Contacts of the strand formed by residues 67 - 74 (chain J) in PDB entry 2ZHX
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 PRO 67 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J ILE* 3.5 34.5 - - + -
57J LEU* 4.6 2.7 - - + -
58J LEU 3.9 5.6 - - - +
59J THR* 4.1 8.3 - - + -
65J TYR 3.3 10.3 - - - +
66J LYS* 1.4 92.1 - - + +
68J TRP* 1.3 62.8 + - - +
84J LEU* 4.1 18.7 - - + +
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Residues in contact with TRP 68 (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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29J VAL* 4.0 2.9 - - + -
33J ILE* 3.7 28.5 - - + -
35J ASN* 2.8 41.7 - - + -
36J LYS 4.3 0.7 - - - -
37J PRO* 3.3 34.3 - - + +
38J GLU* 4.7 12.1 - - + +
41J ILE* 3.3 26.5 - - + -
57J LEU* 4.8 0.2 - - - +
58J LEU* 2.9 20.2 + - + +
59J THR* 4.5 3.6 - - - -
60J SER 5.0 0.4 - - - +
66J LYS 4.3 3.6 - - - +
67J PRO* 1.3 78.1 - - - +
69J ALA* 1.3 74.0 + - + +
83J MET* 3.7 4.9 - - - +
84J LEU* 3.0 33.2 + - - +
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Residues in contact with ALA 69 (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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33J ILE* 4.2 19.5 - - + -
57J LEU* 3.4 13.2 - - - +
58J LEU* 3.1 31.0 + - + -
68J TRP* 1.3 98.5 - - + +
70J LEU* 1.3 61.9 + - - +
71J VAL 4.3 0.2 - - - -
81J ILE* 5.0 5.8 - - + -
82J LYS 4.0 9.6 - - - +
83J MET* 4.6 4.7 - - - -
84J LEU* 3.9 7.5 - - - +
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Residues in contact with LEU 70 (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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7J ILE 4.9 1.1 - - - +
8J ILE* 4.6 20.0 - - + -
11J GLU* 3.8 33.9 - - + -
12J THR* 3.9 14.4 - - + -
55J VAL* 4.4 7.6 - - + -
56J MET 3.5 10.3 - - - +
57J LEU* 5.0 5.6 - - + -
69J ALA* 1.3 76.8 - - - +
71J VAL* 1.3 77.1 + - - +
72J ILE* 3.4 25.4 - - + -
80J LYS 3.5 13.9 - - - +
81J ILE* 3.8 0.8 - - - -
82J LYS* 3.4 27.2 + - + +
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Residues in contact with VAL 71 (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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195I LEU* 4.0 16.2 - - + -
33J ILE* 4.5 10.5 - - + -
54J ASN 4.0 0.2 - - - +
55J VAL* 3.8 0.2 - - - -
56J MET* 2.9 50.1 + - + +
58J LEU* 3.5 26.2 - - + -
70J LEU* 1.3 83.0 - - - +
72J ILE* 1.3 65.0 + - - +
73J GLN 4.1 0.7 - - - -
79J ASN* 3.3 39.5 - - + +
80J LYS 4.2 1.8 - - - -
81J ILE* 4.3 13.7 - - + +
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Residues in contact with ILE 72 (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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12J THR* 3.8 26.0 - - + -
53J GLU* 3.4 42.0 - - + +
54J ASN 3.7 3.4 - - - +
55J VAL* 4.5 11.4 - - + -
70J LEU* 3.4 13.5 - - + -
71J VAL* 1.3 81.6 - - - +
73J GLN* 1.3 60.6 + - - +
78J GLU 3.4 3.5 - - - +
79J ASN* 3.3 4.5 - - - -
80J LYS* 3.1 49.2 + - + +
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Residues in contact with GLN 73 (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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96I ASN* 5.5 0.3 + - - -
194I PRO* 3.0 35.4 + - - +
195I LEU* 5.0 1.0 - - - +
198I SER* 5.7 2.4 + - - -
53J GLU* 3.2 7.7 - - - -
54J ASN* 2.9 61.1 + - + +
56J MET* 3.6 15.5 - - + +
72J ILE* 1.3 71.7 - - - +
74J ASP* 1.3 72.0 + - - +
77J GLY* 4.0 16.9 + - - -
78J GLU 3.7 1.1 - - - -
79J ASN* 3.3 26.0 + - - +
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Residues in contact with ASP 74 (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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52J ASP 4.0 5.4 - - - +
53J GLU* 4.3 11.2 - - + +
72J ILE 3.8 1.0 + - - -
73J GLN* 1.3 78.7 - - - +
75J SER* 1.3 57.0 + - - +
76J ASN* 2.7 26.1 + - - +
77J GLY* 2.8 33.3 + - - -
78J GLU* 2.9 42.0 + - - +
80J LYS* 3.6 19.3 + - - +
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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