Contacts of the strand formed by residues 68 - 72 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 3.0 1.2 + - - -
37C GLY* 3.3 3.6 - - - -
38C LEU* 3.1 21.6 + - - +
66C LEU* 4.5 4.0 - - - +
67C THR* 1.3 112.1 + - - +
69C VAL* 1.3 63.2 + - - +
234C LYS* 4.8 0.7 - - - -
235C ASN* 3.4 39.2 + - + +
237C SER* 5.3 1.1 - - - +
254C ASP* 4.8 4.9 + - - -
298C ILE* 3.6 35.9 - - + -
299C GLU 4.9 7.1 + - - -
301C LEU* 3.9 17.3 - - + +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.2 24.9 - - + +
40C LEU* 5.7 1.1 - - + -
66C LEU* 5.6 3.6 - - + -
68C HIS* 1.3 77.8 - - - +
70C SER* 1.3 63.4 + - - +
79C ALA* 3.7 29.2 - - + +
82C LEU* 4.6 12.1 - - + -
83C ALA* 3.7 23.3 - - + +
234C LYS* 3.7 27.1 - - + -
235C ASN 2.8 13.1 + - - +
236C LEU* 3.3 3.6 - - + +
237C SER* 2.9 23.1 + - - -
298C ILE* 4.9 0.9 - - - -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 2.7 7.9 + - - +
39C VAL* 3.3 18.6 - - - -
40C LEU* 3.0 22.5 + - - +
69C VAL* 1.3 74.8 - - - +
71C GLY* 1.3 65.3 + - - +
79C ALA* 3.8 11.8 - - - +
237C SER* 3.2 27.9 + - - -
239C VAL* 4.5 4.2 - - - +
296C PRO* 3.9 18.9 - - - +
297C GLU 4.8 2.7 + - - -
298C ILE* 4.3 14.8 - - - +
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Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 5.2 0.9 - - - -
40C LEU 3.4 13.2 - - - -
70C SER* 1.3 82.6 + - - +
72C ALA* 1.3 59.0 + - - -
75C GLY 3.6 15.0 - - - -
76C ALA* 4.0 6.4 - - - +
79C ALA* 4.3 2.2 - - - +
237C SER 3.0 4.9 + - - +
238C VAL* 3.4 13.3 - - - +
239C VAL* 3.4 21.2 + - - -
296C PRO* 5.2 1.1 - - - -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU 3.3 7.0 + - - +
41C SER 3.4 9.9 - - - +
42C GLY* 3.9 15.3 - - - +
71C GLY* 1.3 74.9 - - - +
73C SER* 1.3 74.6 + - - +
75C GLY* 3.0 13.0 + - - -
76C ALA* 3.9 1.9 - - - +
239C VAL* 3.7 26.0 - - + +
268C SER* 3.3 6.7 - - - -
289C GLY 3.8 17.0 - - - +
294C ASN* 5.5 0.7 - - - +
296C PRO* 4.8 5.2 - - + -
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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