Contacts of the strand formed by residues 58 - 62 (chain A) in PDB entry 2KBS
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 GLN 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.3 3.6 + - - +
35A PRO 5.5 0.8 + - - -
36A GLY* 3.5 7.0 - - - -
37A ILE 2.8 38.5 + - - +
38A PHE* 3.6 30.9 - - + +
57A ASP* 1.3 74.6 - - - +
59A ILE* 1.3 72.7 + - - +
60A VAL* 3.3 11.1 + - - +
67A PHE 4.3 3.1 - - - +
68A SER* 5.3 2.1 + - - +
89A ILE* 3.4 7.5 - - - +
90A VAL 3.0 23.7 + - - +
93A ALA* 3.1 49.1 + - + +
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Residues in contact with ILE 59 (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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25A CYS* 5.6 1.8 - - - -
27A ILE* 4.2 15.5 - - + -
37A ILE* 3.1 21.2 + - + +
39A ILE* 3.7 30.5 - - + -
53A LEU* 5.6 0.4 - - + -
58A GLN* 1.3 72.8 - - - +
60A VAL* 1.3 58.8 + - - +
61A GLU 3.2 26.2 - - - +
62A VAL* 3.4 17.3 - - + -
67A PHE* 2.9 34.1 - - + +
79A LEU* 5.5 7.6 - - + -
87A ILE* 4.2 23.1 - - + -
88A SER 3.7 6.7 - - - +
89A ILE* 4.0 9.6 - - + +
118B LEU* 5.8 1.1 - - + -
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Residues in contact with VAL 60 (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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10A GLU* 4.8 9.2 - - + +
58A GLN* 3.3 19.5 + - - +
59A ILE* 1.3 73.7 - - - +
61A GLU* 1.3 61.3 + - + +
66A ASP* 3.9 4.5 - - - +
67A PHE* 3.1 24.5 + - - +
68A SER* 4.1 11.8 + - - +
88A SER* 2.7 28.7 + - - +
90A VAL* 3.3 33.4 - - + -
93A ALA* 4.7 7.9 - - + -
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Residues in contact with GLU 61 (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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12A LYS* 4.9 4.0 + - - -
59A ILE* 3.2 5.6 - - - +
60A VAL* 1.3 83.3 - - + +
62A VAL* 1.3 76.9 + - - +
63A ASN 3.8 3.5 + - - -
64A GLY* 3.4 38.5 + - - +
65A VAL 3.2 15.9 - - - +
66A ASP* 4.4 5.8 - - - +
67A PHE* 3.5 2.5 - - - +
86A THR* 4.1 4.3 - - - +
87A ILE* 3.2 0.5 - - - -
88A SER* 2.7 52.8 + - - +
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Residues in contact with VAL 62 (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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59A ILE* 3.4 6.5 - - + -
61A GLU* 1.3 88.1 - - - +
63A ASN* 1.3 70.9 + - + +
64A GLY 3.1 0.2 - - - -
65A VAL* 2.9 27.2 + - - +
67A PHE* 3.0 41.7 - - + -
78A VAL* 4.3 5.6 - - + +
79A LEU* 3.4 20.0 - - + -
85A LEU* 4.2 17.7 - - + -
86A THR 3.3 4.3 - - - +
87A ILE* 3.3 26.2 - - + -
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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