Contacts of the strand formed by residues 32 - 36 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.5 13.8 - - + +
11B VAL* 4.7 2.9 - - + -
22B ALA* 3.6 36.6 - - + +
25B ALA* 3.7 10.8 - - + +
26B ALA* 3.4 21.5 + - - -
30B PHE* 3.3 17.8 + - - +
31B LYS* 1.3 75.4 - - - +
33B VAL* 1.3 72.1 + - - +
111B LYS 4.3 4.9 + - - +
112B VAL* 3.6 7.7 - - + -
113B VAL* 2.9 28.0 + - - +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.5 8.1 - - + -
6B ASP 4.3 5.2 - - - +
7B ALA* 3.4 22.2 - - + -
9B VAL 3.1 5.9 + - - +
10B THR* 3.0 40.1 - - + +
11B VAL* 3.0 23.9 + - - +
31B LYS* 5.8 1.6 - - + -
32B THR* 1.3 75.0 - - - +
34B CYS* 1.3 60.7 + - - +
35B ILE* 4.9 0.9 - - + -
113B VAL* 3.1 27.1 - - + +
115B VAL* 4.5 2.5 - - + -
139B ILE* 3.8 24.7 - - + -
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Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.4 17.5 - - + -
13B GLY 3.5 24.7 - - - -
14B SER* 4.0 13.2 - - - -
18B GLY 4.8 0.9 - - - -
22B ALA* 4.2 1.1 - - + -
33B VAL* 1.3 72.4 - - - +
35B ILE* 1.3 63.1 + - - +
41B LEU* 5.2 1.1 - - - -
107B PHE* 3.5 40.8 - - + -
112B VAL* 4.1 7.8 - - + +
113B VAL 2.8 11.2 + - - +
114B HIS* 3.6 7.4 + - - -
115B VAL* 2.9 26.1 + - - +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 3.6 21.3 - - + -
11B VAL 3.0 10.9 + - - +
12B ILE* 4.4 7.4 - - + -
13B GLY* 2.8 30.8 + - - -
33B VAL* 5.0 0.7 - - + -
34B CYS* 1.3 73.4 - - - +
36B GLU* 1.3 59.3 + - - +
115B VAL* 3.2 25.4 - - + +
117B GLY 3.3 23.1 - - - +
119B GLY* 3.8 18.2 - - - +
127B VAL* 3.6 30.5 - - + +
129B ALA* 4.2 12.3 - - + -
139B ILE* 3.7 15.7 - - + -
480B FAD 3.6 6.7 - - + -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B SER* 2.4 46.9 + - - +
34B CYS* 4.0 0.8 + - - +
35B ILE* 1.3 73.7 - - - +
37B LYS* 1.3 65.4 + - - +
38B ASN* 2.8 30.1 + - - +
40B THR 3.4 18.8 - - - +
41B LEU* 3.7 18.6 - - + -
114B HIS* 3.9 5.2 - - + +
115B VAL 3.1 7.5 + - - -
116B ASN* 3.6 9.4 - - - +
117B GLY 3.1 19.1 + - - -
480B FAD 2.8 40.2 + - - +
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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
------------------------------------------------------------
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