Contacts of the strand formed by residues 92 - 100 (chain C) in PDB entry 5D4P
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.9 1.3 - - - +
105B LYS* 3.6 21.5 - - - -
106B PHE* 3.8 16.8 - - + -
202B BCT 3.5 8.3 - - - +
13C GLU 3.7 0.7 - - - +
14C ILE* 3.6 2.3 - - - -
15C ILE* 2.9 50.4 + - + +
86C PHE* 3.7 2.3 - - - -
91C GLY* 1.3 80.4 - - - +
93C VAL* 1.3 64.1 + - - +
94C PHE* 3.5 31.9 - - + -
201C ADP 3.7 24.9 - - + +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLN 4.1 2.3 - - - +
100B VAL* 3.8 3.8 - - - +
202B BCT 2.6 36.7 + - - +
204B BCT 4.6 7.4 - - - +
12C LEU* 4.4 15.9 - - + -
13C GLU 3.4 6.5 - - - +
14C ILE* 4.4 13.2 - - + -
79C LEU* 3.8 27.8 - - + -
82C PHE* 4.9 7.0 - - + -
86C PHE* 3.3 35.4 - - + -
92C VAL* 1.3 74.1 - - - +
94C PHE* 1.3 79.3 + - - +
95C VAL* 4.1 3.7 + - + +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 3.7 15.7 - - + -
67B ILE* 4.1 9.6 - - + -
69B ALA* 3.4 28.7 - - + -
98B ILE* 3.6 19.7 - - + -
99B GLN 3.9 2.5 - - - -
100B VAL* 4.1 3.6 - - + -
106B PHE* 3.9 11.9 - + - -
11C LYS 3.4 2.1 - - - +
12C LEU* 3.4 5.7 - - - -
13C GLU* 2.9 63.0 + - + +
15C ILE* 3.8 20.4 - - + -
92C VAL* 3.5 26.9 - - + -
93C VAL* 1.3 78.8 - - - +
95C VAL* 1.3 62.5 + - - +
96C HIS* 3.7 16.8 + - + -
201C ADP 3.8 11.4 - + - -
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.5 8.7 - - + -
98B ILE* 3.2 6.8 - - - -
99B GLN* 2.8 63.1 + - + +
100B VAL* 5.5 0.2 - - - -
10C LYS* 4.1 25.1 - - + -
11C LYS 3.8 2.5 - - - -
12C LEU* 4.4 21.1 - - + -
75C VAL* 4.6 10.1 - - + -
79C LEU* 4.4 21.5 - - + -
93C VAL* 4.4 13.0 - - + +
94C PHE* 1.3 76.5 - - - +
96C HIS* 1.3 61.8 + - - +
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Residues in contact with HIS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 4.0 21.3 - + + -
11B LYS* 3.0 22.3 + - - -
96B HIS* 4.1 11.7 - + + -
97B ASP 4.5 6.5 - - - +
98B ILE* 3.4 26.4 - - + +
10C LYS* 3.2 12.7 - - - +
11C LYS* 2.9 55.9 + - + +
13C GLU* 3.4 31.3 + - + -
94C PHE* 3.7 13.5 + - + -
95C VAL* 1.3 75.7 - - - +
97C ASP* 1.3 67.5 + - - +
98C ILE* 4.3 4.3 - - + -
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL 4.7 1.0 - - - +
96A HIS* 4.8 8.0 - - - +
97A ASP 5.0 2.8 + - - -
97B ASP 4.9 4.0 + - - -
99B GLN* 5.4 2.9 - - - +
9C LEU 3.8 3.9 - - - +
10C LYS* 2.5 36.3 + - - +
95C VAL 4.5 0.2 + - - -
96C HIS* 1.3 74.3 - - - +
98C ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.8 30.7 - - + -
95A VAL 3.4 11.7 - - - +
96A HIS* 3.7 34.3 - - + +
8C PRO* 3.5 5.5 - - - +
9C LEU* 2.9 46.0 + - + +
10C LYS 4.0 10.3 - - - +
11C LYS* 3.9 25.6 - - + -
69C ALA* 4.3 5.2 - - + -
96C HIS* 4.3 1.6 - - + -
97C ASP* 1.3 80.0 - - - +
99C GLN* 1.3 66.2 + - - +
100C VAL* 3.9 14.4 - - + -
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.5 13.0 + - - -
94A PHE* 3.9 0.9 - - - -
95A VAL* 2.9 52.0 + - + +
97A ASP* 5.1 5.2 - - - +
6C LEU* 3.8 44.2 + - + +
7C TYR 3.1 12.4 - - - +
8C PRO* 4.8 3.7 - - + +
98C ILE* 1.3 78.8 - - - +
100C VAL* 1.3 68.8 + - - +
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 4.1 5.2 - - - +
94A PHE* 4.3 1.3 - - + -
95A VAL* 5.5 0.7 - - - -
6C LEU* 3.5 8.1 - - - +
7C TYR* 2.7 43.3 + - + +
9C LEU* 3.8 36.6 - - + -
98C ILE* 3.9 13.5 - - + -
99C GLN* 1.3 80.1 - - - +
101C GLY* 1.3 61.5 + - - +
102C ARG 4.2 9.2 - - - +
103C PRO* 4.4 3.6 - - + -
106C PHE* 3.8 33.4 - - + -
202C BCT 3.5 13.2 - - - +
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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