Contacts of the helix formed by residues 2 - 17 (chain A) in PDB entry 1ESQ
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 ASP 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 79.6 + - - +
3A ALA* 1.3 67.7 + - - +
4A GLN* 3.0 48.9 + - - +
5A SER* 3.0 18.2 + - - -
6A ALA* 3.1 12.3 + - - +
266A ILE* 3.9 16.5 - - + +
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Residues in contact with ALA 3 (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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2A ASP* 1.3 77.4 - - - +
4A GLN* 1.3 56.3 + - - +
6A ALA* 3.4 4.2 + - - +
7A ALA* 3.0 30.7 + - - +
260A VAL* 3.9 2.6 - - - +
261A GLN* 3.5 29.0 - - - +
264A ALA* 3.9 34.1 - - + +
266A ILE* 4.1 5.0 - - - +
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Residues in contact with GLN 4 (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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2A ASP* 3.0 36.7 + - - +
3A ALA* 1.3 79.3 - - - +
5A SER* 1.3 70.3 + - - +
7A ALA* 3.7 2.3 + - - +
8A LYS* 3.2 22.9 + - - +
257A GLU* 5.1 1.0 - - - +
261A GLN* 4.3 19.0 - - + +
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Residues in contact with SER 5 (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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1A MET* 3.5 30.4 - - - -
2A ASP* 3.0 18.9 + - - -
4A GLN* 1.3 79.5 - - - +
6A ALA* 1.3 69.3 + - - +
8A LYS* 3.2 8.3 + - - +
9A CYS* 3.1 23.5 + - - -
216A PHE* 6.1 0.7 - - - -
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Residues in contact with ALA 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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1A MET* 4.0 2.8 - - - +
2A ASP 3.1 11.9 + - - +
3A ALA* 3.6 9.0 - - - +
5A SER* 1.3 75.7 - - - +
7A ALA* 1.3 65.7 + - - +
9A CYS* 2.8 16.3 + - - +
10A LEU* 3.1 11.2 + - - +
220A ALA* 3.8 34.0 - - - +
223A SER* 4.5 5.2 - - - -
224A SER* 4.6 1.9 + - - -
260A VAL* 4.0 11.7 - - + -
264A ALA* 5.2 0.2 - - + -
266A ILE* 4.2 15.3 - - + -
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Residues in contact with ALA 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 ALA 3.0 13.8 + - - +
4A GLN 4.0 2.9 - - - +
6A ALA* 1.3 78.8 - - - +
8A LYS* 1.3 62.8 + - - +
10A LEU* 3.1 17.2 + - - +
11A THR 3.2 9.7 + - - -
257A GLU* 3.0 47.2 - - + +
260A VAL* 3.5 16.3 - - + +
261A GLN* 3.8 10.3 - - + +
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Residues in contact with LYS 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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4A GLN 3.2 11.7 + - - +
5A SER* 3.2 10.7 + - - +
6A ALA 3.1 1.2 - - - -
7A ALA* 1.3 78.4 - - - +
9A CYS* 1.3 62.9 + - - +
11A THR* 3.4 16.3 + - - +
12A ALA* 3.2 19.6 + - - +
257A GLU* 3.3 31.5 + - - +
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Residues in contact with CYS 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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1A MET* 4.3 10.3 - - - -
5A SER* 3.1 20.3 + - - -
6A ALA 2.8 8.1 + - - +
8A LYS* 1.3 75.2 - - - +
10A LEU* 1.3 65.0 + - - +
12A ALA* 3.3 8.3 + - - +
13A VAL* 3.1 26.2 + - - +
207A PHE* 4.0 9.2 - - + -
210A VAL* 4.1 3.8 - - + +
211A GLU* 4.1 33.9 - - + -
220A ALA* 3.8 22.0 - - + -
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Residues in contact with LEU 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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6A ALA 3.1 6.2 + - - +
7A ALA* 3.1 10.5 + - - +
9A CYS* 1.3 78.0 - - - +
11A THR* 1.3 62.5 + - - +
13A VAL* 3.3 4.1 + - + +
14A ARG* 3.3 42.8 + - - +
39A LEU* 3.5 32.8 - - + -
207A PHE* 3.8 15.6 - - + -
224A SER* 3.7 18.2 - - - +
255A VAL* 3.8 20.0 - - + -
256A THR 4.3 8.3 - - - +
257A GLU 4.7 1.3 - - - +
260A VAL* 3.6 28.0 - - + -
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Residues in contact with THR 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 ALA 3.2 2.2 + - - -
8A LYS* 3.6 22.2 - - - +
9A CYS 3.3 0.2 - - - -
10A LEU* 1.3 79.6 - - - +
12A ALA* 1.3 58.4 + - - +
14A ARG* 3.4 13.5 + - + +
15A ARG* 2.9 31.0 + - + +
257A GLU* 3.3 38.7 + - - +
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Residues in contact with ALA 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 LYS 3.2 12.0 + - - +
9A CYS* 3.6 10.5 - - - +
10A LEU 3.2 0.8 - - - -
11A THR* 1.3 75.6 - - - +
13A VAL* 1.3 65.9 + - - +
15A ARG* 4.2 7.4 - - - +
16A HIS* 3.0 42.3 + - + +
210A VAL* 4.0 17.0 - - + +
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Residues in contact with VAL 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 CYS 3.1 18.0 + - - +
10A LEU* 3.3 9.4 + - + +
12A ALA* 1.3 75.2 - - - +
14A ARG* 1.3 55.7 + - - +
17A SER* 2.7 30.7 + - - -
18A PRO* 3.0 26.9 - - + +
39A LEU* 4.1 28.7 - - + +
40A GLY 3.7 3.0 - - - +
41A ALA* 4.5 6.3 - - + -
206A ALA* 3.7 22.4 - - + +
207A PHE* 3.7 25.6 - - + -
210A VAL* 3.8 11.2 - - + -
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Residues in contact with ARG 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 LEU* 3.3 35.1 + - + +
11A THR* 3.6 12.9 + - + +
12A ALA 3.1 0.4 - - - -
13A VAL* 1.3 77.9 - - + +
15A ARG* 1.3 62.6 + - - +
16A HIS 3.5 0.2 + - - -
17A SER* 3.8 7.8 + - - -
38A ALA 5.3 0.2 + - - -
39A LEU 3.2 24.8 + - - +
40A GLY* 4.2 12.4 - - - +
252A LEU 3.2 16.6 + - - -
253A SER 3.6 12.9 + - - -
255A VAL* 2.7 50.3 + - - +
256A THR* 4.2 6.1 - - - +
257A GLU 4.7 2.2 - - - +
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Residues in contact with ARG 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 THR* 2.9 23.5 + - + +
12A ALA* 3.8 8.5 - - - +
14A ARG* 1.3 79.5 - - - +
16A HIS* 1.3 87.0 + - + +
17A SER* 5.3 0.5 - - - -
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Residues in contact with HIS 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 ALA* 3.0 34.7 + - + +
15A ARG* 1.3 114.4 + - + +
17A SER* 1.3 73.7 + - - +
18A PRO* 3.4 3.1 - - + +
210A VAL* 4.2 23.8 - - + -
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Residues in contact with SER 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 VAL 2.7 13.9 + - - -
14A ARG 3.8 5.8 + - - -
15A ARG 3.6 1.6 - - - -
16A HIS* 1.3 76.4 - - - +
18A PRO* 1.3 69.2 - - - +
19A LEU* 3.5 1.7 + - - +
40A GLY 3.2 23.2 + - - -
41A ALA 3.9 2.6 - - - -
42A SER* 3.0 23.8 + - - -
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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