Contacts of the strand formed by residues 30 - 34 (chain P) in PDB entry 2ZCH
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLN* 2.8 25.1 + - + +
28P PRO 4.4 4.0 - - - +
29P TRP* 1.3 84.2 - - + +
31P VAL* 1.3 80.3 + - - +
43P GLY* 4.0 10.4 - - - -
44P GLY 3.8 6.6 + - - +
66P LEU 4.6 0.2 - - - +
67P LEU* 4.4 10.4 - - - -
68P GLY 4.5 3.8 + - - -
69P ARG 5.6 1.8 + - - +
139P SER* 2.6 41.8 + - - +
140P GLY* 4.2 9.8 - - - -
141P TRP* 3.8 29.4 - - + -
155P LEU* 4.0 10.8 - - + -
197P GLY* 4.6 0.2 - - - -
198P PRO* 3.3 19.1 - - - +
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Residues in contact with VAL 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P PRO 5.9 0.2 - - - +
29P TRP 3.5 11.4 - - - +
30P GLN* 1.3 97.5 - - - +
32P LEU* 1.3 65.2 + - - +
33P VAL* 4.7 3.4 - - + -
43P GLY* 3.5 2.3 - - - -
44P GLY* 3.1 41.7 + - - +
46P LEU* 4.2 14.8 - - + +
52P VAL* 3.7 22.2 - - + -
65P ILE* 4.2 6.7 - - + -
66P LEU 3.6 10.8 - - - +
67P LEU* 3.5 27.4 - - + -
141P TRP* 3.6 7.2 - - - -
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Residues in contact with LEU 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P VAL* 1.3 73.9 - - - +
33P VAL* 1.3 75.3 + - - +
34P ALA* 4.2 10.8 - - + -
39P ALA* 3.9 27.4 - - + -
42P CYS 3.5 19.3 - - - +
64P VAL 3.7 0.5 - - - +
65P ILE* 3.4 7.1 - - - +
66P LEU* 3.2 52.2 + - + +
72P LEU* 4.2 13.9 - - + -
141P TRP* 3.4 37.5 - - + -
193P GLY 5.9 1.3 - - - +
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Residues in contact with VAL 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P VAL* 4.7 4.5 - - + -
32P LEU* 1.3 76.4 - - - +
34P ALA* 1.3 63.8 + - - +
39P ALA* 3.8 2.6 - - - -
41P VAL* 2.9 30.4 + - + -
42P CYS* 2.8 25.6 + - + +
43P GLY 4.1 4.3 - - - +
44P GLY 4.5 0.9 - - - +
54P THR* 3.9 27.8 - - + -
58P CYS* 5.3 7.2 - - + +
60P ARG* 6.4 0.4 - - + -
63P SER* 4.2 21.8 - - - +
64P VAL 3.4 10.8 - - - +
65P ILE* 4.7 7.2 - - + -
106P LEU* 4.3 17.9 - - + -
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Residues in contact with ALA 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P LEU* 3.9 13.8 + - + -
33P VAL* 1.3 75.9 - - - +
35P SER* 1.3 60.1 + - - +
37P GLY* 4.4 10.5 - - - +
38P ARG 3.0 21.3 - - - +
41P VAL* 4.0 2.2 - - - -
63P SER* 3.3 5.7 - - - -
64P VAL* 3.0 47.0 + - + +
66P LEU* 4.9 5.4 - - + -
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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