Contacts of the strand formed by residues 57 - 60 (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 SER 57 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310G LYS 3.6 7.3 + - - -
311G LYS* 4.7 7.7 - - - +
51J ILE* 3.5 1.6 - - - +
52J SER* 2.9 40.5 + - - -
54J ARG* 4.0 9.4 - - - -
56J ASP* 1.3 86.5 + - - +
58J THR* 1.3 65.9 + - - +
104J TRP* 3.0 20.9 + - - -
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Residues in contact with THR 58 (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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309G GLU* 3.5 2.8 - - - +
310G LYS* 2.7 51.1 + - + +
50J GLY 3.4 4.9 - - - -
51J ILE* 3.8 16.6 - - - +
55J GLY 4.2 6.3 + - - -
56J ASP 5.2 1.6 - - - -
57J SER* 1.3 78.0 + - - +
59J GLY* 1.3 58.4 + - - +
60J TYR* 3.0 42.0 - - + +
70J ILE* 3.7 12.7 + - + +
104J TRP* 3.6 7.8 - - - +
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Residues in contact with GLY 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G GLU 3.3 9.0 - - - -
47J PHE* 4.3 4.3 - - - -
49J SER* 3.0 23.6 + - - -
50J GLY 3.0 17.3 + - - -
58J THR* 1.3 74.7 - - - +
60J TYR* 1.3 67.9 + - - -
104J TRP* 3.4 23.9 - - - -
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Residues in contact with TYR 60 (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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307G LEU* 3.3 6.7 - - - +
308G GLU* 2.7 57.8 + - + +
310G LYS* 5.3 8.1 - - + -
47J PHE* 4.1 6.6 - - - -
48J VAL 3.5 3.6 - - - -
49J SER* 3.5 20.6 - - - -
58J THR* 3.0 27.4 - - + +
59J GLY* 1.3 83.8 - - - -
61J ALA* 1.3 66.8 + - - +
64J VAL* 4.3 13.5 - - + -
65J LYS* 4.5 8.1 - - - -
66J GLY 5.8 0.2 - - - -
68J PHE* 3.0 31.6 - - + -
69J THR* 3.3 11.7 - - - +
70J ILE* 2.8 30.7 + - + +
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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