Contacts of the strand formed by residues 78 - 83 (chain J) in PDB entry 4KRM
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 THR 78 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J THR* 5.8 3.1 - - - -
22J CYS 3.3 13.9 - - - +
23J ALA* 4.6 9.2 - - + -
24J ALA* 5.7 0.4 - - - -
72J ARG* 3.3 7.4 + - - +
73J ASP* 3.1 42.2 + - - +
74J ASN* 4.7 2.5 - - - +
76J LYS* 3.4 17.0 - - + +
77J ASN* 1.3 82.1 - - - +
79J VAL* 1.3 62.9 + - - +
80J ASP* 4.0 13.3 + - - -
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Residues in contact with VAL 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J THR* 3.8 0.5 - - - -
22J CYS* 2.9 48.7 + - + +
34J MET* 4.0 24.5 - - + -
35J GLY 5.9 0.7 - - - +
36J TRP* 3.8 17.9 - - - +
51J ILE* 4.1 14.8 - - + -
70J ILE* 4.0 15.5 - - + -
71J SER 3.1 19.3 - - - +
72J ARG* 4.0 4.5 - - + +
78J THR* 1.3 76.6 - - - +
80J ASP* 1.3 62.9 + - - +
96J CYS* 4.0 11.9 - - - -
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Residues in contact with ASP 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ARG* 2.8 44.3 + - - +
20J LEU 3.2 4.9 - - - +
21J THR* 3.3 26.9 - - - +
36J TRP* 4.0 3.0 + - - -
70J ILE* 3.5 9.7 - - - +
71J SER* 2.7 39.6 + - - +
72J ARG* 6.3 0.2 - - - -
78J THR* 4.0 16.3 + - - -
79J VAL* 1.3 82.6 + - - +
81J LEU* 1.3 60.1 + - - +
82J GLN 4.2 0.4 - - - -
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Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ARG* 3.4 4.9 - - - -
20J LEU* 2.8 40.3 + - + -
36J TRP* 3.7 40.4 - - + +
48J VAL* 4.3 6.3 - - + -
49J SER* 4.2 20.4 - - - -
68J PHE* 4.1 27.1 - - + -
69J THR 3.4 19.7 - - - +
70J ILE* 4.2 4.7 - - + -
80J ASP* 1.3 75.7 - - - +
82J GLN* 1.3 60.2 + - - +
83J MET* 3.5 28.5 - - + +
94J TYR* 4.6 2.9 - - + -
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Residues in contact with GLN 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 4.8 3.6 - - - -
18J LEU 3.8 5.9 + - - -
19J ARG* 3.1 52.2 + - + +
67J ARG 3.8 0.7 - - - +
68J PHE* 3.2 8.8 - - - +
69J THR* 2.8 51.5 + - - +
80J ASP 4.2 0.4 - - - -
81J LEU* 1.3 70.2 - - - +
83J MET* 1.3 66.2 + - - +
84J ASN* 3.1 34.6 + - - +
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Residues in contact with MET 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 3.2 6.9 - - - -
18J LEU* 2.7 41.8 + - - +
20J LEU* 3.6 34.1 - - - -
68J PHE* 3.3 36.6 - - + -
81J LEU* 3.5 22.7 - - + +
82J GLN* 1.3 72.9 - - - +
84J ASN* 1.3 62.8 + - - +
86J LEU* 3.5 23.4 - - + +
94J TYR* 3.3 37.7 - - + +
120J VAL* 4.5 6.3 - - + -
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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