Contacts of the strand formed by residues 99 - 106 (chain B) in PDB entry 1SN8
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 GLU 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A SER 4.2 0.9 - - - +
122A LEU* 3.6 31.6 - - + +
123A ALA* 2.8 50.7 + - + +
125A SER* 5.8 0.5 - - - -
43B LYS* 3.4 28.8 + - + +
44B GLY 3.0 15.3 - - - +
45B LYS* 4.4 21.5 - - + +
77B TYR* 4.0 4.2 - - - -
98B GLN* 1.3 81.2 + - - +
100B VAL* 1.3 65.9 + - - +
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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
----------------------------------------------------------
122A LEU* 4.4 2.2 - - - -
42B TYR 3.6 0.2 - - - +
43B LYS* 3.5 3.6 - - - +
44B GLY 2.8 38.9 + - - +
46B ILE* 4.1 28.7 - - + -
58B VAL* 4.2 7.6 - - + -
68B LEU* 4.2 10.3 - - + -
73B ILE* 6.3 0.4 - - + -
77B TYR* 3.7 28.9 - - + +
94B LEU* 4.5 12.1 - - + -
98B GLN* 4.6 2.2 - - + -
99B GLU* 1.3 79.0 - - - +
101B ILE* 1.3 63.9 + - - +
102B VAL* 3.5 24.4 + - + -
118B THR* 4.3 4.7 - - + -
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Residues in contact with ILE 101 (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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41A ILE* 3.8 18.2 - - + -
101A ILE* 4.5 11.0 - - + -
120A ILE* 3.9 33.7 - - + -
122A LEU* 3.8 26.9 - - + -
41B ILE* 3.6 29.2 - - + -
42B TYR 3.4 3.8 - - - +
43B LYS* 5.4 0.4 - - - -
77B TYR* 3.1 13.6 + - - +
100B VAL* 1.3 72.0 - - - +
102B VAL* 1.3 62.8 + - - +
118B THR* 3.4 27.4 - - - +
120B ILE* 4.0 11.3 - - + +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.4 5.4 - - - +
42B TYR* 2.8 50.3 + - + +
44B GLY* 4.6 4.7 - - - +
60B TYR* 4.4 8.3 - - + -
68B LEU* 4.5 4.7 - - + -
100B VAL* 3.5 25.6 - - + +
101B ILE* 1.3 79.2 - - - +
103B GLN* 1.3 63.0 - - - +
116B LEU* 4.0 35.7 - - + -
117B THR 3.1 15.5 - - - +
118B THR* 4.1 8.3 - - + -
120B ILE* 3.6 4.3 - - - -
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Residues in contact with GLN 103 (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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43A LYS* 4.4 3.1 + - - -
40B ASN* 3.4 32.2 + - - +
42B TYR* 4.6 2.0 - - - -
102B VAL* 1.3 74.5 - - - +
104B ILE* 1.3 64.3 + - - +
105B ASP* 3.3 20.4 + - - +
116B LEU* 3.4 8.9 - - - +
117B THR* 3.0 47.0 + - + +
119B PHE 4.0 2.6 + - - -
120B ILE* 3.5 16.9 - - + +
121B SER* 2.8 50.6 + - - +
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Residues in contact with ILE 104 (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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40B ASN* 2.8 36.3 + - - +
42B TYR* 3.9 28.9 - - + +
60B TYR* 3.9 21.5 - - + +
103B GLN* 1.3 73.5 + - - +
105B ASP* 1.3 61.3 + - - +
106B LYS 3.4 32.3 - - - +
107B GLU* 3.7 31.8 - - - +
114B ALA* 3.8 14.1 - - + -
115B ALA 3.7 3.1 - - - -
116B LEU* 3.9 10.5 - - + -
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Residues in contact with ASP 105 (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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72B GLU* 4.2 10.4 - - - +
103B GLN* 3.3 26.5 + - - -
104B ILE* 1.3 73.0 - - - +
106B LYS* 1.3 64.4 + - + +
115B ALA* 2.8 21.1 + - + +
116B LEU 4.9 1.0 - - - -
117B THR* 3.4 26.8 - - - +
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Residues in contact with LYS 106 (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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104B ILE* 3.4 7.0 - - - +
105B ASP* 1.3 84.3 - - + +
107B GLU* 1.3 63.1 + - - +
109B ARG* 3.9 34.0 - - - +
114B ALA* 3.2 3.8 - - - -
115B ALA* 2.9 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