Contacts of the strand formed by residues 58 - 61 (chain C) in PDB entry 2N9P
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 ARG 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU* 2.6 49.2 + - - -
43C LYS* 4.6 0.2 - - - +
56C LYS 3.4 7.9 + - - +
57C GLN* 1.3 77.6 + - - +
59C LEU* 1.3 60.6 + - - +
60C ILE* 3.5 9.5 + - + -
65C VAL* 3.5 29.5 - - + +
66C LEU 4.6 2.0 - - - +
67C GLN* 6.1 1.5 - - + +
83C HIS 3.5 8.5 - - - +
84C LEU* 3.4 14.7 - - - +
85C VAL* 3.6 23.4 + - + +
87C ARG* 3.1 32.2 - - + +
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Residues in contact with LEU 59 (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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21C VAL* 4.5 4.3 - - + -
39C VAL* 4.4 12.6 - - + -
42C PHE* 3.8 18.4 - - + -
43C LYS* 3.6 30.0 - - + +
46C ILE* 4.2 9.9 - - + -
57C GLN* 4.1 12.1 + - - +
58C ARG* 1.3 70.7 - - - +
60C ILE* 1.3 57.8 + - - +
64C ARG 3.4 0.2 - - - +
65C VAL* 3.5 2.6 - - - -
66C LEU* 2.6 60.4 + - + +
72C LEU* 5.8 0.4 - - + -
82C ILE* 3.8 27.4 - - + -
83C HIS 4.0 0.9 - - - -
84C LEU* 3.6 23.8 - - + -
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Residues in contact with ILE 60 (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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14A HIS* 4.3 2.0 - - + -
35A GLY 5.1 1.8 - - - +
36A PHE* 4.5 3.6 - - - +
37A ILE 2.9 31.9 - - - +
38A GLU* 3.7 35.2 - - + +
58C ARG* 3.9 11.4 - - + +
59C LEU* 1.3 77.7 - - - +
61C TYR* 1.3 60.4 + - - +
63C GLY* 3.7 7.9 - - - +
64C ARG 3.2 13.7 - - - +
65C VAL* 5.2 0.7 - - - -
82C ILE* 3.4 1.9 - - - +
83C HIS* 2.8 49.6 + - + +
85C VAL* 3.6 40.4 - - + -
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Residues in contact with TYR 61 (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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60C ILE* 1.3 75.8 - - - +
62C GLN* 1.3 105.1 + - + +
63C GLY 3.1 0.9 - - - -
64C ARG* 2.9 28.3 + - - +
66C LEU* 3.6 23.1 - - + +
75C TYR 4.5 6.1 - - - -
76C ASN 5.0 2.5 - - - -
77C VAL* 4.1 17.0 - - + -
80C LYS* 3.2 44.5 - - + +
81C VAL* 3.2 29.8 - - + -
82C ILE* 4.1 7.6 - - + -
83C HIS* 4.5 10.3 - + - -
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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