Contacts of the helix formed by residues 5 - 18 (chain A) in PDB entry 1A16
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 ARG 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 1.3 72.9 - - - +
6A GLN* 1.3 96.6 + - - +
8A PHE* 3.2 13.2 + - - +
9A GLN* 3.0 26.7 + - - +
12A ARG* 4.6 0.9 + - - -
100A GLU* 3.6 29.7 + - - -
101A LYS 3.4 24.9 + - - +
102A LEU* 3.7 20.6 - - - +
103A GLY* 4.5 5.5 - - - -
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Residues in contact with GLN 6 (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 SER* 3.2 13.9 + - - +
5A ARG* 1.3 112.7 + - - +
7A GLU* 1.3 57.2 - - - +
9A GLN* 3.2 28.9 + - - +
10A ARG* 2.9 46.0 + - - +
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Residues in contact with GLU 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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3A ILE* 3.8 14.0 - - + +
4A SER* 3.3 15.8 + - - +
6A GLN* 1.3 76.2 - - - +
8A PHE* 1.3 65.2 + - - +
10A ARG* 3.2 31.7 + - + +
11A ARG* 3.0 56.7 + - + +
177A SER* 2.6 31.5 + - - -
179A GLU* 3.2 30.0 - - - +
180A GLU* 3.8 0.9 - - - +
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Residues in contact with PHE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.4 34.1 - - + -
4A SER 3.1 20.6 + - - -
5A ARG* 3.2 10.9 + - - +
7A GLU* 1.3 76.6 - - - +
9A GLN* 1.3 62.6 + - - +
11A ARG* 3.4 27.2 + - - +
12A ARG* 3.1 34.9 + - - +
50A TRP* 3.3 34.5 - + - -
51A TYR* 3.3 15.7 - - - -
52A PHE 3.8 10.7 - - - +
53A THR* 3.8 14.6 - - - +
54A GLY* 3.4 21.8 - - - -
102A LEU 5.4 1.3 - - - +
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Residues in contact with GLN 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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5A ARG* 3.0 20.7 + - - +
6A GLN* 3.3 33.9 + - - +
8A PHE* 1.3 74.8 - - - +
10A ARG* 1.3 59.3 + - + +
12A ARG* 3.1 25.5 + - - +
13A GLN* 2.9 38.1 + - + +
103A GLY* 3.2 26.7 - - - +
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 5.9 0.2 + - - -
6A GLN* 2.9 34.8 + - - +
7A GLU* 3.2 42.8 + - + +
9A GLN* 1.3 75.2 - - + +
11A ARG* 1.3 58.1 + - + +
13A GLN* 3.2 8.8 + - - +
14A ALA* 2.8 30.2 + - - +
177A SER* 6.2 0.4 - - - -
179A GLU* 4.6 10.9 + - - +
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Residues in contact with ARG 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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3A ILE* 3.7 13.5 - - - +
7A GLU* 3.0 44.5 + - + +
8A PHE* 3.4 27.1 - - - +
9A GLN 3.2 0.2 - - - -
10A ARG* 1.3 76.1 - - + +
12A ARG* 1.3 61.4 + - - +
14A ALA* 3.3 2.3 + - - -
15A LEU 3.1 17.0 + - - -
50A TRP* 5.7 1.0 - - - -
51A TYR* 2.9 67.9 + - + +
52A PHE* 3.3 24.8 - - + -
172A MET* 3.6 11.3 - - + +
180A GLU* 3.2 28.9 + - - +
268A TYR* 3.3 7.5 + - - -
358A LEU* 5.5 0.2 - - - +
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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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5A ARG 4.6 0.4 + - - -
8A PHE* 3.1 14.9 + - - +
9A GLN* 3.1 36.5 + - + +
11A ARG* 1.3 77.0 - - - +
13A GLN* 1.3 60.0 + - - +
15A LEU* 3.2 3.8 + - - +
16A VAL* 3.0 34.2 + - - +
52A PHE* 2.5 53.5 + - + +
53A THR* 3.9 12.9 + - - +
62A LEU* 3.8 21.8 - - + -
64A LEU* 4.0 22.7 - - + +
74A SER* 5.2 2.6 + - - -
102A LEU* 2.9 29.9 + - - +
103A GLY 3.2 19.6 + - - -
104A VAL* 4.4 12.0 - - - +
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Residues in contact with GLN 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 GLN* 2.9 21.7 + - + +
10A ARG* 3.2 10.1 + - - +
12A ARG* 1.3 78.4 - - - +
14A ALA* 1.3 61.4 + - - +
16A VAL* 3.7 10.6 - - - +
17A GLU* 2.9 30.5 + - - +
72A ASN* 3.2 33.5 + - - +
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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 ARG 2.8 17.2 + - - +
11A ARG* 3.6 7.0 - - - +
12A ARG 3.3 0.4 - - - -
13A GLN* 1.3 76.8 - - - +
15A LEU* 1.3 60.1 + - - +
17A GLU* 3.5 9.0 - - - +
18A GLN* 3.0 30.9 + - - +
172A MET* 3.8 16.2 - - + -
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Residues in contact with LEU 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 ARG 3.1 12.4 + - - +
12A ARG 3.6 7.6 - - - +
13A GLN 3.2 0.2 - - - -
14A ALA* 1.3 75.6 - - - +
16A VAL* 1.3 66.4 + - - +
18A GLN* 3.0 16.9 + - + +
19A MET* 3.0 28.9 + - + +
25A ALA* 4.3 10.8 - - + -
27A ILE* 4.2 12.3 - - + -
52A PHE* 3.8 24.2 - - + -
64A LEU* 3.9 19.3 - - + -
128A TYR* 6.3 1.3 - - + -
165A TRP* 4.9 10.5 - - + -
168A VAL* 4.1 24.7 - - + -
169A VAL* 4.2 13.5 - - + -
172A MET* 4.5 4.0 - - - +
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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
----------------------------------------------------------
12A ARG 3.0 19.3 + - - +
13A GLN* 3.7 15.9 - - - +
15A LEU* 1.3 77.4 - - - +
17A GLU* 1.3 60.8 + - - +
19A MET* 3.0 17.5 + - + -
64A LEU* 4.2 28.9 - - + -
65A ILE 5.7 0.2 - - - +
66A LYS* 2.8 42.4 + - + +
72A ASN* 3.7 39.3 - - + +
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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 GLN 2.9 17.5 + - - +
14A ALA* 3.5 11.4 - - - +
16A VAL* 1.3 77.1 - - - +
18A GLN* 1.3 64.1 + - - +
19A MET 3.8 0.5 - - - +
66A LYS* 3.2 18.0 + - - +
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Residues in contact with GLN 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* 3.0 23.6 + - - +
15A LEU* 3.0 9.2 + - + +
17A GLU* 1.3 81.6 - - - +
19A MET* 1.3 61.9 + - - +
20A GLN* 3.9 1.2 + - - +
128A TYR* 4.4 3.7 + - - -
168A VAL* 3.4 40.9 - - + +
172A MET* 3.8 18.9 - - - +
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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