Contacts of the strand formed by residues 48 - 55 (chain B) in PDB entry 3G65
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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PHE 3.9 0.9 - - - +
44B ALA* 3.3 2.4 - - - -
45B THR* 2.9 28.3 + - - +
46B LYS 3.4 2.8 - - - -
47B ASN* 1.3 82.9 - - - +
49B ILE* 1.3 64.8 + - - -
64B PHE* 4.8 4.9 - - - -
65B ILE 3.5 10.3 - - - -
66B GLN* 4.3 0.7 - - - -
67B ALA* 3.6 5.4 - - - -
73B PHE* 3.8 15.9 - - - -
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Residues in contact with ILE 49 (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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17B LEU* 5.6 5.8 - - + -
19B ALA* 4.7 6.5 - - + -
27B LEU* 5.5 7.2 - - + -
42B CYS* 4.9 6.3 - - + -
43B PHE 3.5 10.5 - - - +
44B ALA* 4.2 12.8 - - + +
48B GLY* 1.3 73.5 - - - -
50B LYS* 1.3 67.0 + - - +
51B VAL* 4.3 19.1 - - + -
63B ALA 4.0 0.6 - - - +
64B PHE* 3.6 5.9 - - - -
65B ILE* 3.0 40.5 + - + +
70B PHE* 3.5 29.4 - - + -
73B PHE* 3.4 24.0 - - + -
82B PHE* 6.5 0.2 - - + -
110B MET* 5.0 13.9 - - + -
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Residues in contact with LYS 50 (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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41B THR 3.5 3.5 - - - +
43B PHE* 2.7 61.3 + - + +
49B ILE* 1.3 77.4 - - - +
51B VAL* 1.3 65.5 + - - +
52B THR* 4.0 11.0 + - - +
60B GLN* 5.3 4.0 - - - +
62B ASN* 4.2 27.3 + - + +
63B ALA 3.3 12.8 - - - +
64B PHE* 4.1 16.8 - - + -
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Residues in contact with VAL 51 (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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27B LEU* 5.8 2.0 - - + -
31B LEU* 3.7 34.3 - - + -
34B ILE* 4.6 4.0 - - + +
40B ALA* 3.8 22.9 - - + -
41B THR 3.2 9.0 - - - +
42B CYS* 4.0 22.9 - - - -
49B ILE* 4.3 13.2 - - + -
50B LYS* 1.3 75.9 - - - +
52B THR* 1.3 63.7 + - - +
53B VAL* 4.9 3.1 - - + -
61B ALA 3.9 1.0 - - - +
62B ASN* 3.8 0.3 - - - -
63B ALA* 2.9 38.5 + - + +
65B ILE* 5.7 5.4 - - + -
86B LEU* 4.9 5.6 - - + -
89B LEU* 6.2 1.6 - - + -
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Residues in contact with THR 52 (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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40B ALA* 3.5 1.4 - - - -
41B THR* 2.8 63.0 + - + +
43B PHE* 6.1 1.6 - - + -
50B LYS* 4.8 13.2 - - - +
51B VAL* 1.3 75.3 - - - +
53B VAL* 1.3 68.8 + - - +
54B GLU* 4.8 4.0 + - - +
60B GLN* 3.4 19.0 + - - +
61B ALA 3.4 3.4 - - - -
62B ASN* 3.1 23.2 + - - -
142B THR* 4.8 11.8 + - + +
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Residues in contact with VAL 53 (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 ILE* 3.2 36.3 - - + +
36B PHE* 3.2 21.0 - - + -
37B ARG* 3.3 33.0 - - + +
39B HIS 3.9 4.5 - - - +
40B ALA* 3.4 29.4 - - + +
51B VAL* 4.9 1.3 - - + -
52B THR* 1.3 74.1 + - - +
54B GLU* 1.3 62.3 + - - +
60B GLN* 3.4 0.3 - - - -
61B ALA 2.7 38.3 + - - -
86B LEU* 3.8 8.7 - - + -
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Residues in contact with GLU 54 (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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36B PHE* 4.1 3.1 - - - -
37B ARG* 3.7 21.5 + - - +
52B THR* 5.2 3.4 - - - +
53B VAL* 1.3 76.8 - - - +
55B ASN* 1.3 61.5 + - - +
57B LYS* 3.6 28.2 + - + +
59B VAL 3.1 17.0 - - - +
60B GLN* 3.3 24.6 - - + +
141B GLU 3.6 5.7 - - - +
142B THR* 3.0 36.8 + - - -
143B LEU* 3.5 17.9 + - - +
145B PHE* 4.9 1.4 - - - -
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Residues in contact with ASN 55 (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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36B PHE* 3.7 23.5 + - + -
37B ARG* 3.2 31.4 + - - +
54B GLU* 1.3 75.8 - - - +
56B ALA* 1.3 79.4 + - - +
57B LYS* 2.8 11.9 + - - +
58B CYS 3.1 9.4 + - - -
59B VAL* 2.9 19.0 + - + +
226B SER 5.4 2.0 + - - -
227B LEU* 3.6 23.8 - - + +
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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