Contacts of the strand formed by residues 68 - 72 (chain G) in PDB entry 4KYI
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 HIS 68 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36G LYS 3.2 2.0 + - - -
37G GLY* 3.3 4.3 - - - -
38G LEU* 3.2 20.3 + - - +
66G LEU* 4.4 5.0 - - - +
67G THR* 1.3 115.9 + - - +
69G VAL* 1.3 62.9 + - - +
234G LYS* 4.7 0.9 - - - -
235G ASN* 3.3 42.1 + - + +
237G SER* 5.8 0.2 - - - +
254G ASP* 5.2 2.6 + - - -
298G ILE* 3.7 33.9 - - + -
299G GLU 4.8 9.0 + - - -
301G LEU* 4.1 15.7 - - + +
601G EDO 4.8 7.4 - - - -
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Residues in contact with VAL 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU* 3.3 36.3 - - + +
40G LEU* 5.7 0.7 - - + -
66G LEU* 5.7 3.1 - - + -
68G HIS* 1.3 74.8 - - - +
70G SER* 1.3 59.3 + - - +
79G ALA* 3.4 40.8 - - + +
82G LEU* 4.5 7.2 - - + -
83G ALA* 3.7 10.5 - - + +
234G LYS* 3.7 26.7 - - + -
235G ASN 3.1 7.4 + - - +
236G LEU* 3.4 5.0 - - - +
237G SER* 3.1 22.9 + - - +
298G ILE* 4.7 0.9 - - - -
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Residues in contact with SER 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU 2.6 15.3 + - - +
39G VAL* 3.9 7.9 - - - -
40G LEU* 2.9 22.1 + - - +
69G VAL* 1.3 74.3 - - - +
71G GLY* 1.3 62.1 + - - +
79G ALA* 3.8 10.8 - - - +
237G SER* 3.1 26.7 + - - -
239G VAL* 4.6 2.8 - - - +
296G PRO* 4.0 17.4 - - - +
297G GLU 4.6 0.2 + - - -
298G ILE* 3.8 24.2 - - - +
601G EDO 4.4 5.6 + - - -
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Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G VAL* 5.1 1.1 - - - -
40G LEU 3.3 13.0 - - - -
70G SER* 1.3 81.4 + - - +
72G ALA* 1.3 61.0 + - - -
75G GLY 3.3 20.2 - - - -
76G ALA* 4.1 2.7 - - - -
79G ALA* 4.3 1.9 - - - +
237G SER 3.0 4.6 + - - -
238G VAL* 3.2 9.4 - - - +
239G VAL* 3.1 25.2 + - - +
296G PRO* 5.1 1.1 - - - -
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Residues in contact with ALA 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU 3.1 11.6 + - - +
41G SER 4.4 1.0 - - - +
42G GLY* 4.1 18.5 + - - +
71G GLY* 1.3 74.2 - - - +
73G SER* 1.3 67.7 + - - +
75G GLY* 2.8 21.4 + - - -
76G ALA* 3.7 2.9 - - - -
239G VAL* 3.7 24.9 - - + +
268G SER* 3.3 7.9 - - - -
289G GLY 4.4 12.8 - - - +
294G ASN* 5.8 1.3 - - - +
296G PRO* 4.7 6.7 - - + -
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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