Contacts of the strand formed by residues 63 - 68 (chain A) in PDB entry 5FOR
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 CYS 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASP 2.8 7.2 + - - +
9A ILE* 4.6 4.9 - - - -
10A LEU 2.9 25.1 + - - -
61A THR* 3.1 6.1 + - - -
62A ARG* 1.3 80.6 - - - +
64A VAL* 1.3 74.4 + - - +
65A VAL* 4.3 12.8 - - - -
94A ARG* 3.5 9.0 - - - +
96A VAL* 4.8 1.6 - - - -
134A VAL* 4.6 9.4 - - - -
137A ALA* 3.7 29.2 - - + +
138A ILE* 3.5 26.9 - - + -
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Residues in contact with VAL 64 (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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10A LEU* 3.4 6.5 - - + +
12A VAL* 3.7 28.5 - - + -
58A PHE* 4.7 3.6 - - + +
61A THR* 3.5 26.7 - - + -
63A CYS* 1.3 73.9 - - - +
65A VAL* 1.3 67.0 + - - +
66A VAL* 3.9 10.3 - - + -
88A ALA* 4.1 19.5 - - + +
89A PHE* 3.8 21.5 - - + -
94A ARG 3.1 9.6 + - - +
95A VAL* 3.6 8.5 - - + +
96A VAL* 2.9 26.9 + - - +
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Residues in contact with VAL 65 (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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9A ILE* 4.1 19.3 - - + -
10A LEU 2.8 11.8 + - - +
11A ILE* 3.4 10.1 - - + +
12A VAL* 2.9 28.6 + - - +
24A LEU* 4.5 11.9 - - + -
28A PHE* 4.7 6.3 - - + -
63A CYS* 4.3 4.0 - - - -
64A VAL* 1.3 75.7 - - - +
66A VAL* 1.3 63.0 + - - +
67A LEU* 3.9 20.4 + - + -
96A VAL* 3.3 21.3 - - + +
98A LEU* 5.3 4.0 - - + +
121A LEU* 5.8 2.2 - - + -
134A VAL* 3.9 27.8 - - + -
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Residues in contact with VAL 66 (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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12A VAL* 3.8 6.1 - - + +
64A VAL* 3.9 17.9 - - + -
65A VAL* 1.3 74.7 - - - +
67A LEU* 1.3 62.7 + - - +
68A LEU* 3.2 11.4 + - + +
72A LEU* 3.8 28.7 - - + -
76A PHE* 4.8 2.2 - - + -
89A PHE* 4.1 28.0 - - + -
95A VAL* 3.9 16.4 - - + -
96A VAL 2.6 17.4 + - - +
97A ARG* 3.3 8.3 - - + +
98A LEU 2.8 27.2 + - - -
118A TRP* 4.3 7.6 - - + -
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Residues in contact with LEU 67 (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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11A ILE* 4.0 6.5 - - + -
12A VAL 2.9 16.3 + - - +
13A TYR* 3.8 23.0 - - + -
17A ALA* 3.8 12.6 - - + +
20A TRP* 3.7 16.4 - - + -
21A CYS* 3.6 35.9 - - + +
24A LEU* 3.7 22.0 - - + -
65A VAL* 4.1 10.5 - - + -
66A VAL* 1.3 75.9 - - - +
68A LEU* 1.3 60.2 + - - +
69A SER* 3.0 10.7 + - - -
72A LEU* 3.6 20.4 - - - +
98A LEU* 3.8 21.3 - - + +
100A CYS* 5.1 2.7 - - + -
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Residues in contact with LEU 68 (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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66A VAL* 3.2 9.4 + - + +
67A LEU* 1.3 68.0 - - - +
69A SER* 1.3 58.5 + - - +
72A LEU* 4.0 7.9 - - + -
73A VAL* 4.0 11.0 - - + -
76A PHE* 3.8 29.4 - - + -
97A ARG* 4.3 4.3 - - + -
98A LEU 2.7 21.7 + - - +
99A LEU* 3.5 24.9 - - + -
100A CYS* 2.8 22.4 + - - +
102A VAL* 3.4 32.0 - - + +
104A ASP* 5.6 0.2 - - - -
108A PHE* 4.1 5.6 - - + -
115A TRP* 3.6 32.3 - - + -
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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