Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 4GS6
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 VAL 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.8 21.3 - - + -
43A GLY 3.6 10.3 - - - +
44A ARG* 3.5 31.9 - - + +
48A GLY* 1.4 73.2 - - - +
50A VAL* 1.4 67.2 + - - +
51A CYS* 4.0 11.0 + - - -
62A ILE 3.3 1.6 - - - +
63A LYS* 3.2 5.3 - - - +
64A GLN* 3.1 38.2 + - + +
66A GLU* 3.5 29.8 - - + +
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Residues in contact with VAL 50 (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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41A VAL* 3.5 4.7 - - - +
42A VAL* 2.7 45.7 + - + -
43A GLY 3.0 20.5 + - - +
45A GLY 5.1 4.7 - - - +
49A VAL* 1.4 76.0 - - - +
51A CYS* 1.3 61.5 + - - +
61A ALA* 4.2 6.5 - - + -
62A ILE 3.2 7.6 - - - +
63A LYS* 4.3 13.5 - - + -
611A 1FM 3.7 68.4 - - + +
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Residues in contact with CYS 51 (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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38A VAL* 4.0 18.4 - - + -
39A GLU 4.7 1.3 - - - -
40A GLU 3.4 9.6 - - - +
41A VAL* 3.9 25.4 - - - -
42A VAL* 4.0 5.4 - - - -
49A VAL* 4.6 14.4 - - - -
50A VAL* 1.3 77.4 - - - +
52A LYS* 1.3 68.5 + - - +
61A ALA* 3.4 5.0 - - - -
62A ILE* 2.8 50.0 + - + -
64A GLN* 5.8 1.3 - - - -
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Residues in contact with LYS 52 (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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39A GLU* 2.8 51.3 + - + +
40A GLU* 2.8 39.9 + - - +
42A VAL* 3.8 11.6 - - + +
51A CYS* 1.3 75.4 - - - +
53A ALA* 1.3 58.3 + - - +
59A ASP* 3.8 22.0 + - - +
60A VAL 3.7 5.2 - - - +
106A TYR* 3.7 46.2 + - + +
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Residues in contact with ALA 53 (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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36A ILE* 3.8 22.2 - - + -
37A GLU 3.3 13.2 - - - +
38A VAL* 4.1 2.7 - - - -
39A GLU* 3.7 9.3 - - - +
52A LYS* 1.3 77.6 - - - +
54A LYS* 1.3 58.8 + - - +
59A ASP* 3.6 6.2 - - - +
60A VAL* 2.8 43.9 + - + +
62A ILE* 3.8 17.5 - - + -
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Residues in contact with LYS 54 (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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35A GLU 3.6 2.8 - - - +
36A ILE* 3.5 4.3 - - - -
37A GLU* 3.0 48.9 + - + +
39A GLU* 4.0 11.2 - - - +
53A ALA* 1.3 73.1 - - - +
55A TRP* 1.3 59.8 + - - +
56A ARG 4.4 0.4 - - - -
57A ALA* 3.4 29.6 - - - +
58A LYS 3.4 9.2 - - - +
59A ASP* 3.1 40.9 + - - +
60A VAL* 4.2 0.2 - - - -
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Residues in contact with TRP 55 (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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29A HIS* 3.8 26.2 - + - -
31A ILE* 3.3 35.7 - - + +
35A GLU* 3.0 45.2 + - + -
36A ILE* 4.0 10.5 - - + -
54A LYS* 1.3 73.5 - - - +
56A ARG* 1.4 103.0 - - + +
58A LYS* 3.0 31.8 + - + +
60A VAL* 3.8 18.9 - - + +
93A TYR* 3.9 33.7 - + + -
103A VAL* 4.2 16.4 - - + -
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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