Contacts of the strand formed by residues 30 - 36 (chain B) in PDB entry 1GJA
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 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.9 21.4 - - + +
27B GLN* 2.9 24.6 + - + +
28B PRO 4.5 2.3 - - - +
29B TRP* 1.3 84.1 - - + +
31B ALA* 1.3 67.6 + - - +
32B ALA* 4.3 2.0 + - + -
40B TYR* 3.5 21.1 - - - -
43B GLY* 3.8 19.7 - - - -
44B GLY 3.6 10.8 - - - -
68B LEU* 3.9 14.7 - - - +
69B GLY 4.6 0.7 + - - -
70B ARG* 5.1 2.4 + - + -
139B THR* 3.7 35.2 - - + -
140B GLY* 4.0 13.7 - - - -
141B PHE* 3.8 25.6 - + - -
155B LEU* 3.9 13.7 - - + -
197B GLY* 4.5 1.1 - - - -
198B PRO* 3.8 9.2 - - + -
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Residues in contact with ALA 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 3.5 1.5 + - - +
30B PHE* 1.3 81.1 - - - +
32B ALA* 1.3 59.6 + - - +
33B ILE* 4.3 1.7 - - + +
43B GLY* 3.3 5.9 - - - -
44B GLY* 2.8 34.8 + - - +
45B SER* 4.3 0.9 - - - +
52B VAL* 3.8 30.5 - - + -
66B VAL* 4.1 9.2 - - + -
67B TYR 3.5 7.4 - - - +
68B LEU* 3.6 18.8 - - + -
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Residues in contact with ALA 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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30B PHE* 4.3 3.3 + - + -
31B ALA* 1.3 72.2 - - - +
33B ILE* 1.3 62.3 + - - +
34B TYR* 3.6 29.5 - - + +
40B TYR* 3.8 17.0 - - + -
66B VAL* 3.5 2.6 - - - +
67B TYR 3.0 36.2 + - - +
70B ARG* 4.6 11.9 - - + -
141B PHE* 4.3 14.8 - - + -
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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 ALA* 4.3 4.9 - - + +
32B ALA* 1.3 78.3 - - - +
34B TYR* 1.3 57.5 + - - +
40B TYR* 3.5 4.3 - - - -
41B VAL* 2.8 33.8 + - + +
42B CYS* 2.9 19.4 + - + +
43B GLY 3.7 24.5 - - - +
44B GLY* 4.3 4.3 - - - +
52B VAL* 4.6 4.9 - - + -
54B SER* 4.0 16.4 - - - +
59B PHE* 3.9 33.7 - - + -
64B TYR* 4.2 14.1 - - + -
65B ILE 3.5 8.1 - - - +
66B VAL* 4.3 20.4 - - + -
106B LEU* 4.4 11.9 - - + -
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Residues in contact with TYR 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 ALA* 3.6 30.0 - - + +
33B ILE* 1.3 75.9 - - - +
35B ARG* 1.3 61.7 + - - +
38B VAL* 3.5 27.6 - - + -
39B THR* 3.1 11.4 - - - +
40B TYR* 3.8 31.4 - + + -
41B VAL* 3.7 4.3 - - - -
64B TYR* 3.2 9.7 - - - -
65B ILE* 2.9 35.0 + - + +
67B TYR* 3.6 28.9 - + - -
70B ARG* 2.9 21.5 + - - -
72B ARG 4.1 0.2 + - - -
73B LEU* 2.8 40.2 + - + +
74B ASN* 4.8 5.4 - - - -
141B PHE* 4.9 0.5 - - - -
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Residues in contact with ARG 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 TYR* 1.3 75.3 - - - +
36B ARG* 1.3 77.0 + - - +
37B HIS* 3.1 29.1 + - - +
38B VAL* 3.2 4.3 - - - -
39B THR* 2.8 36.0 + - - +
41B VAL* 3.6 17.9 - - + +
60B TYR* 3.6 53.8 - - - +
63B ASP* 3.4 9.4 + - + +
64B TYR* 4.3 12.1 - - + -
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Residues in contact with ARG 36 (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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2B CIT 2.8 42.4 + - - -
35B ARG* 1.3 91.2 + - - +
37B HIS* 1.3 97.4 + - + +
38B VAL* 4.4 11.2 - - + +
62B GLU 4.4 9.0 - - - -
63B ASP* 2.8 37.0 + - - +
64B TYR 5.0 0.9 - - - -
65B ILE* 3.4 43.2 - - + +
82B LYS* 4.4 4.0 - - - +
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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