Contacts of the strand formed by residues 101 - 107 (chain A) in PDB entry 1ISR
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 LEU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A MET* 4.3 8.5 - - - +
42A ASP 4.8 1.6 - - - +
43A GLY* 4.7 1.6 - - - -
45A VAL* 3.3 21.8 - - + +
47A ILE* 3.9 21.3 - - + -
86A LEU* 4.0 16.8 - - + +
89A ILE* 3.9 23.6 - - + -
90A ASN* 2.7 30.6 + - - +
96A LEU* 3.6 28.7 - - + -
99A ILE* 4.9 2.7 - - + +
100A THR* 1.3 73.7 - - - +
102A GLY* 1.3 61.1 + - - +
417A ILE 5.7 0.2 - - - +
421A ALA* 4.3 11.7 - - + -
424A LEU* 3.6 28.5 - - + -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A MET* 3.2 18.4 - - - -
42A ASP 4.2 6.5 - - - -
43A GLY* 4.3 0.4 - - - -
45A VAL 2.8 11.6 + - - +
46A ILE* 3.6 12.1 - - - +
47A ILE* 3.1 23.7 + - - +
86A LEU* 4.1 5.2 - - - +
100A THR 3.8 1.8 + - - -
101A LEU* 1.3 76.4 - - - +
103A SER* 1.3 66.2 + - - -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA 4.2 0.2 - - - -
40A ARG* 3.3 6.4 - - - +
41A MET* 2.8 47.4 + - - +
46A ILE* 3.9 8.2 - - - +
47A ILE* 3.4 15.0 - - - -
82A MET* 4.7 5.6 - - - -
83A PHE* 3.8 13.2 - - - -
86A LEU* 3.4 24.2 - - - +
102A GLY* 1.3 75.1 - - - -
104A GLU* 1.3 60.7 + - - +
105A ILE* 3.9 10.3 - - - +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.0 18.4 - - + -
39A ALA 3.6 3.1 - - - -
40A ARG* 4.1 19.3 + - + +
46A ILE* 3.9 14.8 - - + +
47A ILE 3.5 5.7 + - - -
48A GLY* 3.3 4.4 - - - -
49A ALA 3.3 18.0 + - - -
103A SER* 1.3 74.1 - - - +
105A ILE* 1.3 59.4 + - - +
106A ARG* 2.8 35.1 + - - +
121A GLU 4.6 1.7 - - - +
122A PHE* 3.4 22.8 - - + -
154A LYS 5.4 2.4 - - - +
156A ILE* 4.2 18.4 - - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.2 22.3 - - - +
39A ALA* 2.8 25.9 + - + +
49A ALA* 3.4 11.7 - - + +
51A PHE* 3.6 27.8 - - + -
79A VAL* 3.7 19.1 - - + -
82A MET* 3.5 33.9 - - + -
83A PHE* 3.6 28.5 - - + -
103A SER* 4.5 7.2 - - - +
104A GLU* 1.3 74.5 - - - +
106A ARG* 1.3 65.1 + - - +
367A TRP* 3.9 19.6 - - + -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 5.3 2.2 - - - +
37A SER 5.3 1.3 - - - -
38A VAL* 3.2 26.4 - - + +
40A ARG* 3.9 15.0 - - - +
49A ALA 2.9 7.3 + - - -
50A LEU* 3.3 19.9 - - + +
51A PHE 3.3 21.7 + - - +
53A VAL* 5.2 0.2 - - - -
104A GLU* 2.8 34.1 + - - +
105A ILE* 1.3 80.6 - - - +
107A ASP* 1.3 63.7 + - - +
118A GLN* 3.2 39.7 + - + +
121A GLU* 3.4 34.7 + - - +
122A PHE* 3.5 22.9 - - + -
367A TRP* 4.4 6.1 - - - -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 5.6 3.1 - - - +
37A SER 5.0 2.8 + - - +
50A LEU* 4.7 0.6 - - - +
51A PHE 3.6 4.5 - - - -
53A VAL* 3.0 34.6 + - + -
54A HIS* 2.8 27.6 + - - -
67A CYS* 4.6 0.5 - - - -
106A ARG* 1.3 72.4 - - - +
108A SER* 1.3 68.8 + - - +
109A CYS* 3.0 29.5 + - - -
114A VAL* 4.2 5.3 - - + +
118A GLN* 3.2 29.8 + - - +
367A TRP* 4.2 15.4 + - + +
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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