Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 1P57
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 ARG 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A CYS* 4.0 0.3 - - - -
33A SER* 2.9 23.0 + - - -
58A GLU* 3.0 41.9 + - + +
59A LEU 3.1 11.4 - - - +
60A ASP* 3.4 29.7 + - - +
72A PHE* 5.0 0.2 - - - -
95A CYS* 3.5 12.8 - - - -
97A ARG* 3.1 49.8 + - + +
98A GLY* 1.3 77.0 - - - +
100A PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 100 (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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17A ARG* 3.6 47.1 - - + -
18A LEU 5.4 0.2 - - - -
30A LEU* 3.6 39.7 - - + -
31A LEU 3.2 16.4 - - - +
33A SER* 3.9 6.1 - - - +
58A GLU* 3.2 5.0 - - - -
59A LEU* 2.7 65.9 + - + -
60A ASP 3.8 2.5 - - - -
61A VAL* 3.5 33.0 - - + -
64A ALA* 4.2 2.7 - - + -
65A GLY 3.8 3.1 - - - -
72A PHE* 4.2 8.5 - + + -
98A GLY 4.2 2.0 - - - -
99A ARG* 1.3 78.4 - - - +
101A LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.6 2.8 - - - -
18A LEU* 3.1 48.8 + - + +
31A LEU* 3.0 22.0 + - + +
32A CYS 5.3 0.4 - - - +
33A SER* 4.4 2.0 - - - +
37A ASN* 3.7 46.0 - - + +
40A VAL* 3.7 27.1 - - + -
41A ALA* 3.9 4.0 - - - +
56A HIS* 3.7 19.1 - - + +
57A SER 3.6 15.5 - - - +
58A GLU* 4.8 0.4 - - - +
100A PHE* 1.3 79.8 - - - +
102A ALA* 1.3 70.0 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASP 3.7 17.3 - - - +
16A ALA* 3.0 18.8 - - + +
17A ARG* 3.7 0.2 - - - +
18A LEU 4.3 0.2 - - - +
56A HIS* 3.0 8.7 - - - +
57A SER* 3.0 46.8 + - - +
59A LEU* 3.9 16.8 - - + -
101A LEU* 1.3 77.1 - - - +
103A ALA* 1.3 61.1 + - - +
104A ILE* 5.8 0.7 - - + -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.3 15.1 - - - +
16A ALA* 2.7 22.1 + - - +
18A LEU* 3.8 31.3 - - + +
41A ALA* 4.1 20.2 - - + +
45A CYS* 4.3 13.5 - - - -
55A THR 3.7 4.7 - - - +
56A HIS* 4.1 0.2 - - - +
102A ALA* 1.3 76.3 - - - +
104A ILE* 1.3 64.1 + - - +
105A CYS* 3.7 2.4 + - - -
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Residues in contact with ILE 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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16A ALA* 3.7 23.1 - - + -
53A ALA* 3.3 3.2 - - - -
54A LEU* 2.6 49.3 + - + -
55A THR* 2.8 37.7 + - + +
56A HIS* 5.1 1.8 - - - +
57A SER* 6.0 2.0 - - - +
102A ALA* 5.8 0.7 - - + -
103A ALA* 1.3 71.5 - - - +
105A CYS* 1.3 59.7 + - - +
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Residues in contact with CYS 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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11A VAL* 4.9 7.4 - - + +
45A CYS* 2.0 48.7 - - - -
48A MET* 3.8 19.1 - - - -
50A PHE* 3.6 27.5 - - + -
52A ARG 3.2 6.5 - - - -
54A LEU* 4.0 7.3 - - - +
103A ALA* 3.7 10.0 + - - -
104A ILE* 1.3 81.4 - - - +
106A GLN* 1.3 66.2 + - - +
107A ASP* 3.2 4.5 + - - +
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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