Contacts of the helix formed by residues 11 - 22 (chain A) in PDB entry 6B9H
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 GLU 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 1.3 77.4 - - - +
12A LEU* 1.3 59.3 + - - +
13A CYS 3.6 2.3 - - - +
14A GLU* 4.6 5.3 - - - +
15A SER* 3.3 14.0 + - - +
145A SER* 5.3 2.9 - - - +
149A VAL* 3.3 39.3 - - + +
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Residues in contact with LEU 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 ALA* 3.0 13.6 + - - +
11A GLU* 1.3 76.9 - - - +
13A CYS* 1.3 68.1 - - - +
15A SER* 3.4 1.4 + - - -
16A LEU* 3.0 34.3 + - + +
113A ALA 5.5 0.9 - - - +
116A GLY* 3.7 30.3 - - - +
117A ARG* 4.3 5.4 - - + +
120A GLN* 3.8 20.9 - - - +
149A VAL* 3.9 14.8 - - + +
152A THR* 6.3 0.9 - - + -
153A ALA* 3.9 28.9 - - + +
156A GLU* 5.4 2.9 - - - +
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Residues in contact with CYS 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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10A ALA* 5.4 0.6 - - - +
11A GLU 3.6 1.4 - - - +
12A LEU* 1.3 80.6 - - - +
14A GLU* 1.3 60.9 + - + +
16A LEU 3.6 0.7 - - - -
17A LEU* 2.8 29.9 + - - +
32A VAL* 4.3 12.3 - - - -
35A LEU* 5.8 0.2 - - - -
112A ALA* 3.2 42.0 - - + +
113A ALA* 5.4 0.9 - - - -
115A LEU* 3.8 30.3 - - - -
116A GLY* 3.9 11.6 - - - -
119A LEU* 3.8 7.4 - - - +
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Residues in contact with GLU 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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11A GLU* 4.4 5.7 + - - +
12A LEU 3.3 0.2 - - - -
13A CYS* 1.3 79.2 - - + +
15A SER* 1.3 66.8 + - - +
17A LEU* 3.3 13.5 + - + +
18A THR* 3.2 23.7 + - - -
32A VAL* 4.9 17.7 - - + +
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Residues in contact with SER 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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11A GLU* 3.3 22.4 + - - +
12A LEU 3.4 1.0 + - - -
13A CYS 3.4 0.4 - - - -
14A GLU* 1.3 77.3 - - - +
16A LEU* 1.3 66.4 + - - +
18A THR* 3.3 10.1 + - - -
19A TRP* 3.2 17.2 + - - +
145A SER 4.5 0.9 + - - -
146A VAL* 3.9 29.9 + - - +
149A VAL* 3.5 32.3 - - - +
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Residues in contact with LEU 16 (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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12A LEU* 3.0 35.4 + - + +
15A SER* 1.3 77.4 - - - +
17A LEU* 1.3 60.4 + - - +
19A TRP* 3.2 13.3 + - + +
20A ILE* 2.9 30.7 + - - +
116A GLY 4.0 6.3 - - - +
119A LEU* 3.8 23.6 - - + +
120A GLN* 3.6 35.9 - - + +
123A LEU* 4.0 20.9 - - + -
149A VAL* 5.4 0.4 - - + -
150A VAL* 3.9 30.5 - - + +
153A ALA* 4.8 1.8 - - + -
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Residues in contact with LEU 17 (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 CYS* 2.8 18.9 + - - +
14A GLU* 3.5 15.7 - - + +
15A SER 3.3 0.2 - - - -
16A LEU* 1.3 73.6 - - - +
18A THR* 1.3 66.4 + - - +
20A ILE* 3.1 6.5 + - + +
21A GLN* 2.9 36.0 + - - +
29A CYS* 3.5 35.2 - - - +
30A GLN 4.0 18.4 - - - +
31A THR* 4.3 12.3 - - - +
32A VAL* 4.4 11.2 - - + +
35A LEU* 3.7 21.8 - - + -
119A LEU* 4.0 5.8 - - + +
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Residues in contact with THR 18 (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 GLU 3.2 11.5 + - - -
15A SER* 3.3 11.1 + - - -
17A LEU* 1.3 77.9 - - - +
19A TRP* 1.3 62.3 + - - +
21A GLN* 3.2 26.2 + - - +
22A THR* 3.4 14.2 + - + +
142A MET* 3.7 18.8 - - + -
143A GLU* 6.5 1.1 - - - -
146A VAL* 4.3 15.8 - - + +
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Residues in contact with TRP 19 (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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15A SER 3.2 10.7 + - - +
16A LEU* 3.5 20.9 - - + +
17A LEU 3.2 0.2 - - - -
18A THR* 1.3 76.4 - - - +
20A ILE* 1.3 97.4 + - + +
22A THR* 2.7 30.4 + - - -
23A PHE* 3.6 29.9 - + - -
48A ILE* 4.5 0.2 - - + -
119A LEU 4.5 2.5 - - - -
122A ILE* 4.0 8.1 - - + -
123A LEU* 3.6 52.5 - - + -
126A ALA* 3.6 24.9 - - + -
135A TYR* 5.0 8.6 + + + -
138A ALA* 6.2 0.8 - - - +
139A ILE* 3.8 32.0 - - + +
142A MET* 3.8 22.1 - - + +
150A VAL* 5.2 4.9 - - + -
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Residues in contact with ILE 20 (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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16A LEU 2.9 19.7 + - - +
17A LEU* 3.5 11.2 - - + +
19A TRP* 1.3 98.1 - - + +
21A GLN* 1.3 61.1 + - - +
23A PHE* 3.0 24.0 + - - +
24A ASN 4.1 1.4 + - - -
25A VAL* 5.5 2.1 + - + +
29A CYS* 3.4 26.0 - - - +
35A LEU* 5.0 1.8 - - + -
40A VAL* 3.7 18.2 - - + -
41A MET* 5.5 1.3 - - + -
44A VAL* 4.0 25.7 - - + +
119A LEU* 3.9 30.5 - - + -
122A ILE* 4.5 7.2 - - + -
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Residues in contact with GLN 21 (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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17A LEU* 2.9 31.1 + - - +
18A THR* 3.4 23.0 + - - +
19A TRP 3.1 0.4 - - - -
20A ILE* 1.3 75.8 - - - +
22A THR* 1.3 62.0 + - - +
24A ASN* 3.2 16.6 + - - +
29A CYS* 2.9 36.7 + - + +
30A GLN* 3.9 29.5 + - - +
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Residues in contact with THR 22 (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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18A THR* 3.6 14.8 - - + +
19A TRP* 2.7 27.9 + - - +
21A GLN* 1.3 77.9 - - + +
23A PHE* 1.3 65.2 + - - +
24A ASN* 3.2 4.6 + - - +
138A ALA* 6.0 2.9 - - - +
142A MET* 4.0 23.6 - - + -
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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