Contacts of the helix formed by residues 11 - 21 (chain A) in PDB entry 2V4R
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 TYR 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 ASP* 1.3 87.0 - - + +
12A PHE* 1.3 54.6 + - - +
13A TYR 3.5 1.8 - - - -
14A ALA* 3.1 6.0 + - + -
15A GLN* 2.8 57.6 + - + +
18A GLU* 3.4 28.6 + - - -
25A LYS* 5.8 0.5 - - - +
46A THR* 4.8 1.3 - - - +
47A ALA 3.8 9.4 - - - +
48A ASN* 3.5 28.3 - - + -
49A TYR* 3.5 25.4 - + + -
50A GLU* 5.6 2.0 - - - -
52A ARG* 3.4 20.9 - - - +
140A THR* 4.2 8.3 + - - +
161A PRO* 5.1 2.2 - - + -
404A DGT 2.6 31.8 + - - -
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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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9A PHE* 3.8 33.0 - + + -
10A ASP 2.4 10.1 + - - -
11A TYR* 1.3 70.8 - - - +
13A TYR* 1.3 78.5 + + - +
15A GLN* 3.1 7.0 + - - +
16A VAL* 2.8 44.1 + - + +
82A TYR* 3.3 36.1 - - + -
85A VAL* 4.3 8.3 - - + -
86A SER* 3.9 14.8 - - - -
89A ILE* 4.8 2.9 - - + -
105A ILE* 4.1 17.5 - - + -
106A ASP* 3.9 19.7 - - + +
139A ILE* 4.7 7.4 - - + -
404A DGT 2.8 16.8 + - + +
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Residues in contact with TYR 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 TYR 3.3 0.8 + - - -
12A PHE* 1.3 84.5 - + - +
14A ALA* 1.3 66.2 - - - +
16A VAL* 3.0 10.6 + - - +
17A GLU* 3.1 14.7 + - - +
31A VAL* 4.0 11.0 - - + -
45A ALA* 4.1 9.9 - - + -
46A THR* 3.5 11.7 - - + -
77A MET* 3.6 28.5 - - + -
79A LYS* 3.0 29.6 + - + +
82A TYR* 3.6 46.5 - + + -
105A ILE* 3.8 15.8 - - + +
404A DGT 3.7 51.7 + + - -
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Residues in contact with ALA 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 TYR* 3.1 15.1 + - + +
13A TYR* 1.3 77.0 - - - +
15A GLN* 1.3 63.5 + - - +
17A GLU* 3.0 8.5 + - - +
18A GLU* 3.0 24.4 + - - +
29A VAL* 4.4 10.0 - - + +
31A VAL* 3.6 19.8 - - + +
46A THR* 3.6 4.0 - - + +
47A ALA 3.9 5.2 - - - -
48A ASN* 3.5 32.1 - - + +
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Residues in contact with GLN 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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9A PHE 4.5 0.4 - - - -
10A ASP 2.6 38.5 + - - +
11A TYR* 2.8 34.9 + - + +
12A PHE* 3.4 6.2 - - - +
14A ALA* 1.3 70.6 - - - +
16A VAL* 1.3 64.6 + - - +
18A GLU* 3.1 7.4 + - - +
19A VAL* 2.9 29.0 + - + +
138A LYS 4.0 2.1 - - - +
139A ILE* 3.1 27.0 - - + +
140A THR* 2.5 56.1 + - - +
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Residues in contact with VAL 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 PHE* 2.8 54.0 + - + +
13A TYR 3.5 1.1 - - - +
15A GLN* 1.3 72.5 - - - +
17A GLU* 1.3 55.1 + - - +
19A VAL* 2.9 9.8 + - + +
20A LEU* 2.7 42.5 + - + +
81A VAL* 4.3 11.2 - - + -
82A TYR* 3.4 33.0 - - + -
85A VAL* 4.2 27.6 - - + -
139A ILE* 4.7 2.0 - - + -
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Residues in contact with GLU 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 TYR 3.1 11.4 + - - +
14A ALA* 3.0 10.9 + - - +
16A VAL* 1.3 79.3 - - - +
18A GLU* 1.3 56.5 + - - +
20A LEU* 3.4 4.1 + - - +
21A ASN* 2.8 31.5 + - - +
24A LEU* 3.8 5.5 - - + +
29A VAL* 4.7 1.3 - - + -
31A VAL* 4.2 10.5 - - + -
75A LEU* 3.5 35.1 - - + +
76A PRO 3.9 8.0 - - - +
78A ARG* 3.4 34.5 + - - -
82A TYR* 2.5 33.2 + - - +
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Residues in contact with GLU 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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11A TYR* 3.4 33.6 + - - -
14A ALA 3.0 11.0 + - - +
15A GLN* 3.6 7.3 - - + +
16A VAL 3.1 0.2 - - - -
17A GLU* 1.3 74.2 - - - +
19A VAL* 1.3 59.7 + - + +
21A ASN 3.0 7.1 - - - -
22A PRO* 2.8 33.6 - - - +
24A LEU* 4.0 16.7 - - + +
25A LYS* 3.9 40.1 - - + +
26A GLY 4.5 0.3 + - - -
29A VAL* 4.0 7.6 - - + +
48A ASN* 3.1 26.8 + - - +
50A GLU* 4.2 5.2 - - - +
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Residues in contact with VAL 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 GLN* 2.9 22.3 + - + +
16A VAL* 2.9 8.5 + - + +
18A GLU* 1.3 77.9 - - + +
20A LEU* 1.3 72.4 + - + +
21A ASN 3.2 0.2 + - - -
22A PRO* 3.5 14.6 - - - +
25A LYS* 6.4 0.2 - - - +
85A VAL* 6.4 2.5 - - + -
137A GLU 3.7 17.7 - - - +
138A LYS* 3.3 34.1 - - + +
139A ILE* 3.3 17.5 - - + -
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Residues in contact with LEU 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 VAL* 2.7 32.6 + - + +
17A GLU* 3.8 6.1 - - - +
19A VAL* 1.3 83.5 - - + +
21A ASN* 1.3 59.3 + - + +
22A PRO* 3.7 3.7 - - - +
78A ARG* 3.5 28.5 - - - +
81A VAL* 3.7 26.2 - - + -
85A VAL* 5.4 5.4 - - + -
88A ARG* 6.3 1.1 - - - +
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Residues in contact with ASN 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 GLU* 2.8 14.2 + - - +
18A GLU 3.0 6.1 - - - +
20A LEU* 1.3 80.6 - - + +
22A PRO* 1.3 55.5 - - - +
23A SER* 2.8 43.4 + - - +
24A LEU* 2.9 37.7 + - + +
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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