Contacts of the helix formed by residues 7 - 18 (chain A) in PDB entry 1A9Q
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 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 TYR 4.0 0.6 + - - -
6A THR* 1.3 71.5 - - - +
8A GLU* 1.3 69.1 + - - +
10A TYR* 3.2 15.2 + - - +
11A GLN* 3.2 47.1 + - - +
105A LEU* 3.6 23.7 - - + +
152A GLU* 3.7 12.0 + - + +
154A ARG* 3.3 73.7 + - + +
155A PHE* 3.7 36.3 - + - -
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Residues in contact with GLU 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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6A THR* 3.1 22.1 + - - +
7A TYR* 1.3 77.8 + - + +
9A ASP* 1.3 61.6 + - - +
11A GLN* 3.6 17.2 - - - +
12A ASP* 2.9 39.8 + - - +
154A ARG* 3.5 30.6 + - - -
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Residues in contact with ASP 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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4A GLY 4.0 4.0 - - - +
5A TYR* 3.4 27.5 - - + -
6A THR* 2.9 41.7 + - - +
8A GLU* 1.3 78.5 - - - +
10A TYR* 1.3 61.9 + - - +
12A ASP* 3.3 6.0 + - - +
13A THR* 3.2 25.7 + - - -
55A ASN* 3.3 22.3 + - - +
98A PHE* 4.8 1.1 - - - -
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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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3A ASN* 3.1 27.7 + - - -
5A TYR* 3.5 27.3 - - + +
6A THR 3.3 20.6 - - - -
7A TYR* 3.2 8.6 + - - +
9A ASP* 1.3 80.2 - - - +
11A GLN* 1.3 56.6 + - - +
13A THR* 3.2 4.7 + - - -
14A ALA* 2.9 28.4 + - - +
94A TRP* 4.6 2.9 + - - +
98A PHE* 3.5 43.6 - + - -
101A ARG* 3.3 41.7 + - + -
102A VAL* 4.2 9.2 - - + +
105A LEU* 3.7 16.9 - - + +
155A PHE* 3.7 26.0 - + + -
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Residues in contact with GLN 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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7A TYR* 3.2 40.1 + - + +
8A GLU* 3.6 19.8 - - - +
10A TYR* 1.3 77.6 - - - +
12A ASP* 1.3 62.7 + - - +
14A ALA* 3.3 4.6 + - + +
15A LYS* 2.8 56.9 + - + +
105A LEU* 3.7 16.5 - - + +
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Residues in contact with ASP 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 GLU* 2.9 26.2 + - - +
9A ASP* 3.3 8.9 + - - +
11A GLN* 1.3 75.9 + - - +
13A THR* 1.3 66.8 + - - +
15A LYS* 3.2 8.7 + - - +
16A TRP* 2.9 24.3 + - - +
54A PRO* 6.0 2.5 - - + -
55A ASN* 4.4 8.3 + - - +
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Residues in contact with THR 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 ASP 3.2 5.0 + - - -
10A TYR 3.2 8.0 + - - -
12A ASP* 1.3 77.3 - - - +
14A ALA* 1.3 63.9 + - - +
16A TRP* 3.2 7.4 + - - +
17A LEU* 3.1 23.9 + - + +
53A ILE* 3.7 19.3 - - + -
54A PRO* 2.9 29.9 + - - +
55A ASN* 3.2 20.4 + - - +
56A PHE* 4.2 2.9 - - + -
98A PHE* 3.4 19.0 - - + -
102A VAL* 4.0 15.7 - - + -
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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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10A TYR 2.9 16.5 + - - +
11A GLN* 3.6 6.5 - - + +
13A THR* 1.3 76.5 - - - +
15A LYS* 1.3 61.2 + - + +
17A LEU* 3.3 2.1 + - - -
18A LEU* 3.1 30.4 + - + +
102A VAL* 4.0 10.7 - - + +
105A LEU* 3.9 29.8 - - + +
106A LEU* 3.5 21.4 - - + +
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Residues in contact with LYS 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 GLN* 2.8 47.6 + - + +
12A ASP* 3.6 9.0 - - - +
14A ALA* 1.3 73.4 - - + +
16A TRP* 1.3 64.3 + - - +
18A LEU* 3.6 17.5 + - + +
19A SER* 3.1 24.4 + - - -
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Residues in contact with TRP 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 ASP 2.9 13.7 + - - +
13A THR* 3.2 11.4 + - - +
15A LYS* 1.3 75.0 - - - +
17A LEU* 1.3 81.2 + - + +
19A SER* 2.9 9.2 + - - -
20A HIS* 2.7 60.4 + + - -
48A PHE* 3.6 41.1 - + - -
52A GLU* 3.6 27.1 - - - -
53A ILE* 4.2 9.6 - - + -
54A PRO* 3.8 32.2 - - + +
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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 THR* 3.1 21.7 + - + +
14A ALA 3.3 5.8 + - - +
16A TRP* 1.3 98.8 - - + +
18A LEU* 1.3 57.1 + - - +
20A HIS* 2.9 18.7 + - - +
21A THR* 3.2 19.6 + - - +
48A PHE* 4.4 8.0 - - + -
53A ILE* 4.2 21.3 - - + -
56A PHE* 5.3 1.1 - - + -
68A LEU* 4.1 16.6 - - + -
70A PHE* 4.3 24.0 - - + -
102A VAL* 4.0 23.6 - - + -
103A PHE* 6.1 0.2 - - + -
106A LEU* 4.0 21.1 - - + -
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Residues in contact with LEU 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 ALA* 3.1 21.1 + - + +
15A LYS* 3.9 19.3 - - + +
16A TRP 3.4 0.2 - - - -
17A LEU* 1.3 75.4 - - - +
19A SER* 1.3 57.1 + - - +
21A THR* 3.0 19.4 - - + +
23A GLN 5.0 1.1 - - - +
24A ARG* 3.2 52.2 + - - +
25A PRO* 6.3 1.1 - - + -
105A LEU 4.9 9.0 - - - +
106A LEU* 3.5 31.2 - - + +
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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