Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 2ZA5
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 GLN 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TRP* 3.2 20.9 + - + +
28B PRO 3.4 0.4 - - - -
29B TRP* 1.3 82.7 - - + +
31B VAL* 1.3 82.2 + - - +
45B GLY* 4.1 9.9 - - - -
46B GLY 3.8 8.3 + - - +
76B ARG* 3.1 33.6 + - - -
143B THR* 2.6 40.5 + - - +
144B GLY* 4.2 3.2 - - - -
145B TRP* 3.5 32.0 - - + -
160B LEU* 3.8 16.8 - - + -
211B GLY* 4.7 0.4 - - - -
212B PRO* 3.4 12.1 - - - +
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Residues in contact with VAL 31 (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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29B TRP 3.7 10.3 - - - +
30B GLN* 1.3 100.2 + - - +
32B SER* 1.3 61.7 + - - +
33B LEU* 4.3 6.3 - - + -
45B GLY* 3.4 1.9 - - - -
46B GLY* 3.0 42.2 + - - +
48B LEU* 4.3 9.9 - - + +
54B VAL* 3.8 20.2 - - + -
73B VAL* 4.1 12.6 - - + -
74B GLN 3.1 11.0 - - - +
75B LEU* 3.8 27.4 - - + -
145B TRP* 3.4 5.5 - - - -
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Residues in contact with SER 32 (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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31B VAL* 1.3 75.1 - - - +
33B LEU* 1.3 62.6 + - - +
34B ARG* 2.9 25.4 + - - +
42B HIS* 2.6 27.8 + - - -
44B CYS 3.8 4.0 - - - -
73B VAL* 3.7 3.1 - - - +
74B GLN* 2.8 41.9 + - - +
80B LEU* 3.5 8.0 - - - +
145B TRP* 3.7 14.8 - - - -
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Residues in contact with LEU 33 (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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31B VAL* 4.3 13.2 - - + -
32B SER* 1.3 77.9 - - - +
34B ARG* 1.3 61.2 + - - +
42B HIS* 3.4 4.9 - - - -
43B PHE* 3.0 51.5 + - + -
44B CYS* 2.7 29.9 + - + +
45B GLY 4.0 6.5 - - - +
54B VAL* 4.7 2.5 - - + -
56B THR* 3.7 33.7 - - + +
60B CYS* 4.6 3.8 - - + -
61B VAL* 4.9 4.7 - - + -
71B LEU* 4.3 3.8 - - + -
72B ARG 3.7 2.0 - - - +
73B VAL* 3.9 15.5 - - + -
110B LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 34 (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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32B SER* 2.9 26.1 + - - +
33B LEU* 1.3 74.7 - - - +
35B VAL* 1.3 61.0 + - - +
40B TRP* 3.1 45.8 + - + +
41B MET 3.2 1.6 - - - -
42B HIS* 3.5 15.4 - - - +
43B PHE* 3.6 3.1 - - - -
71B LEU* 3.4 10.4 - - - +
72B ARG* 2.9 39.0 + - + +
74B GLN* 3.5 12.5 - - + +
77B GLU* 3.1 17.8 + - - -
80B LEU* 3.5 14.9 - - - +
81B TYR* 3.5 14.6 - - - +
84B ASP* 2.8 42.3 + - - -
86B LEU* 4.0 14.1 - - + +
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Residues in contact with VAL 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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34B ARG* 1.3 74.6 - - - +
36B HIS* 1.3 76.5 + - - +
39B TYR 3.4 2.1 - - - +
40B TRP* 3.5 2.3 - - - -
41B MET* 3.0 56.3 + - + +
43B PHE* 3.6 23.5 - - + -
66B LYS* 6.5 0.7 - - + -
70B ALA* 3.4 13.9 - - + +
71B LEU* 5.4 0.2 - - - -
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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