Contacts of the strand formed by residues 30 - 33 (chain A) in PDB entry 6V65
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 GLY 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.2 6.2 - - - +
25A ASP* 2.9 30.9 + - - +
28A SER 3.4 2.8 - - - -
29A GLY* 1.3 78.6 - - - +
31A TRP* 1.3 69.0 + - - -
32A LEU* 4.6 0.7 - - - +
1214B MET* 3.6 17.4 - - - +
1215B MET 3.7 8.7 - - - -
1216B GLY* 4.5 4.0 - - - -
1217B ASP* 5.6 0.9 - - - -
1222B PRO* 6.5 0.4 - - - -
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Residues in contact with TRP 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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22A MET* 3.7 20.3 - - + +
23A THR 3.4 11.4 - - - -
24A ARG* 3.1 39.8 - - + +
30A GLY* 1.3 74.7 - - - -
32A LEU* 1.3 71.4 + - - +
33A PRO* 4.9 0.2 - - - +
89A PHE* 3.9 17.5 - + + -
91A HIS* 3.5 31.5 - + + -
92A TRP 4.4 0.7 - - - -
98A LYS* 3.7 24.0 - - + -
99A PHE* 3.3 41.1 - - - -
100A GLY* 3.5 2.9 - - - -
1213B THR 4.6 1.0 - - - +
1214B MET* 3.4 1.6 - - - +
1215B MET* 2.6 53.1 + - + +
1216B GLY* 3.9 8.3 - - - -
1217B ASP* 3.1 28.2 + - - +
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Residues in contact with LEU 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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22A MET* 3.3 6.5 - - - -
23A THR* 2.7 45.3 + - + +
25A ASP* 4.7 9.9 - - + +
28A SER* 4.0 21.5 - - - +
30A GLY 4.6 2.7 - - - +
31A TRP* 1.3 82.0 - - - +
33A PRO* 1.3 81.8 - - + +
1210B GLU* 3.7 55.6 - - + +
1211B LEU* 6.2 0.7 - - + -
1213B THR* 4.7 1.6 - - - +
1214B MET* 3.9 21.3 - - + +
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Residues in contact with PRO 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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20A VAL* 3.9 18.2 - - + -
21A VAL 3.2 10.3 - - - +
22A MET* 3.9 19.7 - - + -
23A THR* 4.2 2.4 - - - +
32A LEU* 1.3 101.9 - - + +
34A LEU* 1.3 64.4 + - - +
37A SER* 3.5 22.7 + - - +
1210B GLU* 5.9 2.4 - - + +
1213B THR* 5.1 5.2 - - - +
1250B ARG* 4.2 23.8 - - + +
1252B LEU* 5.2 8.7 - - + -
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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