Contacts of the strand formed by residues 32 - 36 (chain D) in PDB entry 1ZMD
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 THR 32 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.3 10.8 - - + +
11D VAL* 4.5 4.5 - - + -
22D ALA* 3.6 37.9 - - + +
25D ALA* 3.6 11.9 - - + +
26D ALA* 3.4 20.0 + - - +
30D PHE* 2.9 19.6 + - - +
31D LYS* 1.3 75.2 - - - +
33D VAL* 1.3 77.4 + - - +
111D LYS 4.0 6.1 + - - +
112D VAL* 3.7 7.5 - - + -
113D VAL* 3.0 26.2 + - - +
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Residues in contact with VAL 33 (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 ILE* 3.5 30.3 - - + -
6D ASP 5.1 0.2 - - - +
7D ALA* 3.9 15.0 - - + -
9D VAL 2.9 7.0 + - - +
10D THR* 3.3 15.8 - - + +
11D VAL* 2.7 35.4 + - - +
31D LYS* 6.0 1.3 - - + -
32D THR* 1.3 82.1 - - - +
34D CYS* 1.3 62.7 + - - +
35D ILE* 4.2 10.1 - - + -
112D VAL* 4.7 0.2 - - - -
113D VAL* 3.4 16.6 - - + +
115D VAL* 3.6 23.3 - - + -
139D ILE* 4.3 9.0 - - + -
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Residues in contact with CYS 34 (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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11D VAL* 3.4 10.8 - - + -
13D GLY 3.5 25.6 - - - -
14D SER* 3.8 21.8 - - - -
18D GLY 4.7 0.9 - - - -
22D ALA* 4.1 8.3 - - + -
33D VAL* 1.3 75.0 - - - +
35D ILE* 1.3 65.1 + - - +
36D GLU* 5.4 0.7 - - - -
41D LEU* 5.7 0.2 - - - -
107D PHE* 3.7 29.2 - - + -
112D VAL* 3.9 10.2 - - + +
113D VAL 2.9 10.4 + - - +
114D HIS* 3.5 5.9 - - - -
115D VAL 2.9 22.4 + - - +
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Residues in contact with ILE 35 (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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10D THR* 3.5 25.8 - - + -
11D VAL 2.8 12.6 + - - +
12D ILE* 4.3 10.3 - - + -
13D GLY* 2.8 33.4 + - - -
33D VAL* 4.2 7.0 - - + -
34D CYS* 1.3 75.1 - - - +
36D GLU* 1.3 63.9 + - - +
115D VAL* 3.3 23.8 - - + +
117D GLY 3.3 20.9 - - - +
119D GLY* 4.1 5.2 - - - +
127D VAL* 3.6 25.4 - - + -
129D ALA* 4.0 15.0 - - + -
139D ILE* 3.7 11.7 - - + -
480D FAD 3.8 9.5 + - + -
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Residues in contact with GLU 36 (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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14D SER* 2.8 46.6 + - - +
34D CYS* 4.0 1.0 + - - -
35D ILE* 1.3 73.6 - - - +
37D LYS* 1.3 61.9 + - - +
38D ASN* 2.7 30.4 + - - +
40D THR 3.6 20.2 - - - +
41D LEU* 4.0 16.4 - - + -
114D HIS* 4.0 6.1 - - + +
115D VAL 3.0 6.5 + - - -
116D ASN* 3.1 12.8 + - - -
117D GLY 2.9 22.1 + - - -
480D FAD 2.8 41.4 + - - -
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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