Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1ZMQ
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.3 7.2 - - - -
20A CYS 3.5 0.5 - - - +
21A THR* 3.8 3.1 - - - +
22A VAL 2.8 33.8 + - - +
23A MET* 3.8 13.2 - - + +
24A GLY* 1.3 81.0 - - - +
26A ASN* 1.3 65.2 + - - +
27A HIS* 2.7 40.0 + - + -
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.9 4.7 - - - +
19A THR* 4.5 9.1 - - - +
20A CYS 3.9 3.4 - - - -
21A THR* 4.8 6.2 - - - +
24A GLY 4.1 1.6 + - - -
25A ILE* 1.3 78.1 - - - +
27A HIS* 1.3 65.7 + - - +
28A ARG* 2.9 33.1 + - - +
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 4.3 3.6 - - + -
7A ARG* 3.5 16.2 - - - +
8A ARG* 3.6 40.2 + - + +
19A THR* 3.4 6.9 - - - -
20A CYS* 2.7 37.5 + - + +
22A VAL* 3.5 31.9 - - + +
25A ILE* 2.7 50.0 + - + -
26A ASN* 1.3 77.6 - - - +
28A ARG* 1.3 70.6 + - - +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A HIS 3.5 1.2 - - - +
6A CYS* 3.2 6.4 - - - -
7A ARG 2.7 38.8 + - - +
8A ARG* 4.2 13.0 - - - +
9A SER* 5.2 0.2 - - - -
10A CYS* 3.7 8.3 - - - +
16A SER* 3.1 20.7 + - - +
18A GLY* 3.4 17.1 + - - +
19A THR* 2.7 40.8 - - - +
20A CYS* 4.1 1.8 - - - -
26A ASN* 2.9 27.5 + - - +
27A HIS* 1.3 80.9 + - - +
29A PHE* 1.3 59.3 + - - +
30A CYS* 3.6 17.0 - - - -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A CYS* 3.4 27.1 - - + -
5A HIS 3.7 2.5 - - - -
6A CYS* 4.4 8.1 - - - -
17A TYR* 2.7 53.2 + + + +
18A GLY 2.9 21.2 + - - +
20A CYS* 4.2 7.4 - - + +
27A HIS 4.1 0.2 + - - -
28A ARG* 1.3 69.6 - - - +
30A CYS* 1.3 57.3 + - - +
31A CYS* 3.7 19.3 - - - -
22B VAL* 3.5 31.2 - - + -
25B ILE* 5.2 1.3 - - + -
2C PHE* 3.7 33.7 - + + -
4C CYS* 4.8 4.9 - - - -
17C TYR* 3.7 26.9 - + - -
29C PHE* 5.4 0.2 - + - -
31C CYS* 4.8 8.3 - - + -
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Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR 4.0 0.5 - - - +
4A CYS* 3.1 1.7 - - - -
5A HIS 2.7 40.2 + - - +
7A ARG* 3.8 13.7 - - + +
10A CYS* 2.1 52.9 - - + -
14A GLU* 3.3 27.6 - - + +
15A TYR 3.5 5.2 - - - -
28A ARG* 3.6 18.6 - - - -
29A PHE* 1.3 71.4 - - - +
31A CYS* 1.3 59.7 + - - +
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 5.5 1.3 - - + -
3A THR 3.4 3.8 - - - -
4A CYS* 2.1 44.9 - - - -
14A GLU* 3.4 2.1 - - - -
15A TYR* 2.8 41.2 + - - +
17A TYR* 4.1 17.7 - - + -
29A PHE* 3.7 19.7 - - - -
30A CYS* 1.3 74.1 - - - +
32A LEU* 1.3 63.2 + - - +
29C PHE* 4.9 3.6 - - + -
25D ILE* 3.7 22.0 - - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.6 7.9 - - - +
3A THR* 3.0 54.7 + - + +
5A HIS* 5.6 4.3 - - + +
11A TYR* 6.2 1.3 - - + -
13A THR* 3.9 31.4 - - - +
14A GLU* 4.0 16.8 - - + +
31A CYS* 1.3 76.9 - - - +
8D ARG* 4.1 37.1 + - - +
25D ILE* 3.8 14.8 - - - +
27D HIS* 2.6 35.2 + - - -
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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