Contacts of the helix formed by residues 7 - 19 (chain A) in PDB entry 2A7P
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 ASN 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU 3.7 0.6 - - - -
6A PHE* 1.3 81.7 - - - +
8A VAL* 1.3 62.5 + - - +
9A GLU* 3.0 14.8 + - - +
10A ASP* 2.7 53.6 + - - +
11A TYR* 3.3 17.5 - - - -
289A ARG* 3.6 42.0 - - - +
328A LEU* 4.0 9.8 - - - +
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Residues in contact with VAL 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 ASN* 1.3 74.4 - - - +
9A GLU* 1.3 59.5 + - - +
11A TYR* 2.9 25.9 + - + +
12A ARG* 3.0 9.9 + - - +
288A ARG* 3.3 37.4 + - + +
309A ALA* 3.9 21.8 - - + +
312A TYR* 3.5 28.0 - - + -
325A VAL* 4.2 21.8 - - + -
328A LEU* 5.9 2.8 - - + +
329A LEU* 4.2 16.6 - - + -
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Residues in contact with GLU 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 ASN* 3.0 13.8 + - - +
8A VAL* 1.3 79.7 - - - +
10A ASP* 1.3 63.1 + - - +
12A ARG* 2.7 49.1 + - - +
13A LYS* 3.0 43.8 + - - +
288A ARG* 6.2 0.4 - - - +
312A TYR* 5.9 0.4 - - - -
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Residues in contact with ASP 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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4A ASN* 3.3 22.9 - - - +
5A LEU* 3.6 20.0 - - + +
6A PHE* 2.9 27.0 + - - +
7A ASN* 2.7 36.2 + - - +
9A GLU* 1.3 74.5 - - - +
11A TYR* 1.3 61.6 + - - +
13A LYS* 3.5 24.0 + - - +
14A LEU* 3.1 17.8 + - - +
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Residues in contact with TYR 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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5A LEU* 3.4 40.5 + - + +
7A ASN 3.3 15.5 - - - -
8A VAL 2.9 9.0 + - - +
10A ASP* 1.3 76.3 - - - +
12A ARG* 1.3 61.3 + - - +
14A LEU* 3.7 5.4 - - - +
15A ALA* 2.8 30.3 + - - +
312A TYR* 3.8 19.1 - - + +
313A GLY* 3.7 20.2 - - - +
316A ALA* 3.9 9.8 - - + +
317A ARG* 4.3 6.3 - - - -
321A GLY* 4.0 13.7 - - - -
324A GLU* 2.5 45.2 + - + +
325A VAL* 3.9 12.3 - - + -
328A LEU* 3.7 21.3 - - + +
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Residues in contact with ARG 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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8A VAL 3.0 7.1 + - - +
9A GLU* 2.7 47.6 + - - +
11A TYR* 1.3 75.1 - - - +
13A LYS* 1.3 82.3 + - - +
15A ALA* 3.0 2.9 + - - +
16A GLN* 2.8 45.4 + - - +
24A TYR* 2.7 35.9 + - + +
28A GLU* 3.6 22.9 - - - -
312A TYR* 3.5 43.7 - - + +
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Residues in contact with LYS 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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9A GLU* 3.0 40.9 + - - +
10A ASP* 3.6 23.7 + - - +
12A ARG* 1.3 97.6 - - - +
14A LEU* 1.3 62.7 + - - +
16A GLN* 3.2 13.4 + - - +
17A LYS* 3.2 23.1 + - - +
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Residues in contact with LEU 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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5A LEU* 4.0 19.7 - - + -
10A ASP 3.1 14.2 + - - +
11A TYR* 3.7 4.9 - - - +
12A ARG 3.2 0.2 - - - -
13A LYS* 1.3 79.2 - - - +
15A ALA* 1.3 63.2 + - - +
17A LYS* 3.2 32.2 + - - +
18A ARG* 3.2 45.3 + - + +
316A ALA* 3.6 21.1 - - + -
317A ARG* 4.0 23.3 - - + -
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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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11A TYR 2.8 18.6 + - - +
12A ARG* 3.0 7.8 + - - +
14A LEU* 1.3 77.6 - - - +
16A GLN* 1.3 56.5 + - - +
18A ARG* 3.2 0.8 + - - -
19A LEU* 2.8 39.7 + - + +
24A TYR* 4.6 2.5 - - + -
27A LEU* 5.2 1.6 - - + -
312A TYR* 3.8 24.7 - - + +
315A ALA* 3.9 17.5 - - + -
316A ALA* 3.9 10.1 - - - +
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Residues in contact with GLN 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 ARG* 2.8 33.2 + - - +
13A LYS* 3.7 10.5 + - - +
15A ALA* 1.3 76.7 - - - +
17A LYS* 1.3 60.8 + - + +
19A LEU 3.8 12.0 - - - +
24A TYR* 3.6 49.8 - - + +
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Residues in contact with LYS 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 LYS* 3.2 11.6 + - + +
14A LEU* 3.2 34.2 + - - +
16A GLN* 1.3 78.7 - - + +
18A ARG* 1.3 64.5 + - + +
19A LEU 4.7 1.4 - - - +
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Residues in contact with ARG 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 LEU* 3.2 42.4 + - + +
15A ALA 4.1 2.0 - - - +
17A LYS* 1.3 83.2 - - + +
19A LEU* 1.3 63.2 + - - +
20A PRO* 4.0 4.0 - - - +
87A TRP* 5.0 7.6 - - - -
315A ALA 4.5 11.4 - - - +
316A ALA 2.6 36.7 + - - -
317A ARG* 3.8 16.4 - - - +
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Residues in contact with LEU 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 ALA 2.8 19.5 + - - +
16A GLN 3.8 11.1 - - - +
17A LYS 4.7 1.7 - - - +
18A ARG* 1.3 81.6 - - - +
20A PRO* 1.3 80.2 - - + +
21A LYS* 3.4 2.6 + - - -
23A VAL* 4.0 16.4 - - + -
24A TYR* 4.0 28.2 - - + +
27A LEU* 4.0 11.0 - - + -
85A ALA 4.5 1.8 - - - +
86A LEU* 3.8 38.6 - - + +
315A ALA* 3.7 27.6 - - + +
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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