Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 2D4H
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 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 4.0 22.9 - - + +
34B ILE* 3.8 12.6 - - + -
36B GLN* 3.6 35.7 - - + +
37B PRO 2.9 10.1 + - - +
38B MET* 3.2 17.5 - - + -
39B VAL* 2.8 25.9 + - - +
82B CYS* 4.3 17.5 - - + -
83B VAL 3.7 6.5 - - - +
84B PRO* 3.9 15.5 - - + -
85B HIS* 4.4 3.1 - - - -
91B HIS* 1.3 85.4 - - - +
93B LEU* 1.3 70.6 + - - +
94B VAL* 3.7 9.0 + - + -
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Residues in contact with LEU 93 (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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39B VAL* 3.5 17.7 - - + +
41B VAL* 3.8 19.1 - - + -
58B LEU* 3.5 25.8 - - + +
81B TRP 3.2 5.7 - - - +
82B CYS* 3.4 1.0 - - - -
83B VAL* 2.6 53.9 + - + +
85B HIS* 3.8 33.2 - - + +
86B PRO* 4.9 2.0 - - + -
92B ILE* 1.3 71.0 - - - +
94B VAL* 1.3 60.6 + - - +
95B LEU* 3.8 21.5 - - + -
273B ILE* 4.8 3.8 - - + -
274B PHE* 3.7 19.5 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 6.0 0.2 - - + -
31B LEU* 4.8 2.2 - - + -
38B MET* 3.7 49.6 - - + -
39B VAL 3.1 5.8 + - - +
40B VAL* 3.5 15.5 - - + +
41B VAL* 2.8 31.0 + - - +
80B MET* 4.6 7.0 - - + -
81B TRP 3.7 2.2 - - - -
82B CYS* 3.9 20.0 - - - -
92B ILE* 4.3 2.0 - - + -
93B LEU* 1.3 75.1 - - - +
95B LEU* 1.3 61.8 + - - +
96B LEU* 4.3 17.7 - - + -
293B LEU* 4.2 17.0 - - + -
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Residues in contact with LEU 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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41B VAL* 3.4 18.8 - - + +
43B ILE* 5.3 2.5 - - + -
55B MET* 3.3 40.9 - - + +
58B LEU* 3.7 34.5 - - + +
59B ALA* 3.8 25.1 - - + +
79B TRP 3.2 1.0 - - - +
80B MET* 3.0 7.6 - - - -
81B TRP* 2.9 49.2 + - + +
83B VAL* 4.6 2.7 - - + -
93B LEU* 3.8 18.2 - - + -
94B VAL* 1.3 74.6 - - - +
96B LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 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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13B LEU* 3.7 28.5 - - + -
40B VAL* 3.6 28.5 - - + -
41B VAL 2.8 12.4 + - - +
42B ALA* 4.1 9.0 - - + -
43B ILE* 2.6 37.7 + - - +
55B MET* 4.5 0.9 - - - -
78B ILE* 3.9 11.4 - - + -
79B TRP 3.1 12.8 - - - +
80B MET* 4.0 10.1 - - + -
94B VAL* 4.3 8.7 - - + -
95B LEU* 1.3 75.2 - - - +
97B ASP* 1.3 57.8 - - - +
98B THR* 5.9 0.2 - - - -
119B ALA* 4.3 17.7 - - + +
122B LEU* 3.8 28.0 - - + -
293B LEU* 5.6 2.2 - - + -
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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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43B ILE* 3.3 12.7 - - + +
51B LYS* 3.5 31.2 - - - +
52B SER* 5.3 2.6 + - - -
55B MET* 3.9 27.0 - - + +
77B GLY 3.2 1.4 - - - +
78B ILE* 3.1 10.5 - - - +
79B TRP* 3.0 34.4 + - + +
96B LEU* 1.3 75.4 - - - +
98B THR* 1.3 68.6 + - - +
99B GLU* 2.8 36.6 + - - +
593B 5GP 5.0 1.6 + - - -
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Residues in contact with THR 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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43B ILE 3.2 3.9 + - - -
44B VAL* 3.0 46.5 - - + -
45B GLY 3.1 14.7 + - - +
51B LYS* 3.4 16.3 - - - -
77B GLY 3.4 5.6 - - - -
78B ILE* 4.6 1.6 - - + -
96B LEU 5.9 0.2 - - - -
97B ASP* 1.3 74.9 + - - +
99B GLU* 1.3 64.7 + - - +
100B GLY 3.2 7.4 + - - +
101B LEU* 4.0 10.0 - - - +
115B ILE* 4.1 21.1 - - + +
116B PHE* 4.5 4.3 - - - -
119B ALA* 3.9 17.0 - - + -
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Residues in contact with GLU 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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47B TYR* 5.0 8.0 - - - -
51B LYS* 5.2 1.3 - - - +
52B SER* 5.5 3.1 - - - -
76B LYS* 3.4 16.3 - - + +
77B GLY 2.8 35.0 + - - +
79B TRP* 3.5 33.2 - - + +
97B ASP* 2.8 23.6 - - - +
98B THR* 1.3 69.6 - - - +
100B GLY* 1.3 67.5 + - - +
593B 5GP 4.1 20.3 + - - -
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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