Contacts of the strand formed by residues 92 - 100 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 3.6 4.7 - - - +
105A LYS* 3.7 19.5 - - - -
106A PHE* 3.9 12.3 - - + -
202A BCT 3.5 7.6 - - - +
13B GLU 3.7 0.7 - - - +
14B ILE* 3.6 2.3 - - - -
15B ILE* 2.8 46.4 + - + +
86B PHE* 3.7 1.6 - - - -
91B GLY* 1.3 80.0 - - - +
93B VAL* 1.3 65.0 + - - +
94B PHE* 3.6 32.5 - - + -
201B ADP 3.7 35.2 - - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLN 4.1 1.7 - - - +
100A VAL* 3.8 4.2 - - - +
202A BCT 2.8 38.1 + - - +
12B LEU* 4.3 13.9 - - + -
13B GLU 3.3 7.0 - - - +
14B ILE* 4.3 18.6 - - + -
79B LEU* 3.7 30.7 - - + -
82B PHE* 5.0 6.1 - - + -
86B PHE* 3.4 35.4 - - + -
92B VAL* 1.3 74.9 - - - +
94B PHE* 1.3 73.5 + - - +
95B VAL* 4.4 3.7 - - + +
203B BCT 4.7 4.7 - - - +
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Residues in contact with PHE 94 (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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11A LYS* 3.7 15.7 - - + -
67A ILE* 4.0 18.4 - - + -
69A ALA* 3.6 20.9 - - + -
98A ILE* 3.7 21.3 - - + -
99A GLN 4.0 2.5 - - - -
100A VAL* 4.2 2.9 - - + -
106A PHE* 3.8 11.9 - + - -
11B LYS 3.5 5.9 - - - +
12B LEU* 3.5 1.9 - - - -
13B GLU* 2.8 51.4 + - + +
15B ILE* 3.8 20.2 - - + -
92B VAL* 3.6 27.1 - - + -
93B VAL* 1.3 80.6 - - - +
95B VAL* 1.3 61.5 + - - +
96B HIS* 3.5 17.0 + - + -
201B ADP 3.6 18.8 - + - -
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Residues in contact with VAL 95 (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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6A LEU* 4.6 7.2 - - + -
98A ILE* 3.3 6.5 - - - -
99A GLN* 2.9 63.6 + - + +
100A VAL* 5.5 0.4 - - - -
10B LYS* 4.3 16.6 - - + +
11B LYS 3.8 1.8 - - - -
12B LEU* 4.3 21.5 - - + -
75B VAL* 4.6 9.2 - - + -
79B LEU* 4.2 25.1 - - + -
93B VAL* 4.4 10.1 - - + +
94B PHE* 1.3 75.4 - - - +
96B HIS* 1.3 69.8 + - - +
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Residues in contact with HIS 96 (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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11A LYS* 2.9 21.8 + - - -
96A HIS* 3.9 23.1 - + + -
97A ASP 4.7 5.4 - - - +
98A ILE* 3.5 18.1 - - + +
10B LYS* 3.3 14.9 - - - +
11B LYS* 2.8 47.2 + - + +
13B GLU* 3.2 35.7 + - + +
94B PHE* 3.5 19.9 + - + -
95B VAL* 1.3 74.4 - - - +
97B ASP* 1.3 69.8 + - - +
98B ILE* 4.3 11.0 - - + -
96C HIS* 4.1 9.0 - + + -
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Residues in contact with ASP 97 (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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97A ASP 4.9 6.3 + - - +
99A GLN* 5.4 3.0 - - - +
9B LEU 3.9 4.4 - - - +
10B LYS* 2.5 35.5 + - - +
95B VAL 4.3 0.2 + - - -
96B HIS* 1.3 75.5 - - - +
98B ILE* 1.3 66.2 + - - +
96C HIS* 4.5 10.2 - - - +
97C ASP 4.9 2.8 + - - -
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Residues in contact with ILE 98 (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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8B PRO* 3.6 4.5 - - - +
9B LEU* 2.8 47.0 + - + +
10B LYS 4.2 1.6 - - - +
11B LYS* 3.8 29.8 - - + -
69B ALA* 4.1 11.9 - - + -
96B HIS* 4.3 1.3 - - + -
97B ASP* 1.3 81.1 - - - +
99B GLN* 1.3 66.4 + - - +
100B VAL* 4.1 11.4 - - + -
94C PHE* 3.6 32.5 - - + -
95C VAL 3.2 10.1 - - - +
96C HIS* 3.4 38.8 - - + +
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Residues in contact with GLN 99 (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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6B LEU* 3.5 43.3 + - + +
7B TYR 3.1 13.8 - - - +
8B PRO* 4.5 5.4 - - + +
9B LEU 4.6 0.2 - - - +
98B ILE* 1.3 77.7 - - - +
100B VAL* 1.3 69.6 + - - +
10C LYS* 4.2 17.7 + - - -
94C PHE* 3.9 0.5 - - - -
95C VAL* 2.8 51.0 + - + +
97C ASP* 5.1 2.9 - - - +
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Residues in contact with VAL 100 (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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6B LEU* 3.4 9.2 - - - -
7B TYR* 2.7 48.8 + - + +
9B LEU* 4.2 18.8 - - + -
98B ILE* 4.1 20.0 - - + -
99B GLN* 1.3 79.9 - - - +
101B GLY* 1.3 60.7 + - - +
102B ARG 4.4 4.7 - - - +
103B PRO* 4.4 11.2 - - + -
106B PHE* 3.8 36.3 - - + -
202B BCT 3.4 15.0 - - - +
93C VAL 3.8 6.7 - - - +
94C PHE* 4.1 2.0 - - + -
95C VAL* 5.5 0.4 - - - -
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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