Contacts of the strand formed by residues 30 - 35 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TRP* 3.1 17.7 + - + +
29A TRP* 1.3 84.5 - - + +
31A VAL* 1.3 75.1 + - - +
45A GLY* 4.1 5.5 - - - -
46A GLY 3.7 11.0 + - - +
76A ARG* 3.2 28.9 + - - -
143A THR* 2.5 50.0 + - - +
144A GLY* 4.3 2.9 - - - -
145A TRP* 3.7 29.3 - - + -
160A LEU* 4.0 17.9 - - + -
212A PRO* 3.4 15.3 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP 3.3 16.8 - - - +
30A GLN* 1.3 85.9 - - - +
32A SER* 1.3 61.8 + - - +
33A LEU* 3.8 11.4 - - + -
45A GLY* 3.6 2.3 - - - -
46A GLY* 2.9 44.3 + - - -
47A SER 4.2 0.7 - - - -
48A LEU* 3.9 15.3 - - + +
54A VAL* 3.8 20.4 - - + -
73A VAL* 4.1 8.3 - - + -
74A GLN 3.3 13.2 - - - +
75A LEU* 4.1 22.2 - - + -
145A TRP* 3.8 4.7 - - - -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 1.3 74.8 - - - +
33A LEU* 1.3 61.6 + - - +
34A ARG* 2.9 24.8 + - - +
42A HIS* 2.8 26.1 + - - -
44A CYS 3.8 3.1 - - - -
73A VAL* 3.7 3.3 - - - +
74A GLN* 2.8 42.7 + - - +
80A LEU* 3.8 7.3 - - - +
145A TRP* 3.5 19.5 - - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 21.5 - - + -
32A SER* 1.3 78.6 - - - +
34A ARG* 1.3 60.6 + - - +
42A HIS* 3.2 5.5 - - - -
43A PHE* 2.9 52.7 + - + -
44A CYS* 2.8 27.3 + - + +
45A GLY 3.9 12.6 - - - +
46A GLY* 4.7 1.8 - - - -
54A VAL* 4.8 0.7 - - + -
56A THR* 3.5 29.6 - - + +
60A CYS* 4.4 3.6 - - + -
61A VAL* 4.8 4.5 - - + -
71A LEU* 4.4 5.8 - - + -
72A ARG 3.8 2.5 - - - +
73A VAL* 4.4 5.2 - - + -
110A LEU* 4.2 25.4 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 2.9 29.5 + - - +
33A LEU* 1.3 78.8 - - - +
35A VAL* 1.3 60.3 + - - +
40A TRP* 2.9 44.5 + - + +
41A MET 3.1 1.6 - - - -
42A HIS* 3.5 12.6 - - - +
43A PHE* 3.7 3.1 - - - -
70A ALA 3.7 0.2 - - - +
71A LEU* 3.4 9.5 - - - +
72A ARG* 2.9 39.1 + - + +
74A GLN* 3.7 10.4 - - + +
77A GLU* 3.2 17.6 + - - -
80A LEU* 3.8 5.9 - - - +
81A TYR* 3.5 19.4 - - - +
84A ASP* 2.8 43.3 + - - -
86A LEU* 3.9 17.0 - - + +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 1.3 74.8 - - - +
36A HIS* 1.3 74.9 + - - +
37A GLY 3.3 1.7 + - - -
39A TYR 3.4 0.9 - - - +
40A TRP* 3.5 3.4 - - - -
41A MET* 2.9 60.3 + - + +
43A PHE* 3.7 24.2 - - + -
70A ALA* 3.4 13.7 - - + +
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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