Contacts of the strand formed by residues 6 - 15 (chain A) in PDB entry 1A6Z
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 HIS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.8 20.7 + - - +
5A SER* 1.3 80.6 + - - +
7A SER* 1.3 63.1 + - - +
32A ASP* 2.8 30.2 + - - +
103A GLU* 3.6 3.9 - - - +
104A MET* 2.9 37.0 + - + +
105A GLN 6.3 0.7 - - - -
106A GLU* 6.4 0.2 - - - -
169A LEU* 3.7 9.2 - - + +
173A LEU* 3.5 37.2 - - + +
180A LEU* 6.2 0.2 - - + -
181A ASP* 6.4 2.2 - - + -
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Residues in contact with SER 7 (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 HIS* 1.3 77.0 - - - +
8A LEU* 1.3 60.5 + - - +
9A HIS* 3.8 17.3 + - - -
31A VAL* 3.1 5.0 - - - +
32A ASP* 2.7 45.1 + - - -
33A ASP* 4.2 7.3 + - - -
102A CYS 3.6 10.3 - - - -
103A GLU* 4.2 15.3 - - - -
113A TYR* 5.6 2.0 - - - -
169A LEU* 3.5 11.2 - - - +
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Residues in contact with LEU 8 (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 SER* 1.3 75.5 - - - +
9A HIS* 1.3 66.2 + - - +
10A TYR* 3.6 33.0 - - + +
30A TYR 3.3 13.5 - - - +
31A VAL* 4.9 0.4 - - + -
36A PHE* 3.8 15.7 - - + -
101A GLY* 3.1 2.3 - - - -
102A CYS* 2.9 34.9 + - - +
165A CYS* 3.6 35.7 - - - +
168A GLN* 3.8 21.1 - - + +
169A LEU* 3.7 28.0 - - + +
172A LEU* 4.1 6.3 - - + -
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Residues in contact with HIS 9 (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 SER* 3.8 15.6 + - - -
8A LEU* 1.3 73.4 - - - +
10A TYR* 1.3 64.7 + - - +
11A LEU* 3.2 27.8 - - + +
28A LEU 3.9 0.5 - - - +
29A GLY* 3.7 0.7 - - - -
30A TYR* 2.9 62.2 + - + +
33A ASP* 3.8 23.6 - - - -
99A ILE* 4.3 7.4 - - + -
100A LEU 3.2 10.3 - - - +
101A GLY* 3.7 0.4 - - - -
113A TYR* 2.9 30.1 + - + +
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Residues in contact with TYR 10 (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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8A LEU* 3.6 22.8 - - + +
9A HIS* 1.3 76.0 - - - +
11A LEU* 1.3 67.7 + - - +
12A PHE* 3.6 23.3 - - + -
28A LEU 3.1 14.6 - - - +
29A GLY* 3.7 14.8 - - - -
36A PHE* 3.5 16.2 - + - -
37A VAL* 4.2 5.4 - - + -
65A LEU* 3.8 4.1 - - + +
68A SER* 6.1 0.4 - - - -
69A LEU* 3.9 29.4 - - + -
72A TRP* 4.0 18.4 - + - -
98A VAL 4.1 0.2 - - - +
99A ILE* 3.5 1.7 - - - +
100A LEU* 2.6 43.1 + - + +
101A GLY* 5.6 0.7 - - - -
160A TYR* 3.9 16.4 - - - -
168A GLN* 2.8 34.4 + - - -
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Residues in contact with LEU 11 (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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9A HIS* 3.2 35.2 - - + +
10A TYR* 1.3 81.0 - - - +
12A PHE* 1.3 63.4 + - - +
13A MET* 5.3 2.1 - - - +
26A GLU 4.0 0.2 - - - +
27A ALA* 3.2 6.1 - - - +
28A LEU* 2.8 43.2 + - + +
30A TYR* 3.8 14.4 - - + -
98A VAL 3.4 3.4 - - - -
99A ILE* 3.6 12.6 - - + -
55B SER* 3.5 25.1 - - - +
56B PHE* 3.7 44.6 - - + +
63B TYR* 5.7 0.2 - - - +
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Residues in contact with PHE 12 (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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10A TYR* 3.6 22.0 - - + -
11A LEU* 1.3 74.8 - - - +
13A MET* 1.3 63.9 + - - +
25A PHE* 3.6 17.3 - + + -
26A GLU 3.6 2.9 - - - -
27A ALA* 3.5 27.6 - - + -
69A LEU* 4.2 6.7 - - + -
72A TRP* 3.5 50.0 - + + -
76A PHE* 3.9 23.1 - + + -
97A GLN* 3.3 4.1 - - - -
98A VAL* 2.8 49.9 + - + +
100A LEU* 3.6 25.8 - - + -
56B PHE* 3.6 5.4 - - - -
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Residues in contact with MET 13 (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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11A LEU 5.3 2.0 - - - +
12A PHE* 1.3 75.5 - - - +
14A GLY* 1.3 58.5 + - - +
24A LEU* 4.7 3.9 - - + +
25A PHE* 3.3 3.1 - - - -
26A GLU* 3.0 62.3 + - + +
28A LEU* 4.9 7.6 - - - -
76A PHE* 3.9 5.1 - - - -
96A LEU 3.5 7.0 - - - -
97A GLN* 4.1 14.6 - - + -
54B LEU* 3.2 58.6 - - + +
55B SER* 4.0 4.5 - - - +
56B PHE* 4.3 11.0 - - + -
62B PHE* 3.4 23.3 - - + -
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Residues in contact with GLY 14 (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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13A MET* 1.3 75.9 - - - +
15A ALA* 1.3 60.2 + - - +
24A LEU* 3.5 24.5 - - - -
25A PHE* 4.0 0.7 - - - -
76A PHE* 3.6 8.9 - - - -
80A PHE* 3.7 6.3 - - - -
95A THR* 3.4 5.8 - - - -
96A LEU 2.9 30.2 + - - +
97A GLN* 5.3 0.2 - - - +
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Residues in contact with ALA 15 (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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14A GLY* 1.3 74.2 - - - +
16A SER* 1.3 61.2 + - - +
17A GLU* 5.2 3.2 - - - +
23A SER* 2.7 31.5 - - - -
24A LEU* 2.8 30.9 + - + +
80A PHE* 3.6 7.5 - - - -
93A SER* 5.5 1.1 - - - +
94A HIS 3.1 11.0 - - - +
95A THR* 4.4 11.4 - - + -
33B SER* 6.0 2.0 - - - +
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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