Contacts of the strand formed by residues 31 - 35 (chain B) in PDB entry 3GJ9
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 PHE 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.1 12.8 - - + -
29B LEU* 3.7 35.2 - - + -
30B GLY* 1.3 79.4 - - - +
32B SER* 1.3 72.5 + - - +
33B ILE* 3.4 24.7 - - + -
57B VAL* 4.0 3.4 - - + -
59B ARG* 3.1 17.9 - - - +
60B VAL* 4.2 2.0 - - - +
61B SER* 4.5 2.2 + - - +
66B ALA* 3.7 15.0 - - + -
71B LEU* 3.4 27.8 - - + -
77B ILE* 3.9 13.5 - - + -
97B LEU* 4.1 15.5 - - + -
107B LEU* 4.4 5.2 - - + -
444D ALA* 4.0 0.3 - - - -
445D ILE* 2.9 45.9 + - + +
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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 PHE* 1.3 77.0 + - - +
33B ILE* 1.3 66.7 + - - +
57B VAL* 3.4 8.0 - - - -
58B THR* 2.8 36.2 + - - -
59B ARG* 2.9 33.3 + - - +
442D GLU* 4.1 5.4 - - - -
443D SER 3.1 16.6 + - - -
444D ALA* 3.6 14.2 - - - +
445D ILE* 4.6 0.2 - - - -
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Residues in contact with ILE 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 PHE* 3.4 31.4 - - + -
32B SER* 1.3 75.7 - - - +
34B GLY* 1.3 59.7 + - - +
55B ILE* 4.0 8.1 - - + -
56B TYR 3.2 11.0 - - - +
58B THR* 4.1 5.2 - - - -
77B ILE* 4.0 14.6 - - + -
90B HIS* 3.3 19.2 - - + +
93B ALA* 4.0 26.2 - - + -
94B ARG* 4.2 13.5 - - - +
97B LEU* 4.2 12.1 - - + -
442D GLU* 3.2 10.7 - - - +
443D SER* 3.1 38.1 + - - +
445D ILE* 3.9 8.1 - - + -
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Residues in contact with GLY 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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33B ILE* 1.3 74.4 - - - +
35B GLY* 1.3 60.6 + - - -
54B GLY 3.9 0.2 - - - +
55B ILE* 3.6 3.9 - - - +
56B TYR* 2.8 34.1 + - - +
58B THR* 3.7 3.2 - - - +
90B HIS* 3.8 8.7 - - - -
440D ARG* 3.3 26.5 - - - -
441D ARG 3.9 5.2 - - - -
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Residues in contact with GLY 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 GLY* 1.3 75.5 - - - -
36B GLY* 1.3 62.9 + - - -
39B GLN* 3.3 19.1 - - - +
53B LYS* 4.3 1.8 - - - -
54B GLY 3.3 11.2 - - - -
55B ILE* 3.7 5.3 - - - +
56B TYR* 5.5 0.7 - - - -
90B HIS* 3.1 24.7 + - - +
440D ARG* 4.0 14.2 - - - +
441D ARG 4.8 1.2 + - - -
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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