Contacts of the strand formed by residues 37 - 40 (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 GLY 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C HIS* 3.6 1.9 - - - +
36C LYS* 1.3 80.9 - - - +
38C LEU* 1.3 61.5 + - - +
66C LEU* 3.8 10.0 - - - +
68C HIS 3.3 8.7 - - - -
298C ILE* 3.9 4.7 - - - -
301C LEU* 3.8 15.9 - - - -
305C GLU 3.2 5.9 + - - +
306C VAL* 4.2 2.7 - - - -
307C LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLY* 1.3 74.8 - - - +
39C VAL* 1.3 57.0 + - - +
40C LEU* 4.3 11.2 - - + -
53C MET* 4.4 8.1 - - + -
57C LEU* 4.0 27.6 - - + -
63C ILE* 6.3 0.2 - - + -
66C LEU* 3.8 22.2 - - + -
68C HIS 3.1 6.5 + - - -
69C VAL* 3.2 12.9 - - + +
70C SER 2.7 32.3 + - - +
82C LEU* 4.1 26.0 - - + -
298C ILE* 4.0 3.2 - - - +
307C LEU* 3.5 30.7 - - + +
309C VAL* 3.9 21.3 - - + -
372C ILE* 5.6 0.2 - - + -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 1.3 75.9 - - - +
40C LEU* 1.3 66.6 + - - +
70C SER* 3.3 17.0 - - - -
295C MET* 3.7 13.3 - - + +
296C PRO* 3.5 42.4 - - + +
297C GLU* 5.7 0.4 - - - -
298C ILE* 4.7 5.2 - - + -
306C VAL* 3.7 13.0 - - + -
307C LEU 2.9 14.8 + - - +
308C CYS* 3.6 24.5 - - + -
309C VAL 3.0 26.5 + - - +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.3 12.3 - - + -
39C VAL* 1.3 78.5 - - - +
41C SER* 1.3 66.6 + - - +
50C TYR* 4.0 17.5 - - + +
53C MET* 3.6 26.0 - - + -
69C VAL* 5.7 0.2 - - + -
70C SER 3.0 12.2 + - - +
71C GLY* 3.4 2.6 - - - -
72C ALA 3.3 17.8 + - - -
75C GLY* 3.5 31.6 - - - +
78C THR* 3.8 28.9 - - + -
79C ALA* 4.1 8.7 - - + +
82C LEU* 5.5 4.0 - - + -
295C MET* 4.3 1.6 - - - -
296C PRO* 4.5 2.3 - - - +
309C VAL* 3.7 21.5 - - + -
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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
------------------------------------------------------------
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