Contacts of the strand formed by residues 25 - 32 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.9 15.2 - - + -
15A TYR* 3.6 30.3 - - + -
17A TYR* 4.9 2.2 - - + -
31A CYS* 3.7 35.7 - - + +
32A LEU* 3.8 13.2 - - - +
29C PHE* 5.4 1.1 - - + -
20D CYS 3.7 1.0 - - - +
21D THR* 3.3 5.4 - - - +
22D VAL* 2.8 57.4 + - + +
23D MET 3.2 0.4 - - - -
24D GLY* 1.3 72.6 - - - +
26D ASN* 1.3 65.8 + - - +
27D HIS* 3.8 25.8 - - + -
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Residues in contact with ASN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG* 5.1 3.3 - - - +
19D THR* 3.9 8.8 - - + +
20D CYS 3.6 3.1 - - - -
21D THR* 2.7 33.5 + - - +
23D MET 5.6 0.4 + - - -
24D GLY 4.0 8.7 + - - -
25D ILE* 1.3 77.1 - - - +
27D HIS* 1.3 65.2 + - - +
28D ARG* 3.2 26.6 + - - +
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Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA 2.9 24.8 + - - -
2A PHE* 3.3 34.1 - + + -
32A LEU* 2.6 31.5 + - - -
6D CYS* 3.0 23.9 + - + -
7D ARG 3.2 13.8 - - - +
8D ARG* 3.5 26.2 + - + +
19D THR* 3.4 11.4 - - - +
20D CYS 2.8 33.4 + - - +
25D ILE* 3.8 7.6 - - + -
26D ASN* 1.3 76.7 - - - +
28D ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D HIS 3.2 2.6 - - - +
6D CYS* 3.2 5.7 - - - -
7D ARG 2.6 36.8 + - - +
8D ARG 4.0 14.4 + - - +
9D SER* 4.7 2.5 - - - -
10D CYS* 3.7 8.7 - - - +
16D SER* 3.3 19.5 + - - +
18D GLY 3.5 8.0 + - - -
19D THR* 3.1 24.7 + - - +
20D CYS* 4.3 1.3 - - - -
26D ASN* 3.2 39.8 + - - +
27D HIS* 1.3 81.2 + - - +
29D PHE* 1.3 60.4 + - - +
30D CYS* 3.2 17.3 + - - -
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Residues in contact with PHE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 3.7 24.0 - - + -
23C MET* 3.5 32.5 - - + -
4D CYS* 3.5 22.2 - - + -
5D HIS* 3.9 2.9 - - - -
6D CYS* 4.1 6.1 - - - -
15D TYR 3.6 0.3 - - - +
16D SER* 4.2 0.9 - - - -
17D TYR* 2.9 33.8 + - + +
18D GLY 2.9 28.3 + - - +
20D CYS* 3.8 23.1 - - - -
27D HIS 4.1 0.2 + - - -
28D ARG* 1.3 70.7 - - - +
30D CYS* 1.3 60.4 + - - +
31D CYS* 3.4 26.3 + - - -
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Residues in contact with CYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR 3.9 0.5 - - - +
4D CYS* 2.9 3.6 - - - -
5D HIS* 2.7 45.2 + - - +
7D ARG* 3.8 14.6 - - + +
10D CYS* 2.1 52.7 - - + -
14D GLU* 3.4 22.2 - - + +
15D TYR 3.4 5.6 - - - -
28D ARG* 3.5 18.8 - - - -
29D PHE* 1.3 71.2 - - - +
31D CYS* 1.3 60.3 + - - +
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Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D PHE* 4.1 13.2 - - + -
3D THR 3.3 3.4 - - - -
4D CYS* 2.0 45.8 - - - -
13D THR 4.4 0.3 - - - +
14D GLU* 3.4 6.4 - - - -
15D TYR* 2.8 30.1 + - - +
17D TYR* 3.5 33.5 + - + -
29D PHE* 3.4 20.4 - - - -
30D CYS* 1.3 72.3 - - - +
32D LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA 4.2 5.2 - - - +
2D PHE* 3.5 16.9 - - - -
3D THR* 2.9 39.3 + - - +
11D TYR* 5.5 2.5 - - + -
13D THR* 3.3 44.0 - - + +
14D GLU* 3.9 18.1 - - + +
31D CYS* 1.3 75.5 - - - +
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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