Contacts of the strand formed by residues 46 - 54 (chain A) in PDB entry 3GG0
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 GLN 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.8 7.9 - - + +
9A SER 3.1 11.9 - - - +
10A GLN* 4.0 12.8 - - + +
41A LEU 3.5 0.9 - - - +
42A PHE* 3.3 10.0 - - - -
43A ASN* 2.7 54.9 + - - +
44A GLY 3.8 0.2 - - - -
45A LEU* 1.3 88.3 - - - +
47A PHE* 1.3 63.7 + - - +
132A PHE* 3.9 13.9 - - + -
136A GLY 2.7 30.0 + - - -
137A GLY* 3.8 9.4 - - - -
140A CYS* 3.4 30.7 - - - +
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Residues in contact with PHE 47 (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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7A TYR* 5.1 2.5 - - + -
8A ARG* 3.3 8.1 - - - +
9A SER* 2.7 53.4 + - - +
10A GLN 4.6 1.6 - - - -
11A VAL* 3.6 29.8 - - + -
18A VAL* 5.5 6.1 - - + -
20A LEU* 3.7 35.9 - - + -
23A LEU* 5.8 0.2 - - + -
40A LEU* 4.1 20.4 - - + -
41A LEU 3.2 3.6 - - - -
42A PHE* 3.4 26.2 - + + -
46A GLN* 1.3 74.3 - - - +
48A PHE* 1.3 63.1 + - - +
49A GLN 4.3 0.2 - - - -
70A ARG 4.5 5.4 - - - -
71A HIS* 4.0 18.2 - - + -
132A PHE* 3.9 3.8 - - - -
504A FMN 3.8 24.7 - - + -
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Residues in contact with PHE 48 (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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6A ILE* 3.5 24.5 - - + -
7A TYR 3.5 9.6 - - - -
8A ARG* 4.2 7.4 - - + -
39A ILE* 3.9 1.4 - - - +
40A LEU* 3.5 1.9 - - - -
41A LEU* 2.7 42.6 + - + +
47A PHE* 1.3 76.1 - - - +
49A GLN* 1.3 60.2 + - - +
50A VAL* 4.1 9.4 - - + -
77A LEU* 3.5 24.0 - - + -
128A LEU* 3.9 26.2 - - + -
129A LEU* 3.5 34.8 - - + -
132A PHE* 3.5 48.2 - + + -
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Residues in contact with GLN 49 (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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5A LEU 3.8 1.0 - - - +
6A ILE* 3.3 8.3 - - - +
7A TYR* 2.3 82.0 + - + -
39A ILE 3.4 10.8 - - - +
40A LEU* 3.7 11.3 - - + +
47A PHE 4.3 0.2 - - - -
48A PHE* 1.3 75.4 - - - +
50A VAL* 1.3 70.8 + - - +
51A LEU* 4.0 10.5 - - + -
65A ILE* 3.5 4.5 - - - +
92A MET* 3.3 18.6 - - + +
504A FMN 2.9 47.0 + - - -
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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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4A THR* 4.3 3.8 - - + -
5A LEU 3.6 2.9 - - - -
6A ILE* 4.0 23.8 - - + -
38A GLY* 3.2 19.5 - - - -
39A ILE* 3.0 31.6 + - + +
48A PHE* 4.1 17.3 - - + -
49A GLN* 1.3 76.7 - - - +
51A LEU* 1.3 73.1 + - - +
52A GLU* 4.6 1.3 - - + -
87A PHE* 4.0 9.4 - - + -
92A MET* 4.0 0.3 - - - +
125A MET* 3.7 41.3 - - + -
129A LEU* 4.4 5.6 - - + -
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Residues in contact with LEU 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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4A THR* 3.3 6.2 - - - +
5A LEU* 2.7 62.5 + - + +
7A TYR* 4.6 2.0 - - + -
36A ILE* 4.1 8.3 - - + -
37A THR 3.4 1.3 - - - +
49A GLN* 4.0 11.4 - - + +
50A VAL* 1.3 81.8 - - - +
52A GLU* 1.3 63.5 + - - +
58A LEU* 3.5 22.9 - - + +
61A LEU* 3.8 34.3 - - + -
62A PHE* 5.3 2.5 - - + -
65A ILE* 4.1 16.4 - - + -
92A MET* 3.8 22.2 - - + -
504A FMN 4.0 5.8 - - - +
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Residues in contact with GLU 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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2A LEU* 4.7 3.5 - - + +
3A THR 3.4 6.3 - - - +
4A THR* 4.3 9.5 + - - +
36A ILE* 3.1 9.0 - - - +
37A THR* 2.8 53.1 + - - +
50A VAL* 4.6 4.7 - - + -
51A LEU* 1.3 79.2 - - - +
53A GLY* 1.3 58.0 + - - +
58A LEU* 4.0 3.6 - - - -
82A SER* 5.0 0.2 + - - -
84A TYR 3.9 1.7 - - - +
85A ARG* 3.1 19.7 + - + +
86A ARG* 2.7 34.8 + - - +
87A PHE* 2.9 35.9 + - + +
125A MET* 3.5 14.1 - - + +
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Residues in contact with GLY 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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2A LEU* 3.7 15.9 - - - +
3A THR* 2.8 32.3 + - - +
35A GLY 3.5 16.2 - - - -
36A ILE* 4.8 1.8 - - - -
52A GLU* 1.3 74.4 - - - +
54A THR* 1.3 68.6 + - - +
58A LEU* 3.9 8.0 - - - +
85A ARG* 3.9 1.3 - - - -
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Residues in contact with THR 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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1A MET 3.4 24.5 - - - +
2A LEU* 5.6 0.9 - - + -
3A THR* 4.3 0.2 - - - -
35A GLY 4.7 0.8 + - - -
53A GLY* 1.3 76.9 - - - +
55A GLU* 1.3 65.3 + - - +
56A GLU* 3.2 11.2 + - - +
57A ALA* 3.2 24.7 + - + +
58A LEU* 3.1 21.0 + - - +
85A ARG* 6.1 1.1 - - - +
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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