Contacts of the strand formed by residues 12 - 15 (chain B) in PDB entry 3L6D
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 1.3 82.7 - - - +
13B SER* 1.3 74.2 + - - +
14B VAL* 4.7 0.4 - - + -
28B LEU* 4.1 15.5 - - + -
33B LYS* 4.3 5.8 - - + -
34B ARG 3.4 1.9 + - - +
35B VAL* 3.4 27.3 - - + +
36B ALA 3.1 20.8 + - - +
66B SER* 3.1 9.6 + - - -
68B ALA* 3.5 12.8 - - + +
70B ILE* 3.7 27.4 - - + -
156B LEU* 4.0 26.5 - - + -
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Residues in contact with SER 13 (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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12B VAL* 1.3 80.5 - - - +
14B VAL* 1.3 57.5 + - - +
36B ALA* 3.0 19.6 - - - +
62B ALA* 2.6 39.6 + - - -
65B ALA* 4.1 0.2 - - - +
66B SER* 2.8 18.6 + - - -
68B ALA 3.0 7.2 + - - -
69B THR* 3.3 16.3 - - - -
70B ILE 2.7 29.6 + - - -
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.7 0.7 - - + -
13B SER* 1.3 79.8 - - - +
15B ILE* 1.3 66.5 + - - +
16B GLY 3.9 13.5 - - - +
17B LEU* 3.9 4.4 - - + +
21B GLY* 3.9 25.1 - - - +
24B MSE 5.2 1.8 - - + -
25B ALA* 4.2 14.1 - - + +
28B LEU* 4.5 13.5 - - + -
35B VAL* 4.0 19.5 - - + -
36B ALA 2.9 6.3 + - - -
37B ILE* 3.3 15.7 - - + +
38B TRP 3.2 23.2 + - - +
70B ILE* 3.4 23.8 - - + +
72B VAL* 4.7 1.3 - - + -
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Residues in contact with ILE 15 (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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14B VAL* 1.3 78.0 - - - +
16B GLY* 1.3 64.8 + - - +
38B TRP* 3.6 25.8 - - + -
59B VAL* 4.1 27.1 - - + +
62B ALA* 4.0 24.7 - - + -
63B LEU* 4.8 2.0 - - + -
69B THR* 3.7 22.7 - - + -
70B ILE 2.8 12.5 + - - +
71B PHE* 3.7 12.2 - - + -
72B VAL* 3.0 27.5 + - - +
73B LEU* 4.1 16.6 - - + +
82B VAL* 4.6 11.2 - - + -
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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