Contacts of the helix formed by residues 4 - 19 (chain A) in PDB entry 1C06
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 SER 4 (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 6.3 0.4 - - - -
2A LYS 3.3 6.7 + - - -
3A LEU* 1.3 80.4 - - - +
5A GLU* 1.3 70.3 + - - +
6A TYR* 3.3 28.3 - - - -
7A GLY* 3.4 9.8 + - - -
8A LEU* 3.8 15.6 + - - +
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Residues in contact with GLU 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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4A SER* 1.3 72.4 + - - +
6A TYR* 1.3 69.0 + - + +
7A GLY 2.8 3.9 + - - -
8A LEU* 2.9 31.0 + - + +
9A GLN* 3.2 28.9 + - + +
152A LEU* 5.7 5.9 - - + +
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Residues in contact with TYR 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* 3.6 19.7 - - - +
5A GLU* 1.3 80.5 - - + +
7A GLY* 1.3 60.7 + - - +
9A GLN* 3.6 20.0 - - - +
10A LEU* 3.7 7.6 + - - +
155A GLU* 5.2 2.9 - - - -
156A PHE* 6.1 0.3 - - - -
159A ARG* 4.0 40.1 + - - +
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Residues in contact with GLY 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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4A SER* 3.4 8.9 + - - -
5A GLU 2.8 1.6 + - - -
6A TYR* 1.3 76.8 - - - +
8A LEU* 1.3 67.2 + - - +
9A GLN 2.8 3.2 + - - -
10A LEU* 3.2 7.3 + - - +
11A GLN* 2.9 21.8 + - - +
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Residues in contact with LEU 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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3A LEU* 5.7 8.1 - - + -
4A SER 3.8 14.5 + - - +
5A GLU* 2.9 24.0 + - + +
7A GLY* 1.3 75.8 - - - +
9A GLN* 1.3 64.5 + - - +
11A GLN* 3.2 26.2 + - - +
12A GLU* 3.0 26.6 + - + +
152A LEU* 4.7 6.5 - - + -
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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 GLU* 3.2 35.8 + - + +
6A TYR* 3.6 14.3 - - - +
7A GLY 2.8 1.6 + - - -
8A LEU* 1.3 72.5 - - - +
10A LEU* 1.3 57.3 + - - +
11A GLN 2.6 15.6 + - - -
12A GLU* 2.9 14.9 + - - +
13A LYS* 3.2 8.9 + - - +
152A LEU* 3.3 52.8 - - + +
153A ILE* 4.9 2.1 - - - +
155A GLU* 4.2 7.4 + - - +
156A PHE* 5.6 3.6 - - + -
159A ARG* 2.5 34.4 + - - +
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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 TYR 3.7 7.6 + - - +
7A GLY* 3.2 9.0 + - - +
9A GLN* 1.3 79.4 - - - +
11A GLN* 1.3 60.4 + - - +
13A LYS* 3.4 29.9 - - + +
14A GLN* 3.2 36.0 + - + +
156A PHE* 4.0 39.6 - - + -
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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 GLY 2.9 11.2 + - - +
8A LEU* 3.2 37.0 + - - +
9A GLN 2.6 5.5 + - - -
10A LEU* 1.3 71.0 - - - +
12A GLU* 1.3 70.8 + - - +
13A LYS 2.9 4.3 - - - -
14A GLN* 2.7 26.8 + - + +
15A LYS* 3.1 22.0 + - + +
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Residues in contact with GLU 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 LEU* 3.4 13.6 - - + +
9A GLN 2.9 10.4 + - - +
11A GLN* 1.3 77.7 + - - +
13A LYS* 1.3 61.7 + - - +
15A LYS* 2.8 40.5 + - - +
16A LEU* 3.1 25.5 + - - +
147A GLU 4.1 6.3 - - - +
148A ILE* 5.4 0.9 - - - +
149A ASN* 4.0 21.9 + - + +
152A LEU* 4.1 31.6 - - + -
153A ILE* 4.4 8.4 - - + +
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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 GLN 3.2 4.9 + - - +
10A LEU* 3.4 32.6 - - + +
11A GLN 2.8 1.2 + - - -
12A GLU* 1.3 78.8 - - - +
14A GLN* 1.3 64.1 + - - +
16A LEU* 3.5 2.3 + - - +
17A ARG* 2.8 41.2 + - + +
24A GLU* 5.7 8.0 + - - +
27A PHE* 4.2 29.3 - - + -
153A ILE* 4.0 33.1 - - + +
156A PHE* 4.4 22.4 - - + -
157A TYR* 5.1 5.6 - - - -
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Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.4 37.9 + - + +
11A GLN* 2.7 20.4 + - + +
13A LYS* 1.3 74.1 - - + +
15A LYS* 1.3 65.2 + - - +
17A ARG* 2.7 16.4 + - - +
18A HIS* 2.6 39.1 + - + -
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.1 18.5 + - + +
12A GLU* 2.8 51.8 + - - +
14A GLN* 1.3 75.6 - - - +
16A LEU* 1.3 68.3 + - - +
18A HIS* 3.1 11.3 + - - +
19A MET* 2.9 29.2 + - + +
147A GLU* 4.3 10.8 + - - -
148A ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 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 GLU 3.1 15.9 + - - +
13A LYS 3.7 3.6 - - - +
14A GLN 3.0 0.8 - - - -
15A LYS* 1.3 84.1 - - + +
17A ARG* 1.3 61.5 + - - +
19A MET* 2.8 39.4 + - + +
20A TYR* 4.1 15.8 + - + -
22A VAL* 4.9 3.4 - - + +
27A PHE* 4.1 11.2 - - + -
45A PHE* 3.9 27.6 - - + -
46A MET* 5.1 8.3 - - + -
49A LEU* 4.5 11.0 - - + -
148A ILE* 3.9 35.7 - - + -
149A ASN 4.4 2.5 - - - +
153A ILE* 4.2 13.2 - - + -
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Residues in contact with ARG 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* 2.8 28.2 + - + +
14A GLN* 2.7 17.3 + - - +
16A LEU* 1.3 72.8 - - - +
18A HIS* 1.3 76.1 + - - +
21A GLY* 3.3 5.0 + - - -
22A VAL* 3.1 39.7 + - - +
23A ASN* 3.3 19.8 - - - +
24A GLU* 3.0 41.6 + - - +
27A PHE* 3.8 24.4 - - + -
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN* 2.6 51.1 + - + -
15A LYS* 3.6 9.2 + - - +
17A ARG* 1.3 95.5 + - + +
19A MET* 1.3 70.7 + - - +
21A GLY* 3.6 6.7 + - - +
66A ARG* 3.9 6.4 + - - -
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Residues in contact with MET 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 LYS* 2.9 12.6 + - + +
16A LEU* 2.8 21.3 + - + +
18A HIS* 1.3 82.9 - - - +
20A TYR* 1.3 97.0 + - + +
66A ARG* 3.2 11.6 + - - -
145A PRO* 4.7 8.7 - - + -
147A GLU* 4.4 11.9 - - - +
148A ILE* 3.8 33.4 - - + -
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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