Contacts of the strand formed by residues 32 - 36 (chain H) 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 THR 32 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 3.4 17.0 - - + +
11H VAL* 4.6 0.9 - - + -
22H ALA* 3.8 37.7 - - + +
25H ALA* 3.6 12.2 - - + +
26H ALA* 3.2 21.9 + - - +
30H PHE* 3.1 16.6 + - - +
31H LYS* 1.3 73.8 - - - +
33H VAL* 1.3 71.3 + - - +
111H LYS 4.0 4.5 + - - +
112H VAL* 3.8 6.9 - - + -
113H VAL* 2.9 32.3 + - - +
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Residues in contact with VAL 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 3.7 22.0 - - + -
6H ASP 5.2 0.2 - - - +
7H ALA* 3.4 24.9 - - + -
9H VAL 3.0 5.7 + - - +
10H THR* 3.3 14.5 - - - +
11H VAL* 2.7 34.5 + - - +
32H THR* 1.3 81.4 - - - +
34H CYS* 1.3 56.8 + - - +
35H ILE* 4.2 10.8 - - + -
113H VAL* 3.4 14.4 - - + +
115H VAL* 3.8 27.8 - - + -
139H ILE* 4.1 14.8 - - + -
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Residues in contact with CYS 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 3.1 13.2 - - + +
13H GLY 3.4 30.5 - - - -
14H SER* 4.2 6.3 - - - -
18H GLY 4.8 0.9 - - - -
22H ALA* 4.2 8.3 - - + -
33H VAL* 1.3 74.0 - - - +
35H ILE* 1.3 63.9 + - - +
36H GLU* 5.5 0.2 - - - -
41H LEU* 5.9 0.2 - - - -
107H PHE* 3.9 37.0 - - + -
112H VAL* 4.1 9.1 - - + +
113H VAL 2.9 9.8 + - - +
114H HIS* 3.5 10.7 - - - -
115H VAL 3.0 21.8 + - - +
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Residues in contact with ILE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 3.6 22.0 - - + -
11H VAL 2.8 10.2 + - - +
12H ILE* 3.8 7.5 - - + -
13H GLY* 2.8 30.7 + - - -
33H VAL* 4.2 4.9 - - + -
34H CYS* 1.3 74.9 - - - +
36H GLU* 1.3 62.1 + - - +
115H VAL* 3.1 25.1 - - + +
117H GLY 3.2 25.6 - - - +
119H GLY* 4.2 12.6 - - - +
127H VAL* 3.5 31.4 - - + -
129H ALA* 4.3 9.2 - - + -
139H ILE* 4.1 13.7 - - + -
480H FAD 3.8 10.1 + - + -
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H SER* 2.6 43.4 + - - +
34H CYS* 4.0 0.6 + - - +
35H ILE* 1.3 76.8 - - - +
37H LYS* 1.3 56.4 + - - +
38H ASN* 2.6 32.7 + - - +
40H THR 3.5 17.5 - - - +
41H LEU* 4.0 17.3 - - + -
114H HIS* 4.1 7.0 - - + +
115H VAL 3.0 7.1 + - - -
116H ASN* 2.6 33.6 + - - -
117H GLY 2.8 9.9 + - - -
480H FAD 2.8 39.2 + - - -
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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