Contacts of the strand formed by residues 61 - 65 (chain B) in PDB entry 5V6Y
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 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.8 4.7 - - + -
10B VAL 3.2 3.6 + - - -
11B ILE* 3.4 19.4 - - + -
12B TRP 3.0 24.4 + - - -
59B PRO* 3.6 8.0 - - - +
60B ASP* 1.3 85.9 - - + +
62B ILE* 1.3 63.7 + - - +
63B PHE* 3.7 24.7 - - + -
266B ALA* 4.0 14.4 - - + -
267B GLY 3.3 12.1 - - - +
268B ILE* 4.8 0.7 - - + -
278B ALA* 3.8 30.7 - - + +
281B PHE* 4.2 13.2 - - + -
282B LEU* 3.8 28.0 - - + -
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Residues in contact with ILE 62 (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 TRP* 3.6 7.0 - - + +
45B LEU* 3.9 24.5 - - + -
49B PHE* 3.4 63.9 - - + -
59B PRO* 4.6 4.0 - - + -
61B ILE* 1.3 74.8 - - - +
63B PHE* 1.3 69.3 + - - +
64B TRP* 4.8 4.5 - - + +
69B PHE* 3.7 10.5 - - + -
72B TYR* 4.1 15.9 - - + +
78B LEU* 4.5 2.0 - - + -
265B SER 3.5 1.4 - - - +
266B ALA* 3.3 4.0 - - - -
267B GLY* 3.0 43.2 + - - +
269B ASN 5.8 0.9 - - - +
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Residues in contact with PHE 63 (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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11B ILE* 3.6 27.4 - - + -
12B TRP 2.9 20.6 + - - +
13B ILE* 3.6 32.0 - - + +
14B ASN* 4.3 2.1 + - - +
22B LEU* 4.0 15.5 - - + -
45B LEU* 3.8 14.7 - - - +
61B ILE* 3.7 13.9 - - + -
62B ILE* 1.3 76.1 - - - +
64B TRP* 1.3 67.1 + - - +
110B ILE* 3.9 16.4 - - + -
264B LEU* 4.4 14.4 - - + -
265B SER 3.3 7.4 - - - -
266B ALA* 3.6 22.4 - - + -
281B PHE* 5.4 0.2 - + - -
282B LEU* 4.0 5.2 - - + -
286B LEU* 3.5 33.2 - - + -
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Residues in contact with TRP 64 (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 ASN* 3.4 43.7 - - + -
45B LEU* 3.8 27.6 - - + -
46B GLU* 3.2 43.1 - - + -
62B ILE* 4.9 6.1 - - + -
63B PHE* 1.3 78.8 - - - +
65B ALA* 1.3 93.4 + - + +
67B ASP* 4.1 5.1 + - - -
68B ARG* 3.5 31.8 - - + +
69B PHE* 3.1 18.6 - - + -
72B TYR* 5.5 1.6 - - + -
264B LEU* 4.0 10.4 - - - +
265B SER 2.8 27.4 + - - -
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Residues in contact with ALA 65 (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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64B TRP* 1.3 93.2 - - + +
66B HIS* 1.3 64.0 + - - +
67B ASP* 3.0 23.2 + - - +
68B ARG 3.4 1.7 + - - -
69B PHE* 3.2 10.6 - - - -
113B GLU* 4.8 10.1 + - - +
262B GLY* 4.7 2.0 - - - -
263B VAL 3.5 15.3 - - - +
264B LEU* 4.3 4.6 - - - +
332B MET* 3.8 16.8 - - + -
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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
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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