Contacts of the strand formed by residues 5 - 12 (chain C) in PDB entry 1ZMC
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 ILE 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C PRO* 1.3 81.0 - - - +
6C ASP* 1.3 76.3 + - - +
31C LYS* 6.2 0.4 - - + -
33C VAL* 4.6 11.9 - - + -
113C VAL* 5.5 11.0 - - + -
137C GLN* 3.2 25.8 - - - +
138C VAL 2.8 8.7 + - - +
139C ILE* 3.1 25.3 - - + -
140C ASP* 2.9 26.3 + - - +
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Residues in contact with ASP 6 (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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4C PRO 4.2 7.4 - - - +
5C ILE* 1.3 87.7 - - - +
7C ALA* 1.3 66.0 + - - +
31C LYS* 3.0 37.2 + - - +
33C VAL* 4.9 0.3 - - - +
140C ASP* 3.5 25.8 - - - +
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Residues in contact with ALA 7 (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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6C ASP* 1.3 78.2 - - - +
8C ASP* 1.3 63.3 + - - +
9C VAL 4.3 1.8 - - - +
10C THR* 3.8 21.3 - - - +
31C LYS* 3.7 19.9 - - + +
33C VAL* 3.9 18.2 - - + -
139C ILE* 4.1 2.7 - - + -
140C ASP 2.7 13.3 + - - +
141C THR* 3.0 21.9 - - - -
142C LYS* 3.4 13.3 + - - -
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Residues in contact with ASP 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 1.3 75.2 - - - +
9C VAL* 1.3 66.3 + - - +
29C GLY 4.8 1.4 - - - +
30C PHE* 3.5 28.5 - - + -
31C LYS* 2.9 34.9 + - - +
141C THR* 3.4 1.8 - - - -
142C LYS* 3.1 34.7 + - + +
143C ASN* 3.1 31.1 + - - +
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Residues in contact with VAL 9 (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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7C ALA* 4.3 0.6 - - - +
8C ASP* 1.3 85.4 - - - +
10C THR* 1.3 66.6 + - - +
11C VAL* 4.0 21.1 - - + -
25C ALA* 4.3 12.6 - - + -
30C PHE* 3.8 31.2 - - + -
31C LYS 3.2 3.7 + - - +
32C THR* 3.4 15.6 - - + +
33C VAL* 3.0 23.7 + - - +
141C THR* 3.9 0.2 - - - -
143C ASN* 3.9 5.2 - - - +
145C LEU* 4.9 2.7 - - + -
339C VAL* 5.0 2.5 - - + -
342C MET* 3.8 36.3 - - + -
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Residues in contact with THR 10 (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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7C ALA* 3.8 3.8 - - - +
9C VAL* 1.3 74.2 + - - +
11C VAL* 1.3 63.3 + - - +
12C ILE* 3.9 1.6 + - + +
33C VAL* 3.3 15.0 - - + +
35C ILE* 3.8 29.6 - - + -
127C VAL* 4.3 16.6 - - + -
139C ILE* 3.4 24.2 - - + +
141C THR* 3.4 24.2 + - - -
143C ASN 3.3 7.5 + - - -
144C ILE* 3.7 5.0 - - - +
145C LEU 3.0 24.5 + - - +
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Residues in contact with VAL 11 (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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9C VAL* 4.0 15.3 - - + -
10C THR* 1.3 74.3 - - - +
12C ILE* 1.3 62.2 + - - +
13C GLY 3.4 8.5 + - - +
18C GLY* 3.6 35.4 - - - +
21C ALA* 4.5 0.4 - - + -
22C ALA* 4.1 23.6 - - + +
32C THR* 4.5 1.1 - - + -
33C VAL 2.7 13.2 + - - +
34C CYS* 3.2 7.7 - - - -
35C ILE* 2.8 26.7 + - - +
145C LEU* 3.4 34.5 - - + +
147C ALA* 4.1 4.5 - - + -
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Residues in contact with ILE 12 (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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10C THR* 4.5 6.1 - - + +
11C VAL* 1.3 72.8 - - - +
13C GLY* 1.3 57.5 + - - +
35C ILE* 3.9 21.1 - - + -
119C GLY* 4.7 6.5 - - - -
121C ILE* 4.1 13.7 - - + -
127C VAL* 3.8 21.5 - - + -
144C ILE* 4.0 18.6 - - + -
145C LEU 2.9 12.9 + - - +
146C ILE* 4.7 5.2 - - + -
147C ALA 3.0 28.6 + - - -
148C THR* 3.4 12.0 + - + +
287C LEU* 4.2 12.3 - - + -
480C FAD 3.5 39.9 - - + +
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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