Contacts of the strand formed by residues 64 - 68 (chain B) in PDB entry 4D9R
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 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.3 19.7 - - + -
34B GLN 3.3 10.3 - - - +
35B LEU* 4.6 11.4 - - + -
59B LEU* 4.3 28.9 - - + -
61B ALA* 4.8 5.6 - - + -
62B GLY 3.4 14.8 + - - +
63B LYS* 1.3 72.0 - - - +
65B GLN* 1.3 67.4 + - - +
84B ASP* 4.0 4.7 - - - +
85B VAL* 3.6 39.2 + - + +
106B LEU* 5.4 2.5 - - + -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER 3.6 0.9 - - - +
33B VAL* 3.6 3.6 - - - +
34B GLN* 2.7 44.9 + - + +
37B ASN* 5.5 0.2 - - - -
38B GLY* 4.6 14.7 + - - -
63B LYS* 4.0 25.6 - - + +
64B VAL* 1.3 79.0 - - - +
66B VAL* 1.4 63.2 + - - +
67B LEU 4.0 0.4 - - - -
82B LEU* 3.4 42.6 + - + +
83B TYR 3.4 15.2 + - - +
84B ASP* 3.5 21.5 + - - +
85B VAL* 4.3 1.3 - - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.8 27.1 - - + -
32B SER 3.5 5.4 - - - +
33B VAL* 4.5 8.7 - - + -
52B VAL* 3.9 19.3 - - + -
65B GLN* 1.4 75.1 - - - +
67B LEU* 1.3 62.3 + - - +
68B LEU* 4.2 8.5 - - + -
82B LEU* 4.4 0.7 - - - -
83B TYR* 3.0 38.9 + - - +
85B VAL* 3.8 20.1 - - + +
106B LEU* 4.1 25.6 - - + -
108B LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B MET 4.5 0.2 - - - +
31B ALA* 3.5 5.0 - - - -
32B SER* 2.9 51.1 + - - +
34B GLN* 3.4 22.2 - - - +
65B GLN 4.0 0.8 - - - -
66B VAL* 1.3 69.8 - - - +
68B LEU* 1.3 59.5 + - - +
70B ALA* 4.0 21.5 + - + +
73B LEU* 4.3 13.9 - - + +
80B LYS* 3.6 42.0 - - + +
81B ARG 3.7 19.1 - - - +
82B LEU* 3.7 23.8 - - + +
141B TRP* 5.5 1.6 - - + -
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Residues in contact with LEU 68 (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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28B PRO 4.6 4.0 - - - +
30B MET 4.5 11.9 - - - +
31B ALA* 4.7 3.1 - - + -
46B LEU* 4.1 27.1 - - + -
52B VAL* 4.3 1.3 - - + -
66B VAL* 3.6 19.2 + - + -
67B LEU* 1.3 72.9 - - - +
69B GLY* 1.3 64.7 + - - +
70B ALA* 3.3 5.0 + - - +
79B SER 3.7 1.8 - - - +
80B LYS* 3.5 1.7 - - - -
81B ARG* 3.1 28.7 + - - +
83B TYR* 3.7 27.8 - - + -
108B LEU* 3.8 28.5 - - + -
112B ALA* 4.6 1.6 - - + -
120B VAL* 3.5 36.8 - - + -
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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
------------------------------------------------------------
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