Residues in contact with GLU 122 (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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57A ARG* 3.7 8.3 - - + +
59A VAL* 3.7 1.6 - - - +
100A ILE 4.3 0.2 - - - +
101A PRO* 3.7 9.9 - - + +
102A LEU* 2.9 50.0 + - - +
104A TYR* 3.4 19.5 - - + +
121A MET* 1.3 94.8 - - - +
123A ARG* 1.3 74.9 + - - +
124A LEU* 3.7 13.6 + - + +
177A LYS* 5.2 11.4 + - + +
183A TYR* 4.1 18.1 + - - -
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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