Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 1S5H
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 ALA 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 4.1 20.4 - - + -
39B GLN 3.2 18.4 - - - +
40B ARG* 3.6 12.8 - - - +
41B PRO* 4.6 4.7 - - - -
90B ASP 3.3 4.7 + - - +
91B SER* 1.3 77.1 - - - +
93B VAL* 1.3 69.2 + - - +
94B TYR* 3.4 9.9 - - + -
113B THR* 4.6 2.9 - - - -
114B VAL 2.9 29.9 + - - -
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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
----------------------------------------------------------
37B VAL 3.9 0.5 - - - +
38B LYS* 3.8 1.6 - - - -
39B GLN* 2.9 41.3 + - + +
92B ALA* 1.3 76.1 - - - +
94B TYR* 1.3 62.0 + - - +
95B TYR* 3.6 40.0 + - + +
110B ALA 4.9 1.1 - - - +
111B GLY* 4.2 11.9 - - - -
112B THR 3.5 9.0 - - - +
113B THR* 3.7 23.1 - - + +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 2.8 18.8 - - - +
20B LEU* 3.8 18.2 - - + -
36B TRP* 4.8 3.8 - - + -
37B VAL 3.5 2.0 - - - +
38B LYS* 3.8 28.4 + - + +
48B ILE* 3.5 31.9 - - + -
81B MET* 3.5 14.1 - - + -
83B LEU* 3.8 22.0 - - + +
90B ASP* 2.6 44.7 + - - +
92B ALA 3.4 17.9 - - - -
93B VAL* 1.3 72.0 - - - +
95B TYR* 1.3 61.7 + - - +
112B THR* 2.9 22.0 + - - +
114B VAL* 3.5 25.1 - - + -
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Residues in contact with TYR 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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38A GLN* 3.1 23.7 + - - -
41A ASN 5.5 1.2 - - - -
42A GLY 3.3 8.2 + - - -
43A SER* 3.5 23.3 - - - -
44A PRO* 4.0 5.8 - - + -
6B GLN* 3.6 3.4 - - - +
36B TRP* 3.2 8.3 - - - -
37B VAL* 2.8 43.3 + - + +
39B GLN* 3.3 28.2 + - + -
45B LEU* 4.7 2.2 - - + -
93B VAL* 3.6 26.5 - - + +
94B TYR* 1.3 74.7 - - - +
96B CYS* 1.3 61.6 + - - +
108B TRP* 3.7 26.9 - + + -
109B GLY 3.5 17.9 - - - -
110B ALA 3.6 13.9 - - - -
111B GLY* 3.7 6.1 - - - -
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Residues in contact with CYS 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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4B LEU* 4.0 12.6 - - - -
6B GLN* 3.1 33.4 - - - +
22B CYS* 2.7 45.5 - - + -
34B ILE* 4.5 1.8 - - + -
35B HIS 3.1 10.3 - - - +
36B TRP* 4.0 15.9 - - + -
37B VAL* 6.3 0.2 - - - -
95B TYR* 1.3 76.0 - - - +
97B ALA* 1.3 63.4 + - - +
108B TRP* 3.5 1.9 - - - +
109B GLY 2.8 24.6 + - - -
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Residues in contact with ALA 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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4B LEU* 3.5 5.4 - - - -
34B ILE* 3.4 6.4 - - - +
35B HIS* 2.8 35.9 + - + +
37B VAL* 5.5 2.0 - - + -
96B CYS* 1.3 76.9 - - - +
98B ARG* 1.3 62.2 + - - +
105B PHE* 3.9 24.9 - - + -
107B VAL 3.2 14.1 - - - +
108B TRP* 3.9 24.2 - - + -
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Residues in contact with ARG 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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3B GLN* 3.1 22.6 - - - +
4B LEU* 3.6 11.0 - - + +
24B ALA* 3.6 21.4 - - - +
25B SER 3.1 24.0 + - - -
27B TYR 3.4 18.2 + - - +
28B THR* 3.8 11.9 - - - +
32B ASP* 4.2 9.0 + - - +
33B TRP 3.7 3.6 - - - +
34B ILE* 4.0 17.3 - - + +
97B ALA* 1.3 73.8 - - - +
99B GLU* 1.3 70.0 - - - +
100B ARG* 3.0 44.6 + - - +
105B PHE* 3.7 3.5 - - - -
106B ALA* 3.2 27.3 + - - +
107B VAL* 2.9 28.5 + - + -
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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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96A PHE* 3.8 6.6 - - + -
32B ASP* 3.5 2.1 - - - -
33B TRP* 2.8 40.3 + - - +
35B HIS* 2.9 26.3 + - + +
97B ALA 4.1 0.2 + - - -
98B ARG* 1.3 77.2 - - - +
100B ARG* 1.3 61.8 + - - +
101B GLY* 3.1 14.9 + - - +
103B GLY* 2.7 31.8 + - - +
104B TYR 3.3 24.2 - - - +
105B PHE* 4.2 4.5 - - + -
106B ALA 5.0 0.2 - - - +
52C ARG* 2.7 42.5 + - - -
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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