Contacts of the strand formed by residues 57 - 65 (chain C) in PDB entry 1ZXN
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 VAL 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C SER* 4.4 7.9 - - - +
55C GLU 3.6 9.2 - - - +
56C LEU* 1.3 79.8 - - - +
58C THR* 1.3 62.5 + - - +
59C GLN* 4.1 13.0 - - - +
75C VAL 3.3 0.7 - - - +
76C THR* 2.9 25.4 - - - -
77C PHE* 2.8 46.3 + - + +
79C PRO* 3.8 22.0 - - + -
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Residues in contact with THR 58 (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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57C VAL* 1.3 74.8 - - - +
59C GLN* 1.3 63.4 + - - +
74C GLU* 3.3 41.1 - - + +
75C VAL 3.1 3.1 - - - +
76C THR* 3.1 25.1 + - - +
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Residues in contact with GLN 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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57C VAL* 4.1 15.1 - - + +
58C THR* 1.3 76.9 - - - +
60C GLN* 1.3 63.4 + - - +
61C MET* 2.8 39.3 + - + +
74C GLU* 4.1 2.7 - - - -
75C VAL* 2.6 38.7 + - - +
77C PHE* 4.1 11.2 - - + -
79C PRO* 5.9 0.2 - - - +
320C SER* 6.0 4.0 - - - -
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Residues in contact with GLN 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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59C GLN* 1.3 77.1 + - - +
61C MET* 1.3 64.7 + - - +
72C TYR* 3.3 42.3 + - + +
73C ARG* 3.1 6.5 - - - +
74C GLU* 3.8 28.4 + - + +
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Residues in contact with MET 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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59C GLN* 2.8 48.2 - - + +
60C GLN* 1.3 75.8 - - - +
62C TRP* 1.3 63.8 + - - +
63C VAL* 3.7 3.9 + - + +
71C ASN 3.7 0.7 - - - +
72C TYR* 3.5 16.0 - - - -
73C ARG* 2.8 27.3 + - - +
75C VAL* 3.9 16.9 - - + +
77C PHE* 3.4 22.0 - - + -
238C LEU* 3.2 35.4 - - + -
241C ARG* 5.2 4.0 - - - +
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Residues in contact with TRP 62 (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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61C MET* 1.3 75.8 - - - +
63C VAL* 1.3 63.2 + - - +
70C ILE* 4.0 10.5 - - + -
71C ASN* 3.5 20.4 - - - -
72C TYR* 3.4 55.6 - + + -
241C ARG* 2.6 37.2 + - - +
274C TYR* 3.2 52.6 - + + +
309C GLN* 4.5 9.4 + - - -
311C ILE* 4.0 14.5 - - + +
361C TRP* 3.7 33.0 - + - -
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Residues in contact with VAL 63 (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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61C MET* 4.4 2.2 - - - +
62C TRP* 1.3 75.0 - - - +
64C TYR* 1.3 60.8 + - - +
65C ASP* 3.7 8.7 - - - +
69C GLY 3.7 0.5 - - - +
70C ILE* 3.5 8.1 - - - +
71C ASN 3.0 32.6 + - - +
73C ARG* 3.7 33.2 - - - +
75C VAL* 3.6 20.4 - - + -
234C ASP 4.7 0.7 - - - +
237C ALA* 3.6 16.4 - - + +
238C LEU* 3.2 38.8 - - + +
241C ARG* 4.1 4.7 - - - -
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Residues in contact with TYR 64 (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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63C VAL* 1.3 73.3 - - - +
65C ASP* 1.3 67.9 + - - +
66C GLU* 3.9 3.8 + - - -
67C ASP 5.4 2.0 - - - -
69C GLY* 3.6 23.6 - - - -
70C ILE* 3.6 15.3 - - + -
237C ALA* 2.9 32.2 + - - +
240C VAL* 3.9 18.0 - - + +
241C ARG* 3.8 19.3 - - + +
244C TYR* 3.3 41.3 + + - -
273C MET* 3.2 31.4 - - + +
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Residues in contact with ASP 65 (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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63C VAL* 3.7 2.9 - - - +
64C TYR* 1.3 79.2 - - - +
66C GLU* 1.3 63.0 + - - +
67C ASP 3.3 1.0 + - - -
68C VAL* 3.6 23.1 - - + +
69C GLY* 2.8 34.1 + - - -
71C ASN* 2.8 20.1 + - - +
73C ARG* 2.4 46.4 + - - -
233C LYS* 5.0 3.1 - - - +
237C ALA* 3.8 10.0 - - - +
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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