Contacts of the helix formed by residues 5 - 18 (chain A) in PDB entry 3C98
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 GLY 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 1.3 77.4 - - - +
6A LEU* 1.3 66.5 + - - -
7A LYS* 3.2 3.1 - - - -
8A ALA* 3.1 8.3 + - - +
9A VAL* 3.0 20.1 + - - +
142A SER* 3.8 26.2 - - - -
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Residues in contact with LEU 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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5A GLY* 1.3 71.4 - - - -
7A LYS* 1.3 63.8 + - - +
9A VAL* 3.1 7.1 + - + +
10A VAL* 2.9 29.1 + - - +
137A PHE* 4.5 12.3 - - + -
139A PRO* 3.8 11.4 - - + -
141A GLU 3.6 11.4 - - - +
142A SER* 3.2 21.1 + - - +
143A GLN 4.5 2.2 - - - -
144A VAL 3.9 26.2 - - - +
145A TYR* 4.0 22.4 - - + -
179A LEU* 4.5 9.2 - - + -
183A LEU* 4.3 31.6 - - + -
566A LEU* 4.3 15.7 - - + -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLY 3.2 1.3 - - - -
6A LEU* 1.3 76.9 - - - +
8A ALA* 1.3 57.3 + - - +
11A GLY* 2.9 27.9 + - - -
43A SER* 2.7 34.4 + - - +
44A CYS* 3.6 10.7 - - + +
139A PRO* 2.8 33.3 + - + +
140A TYR* 3.1 24.6 + - - +
141A GLU 4.4 4.1 + - - +
142A SER* 4.8 0.4 - - - +
282A ASP* 5.2 7.4 - - - +
283A GLU* 3.7 45.1 - - + +
284A ASP* 5.9 1.8 - - - +
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Residues in contact with ALA 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 ILE* 3.6 21.5 - - + -
5A GLY* 3.1 15.4 + - - +
7A LYS* 1.3 78.0 - - - +
9A VAL* 1.3 64.8 + - - +
11A GLY* 4.9 0.7 - - - -
12A GLU* 3.0 40.0 + - + +
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Residues in contact with VAL 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 ILE* 3.9 28.0 - - + +
5A GLY 3.0 17.6 + - - +
6A LEU* 3.1 12.1 + - + +
8A ALA* 1.3 79.6 - - - +
10A VAL* 1.3 63.0 + - + +
12A GLU* 4.3 3.5 - - - +
13A LYS* 3.5 20.1 + - - +
137A PHE* 6.0 0.2 - - + -
182A THR* 3.7 31.0 - - + +
183A LEU* 4.4 23.1 - - + -
536A ARG* 6.1 1.1 - - - +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 10.8 + - + +
9A VAL* 1.3 78.4 - - + +
11A GLY* 1.3 66.8 + - - +
13A LYS* 3.5 1.9 + - - +
14A ILE* 3.2 37.2 + - + +
40A MET* 4.3 10.3 - - + -
44A CYS* 3.8 12.6 - - - -
135A ILE* 4.2 21.3 - - + +
137A PHE* 3.5 32.5 - - + -
139A PRO* 3.5 33.4 - - + -
182A THR* 4.9 0.7 - - + -
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 2.9 20.4 + - - -
8A ALA* 3.8 0.9 - - - -
10A VAL* 1.3 76.6 - - - +
12A GLU* 1.3 65.1 + - - +
14A ILE* 4.2 1.1 - - - +
15A MET* 3.2 30.8 + - - +
44A CYS* 3.6 22.9 - - - -
45A CYS* 4.7 2.4 - - - -
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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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4A ILE* 3.9 20.1 - - - +
8A ALA* 3.0 29.1 + - - +
9A VAL* 4.3 3.4 - - - +
11A GLY* 1.3 74.8 - - - +
13A LYS* 1.3 57.6 - - - +
15A MET* 3.3 5.6 + - - +
16A HIS* 2.8 34.7 + - + +
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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 VAL 3.5 15.8 + - - +
10A VAL 4.1 3.1 - - - +
11A GLY 3.3 0.4 - - - -
12A GLU* 1.3 80.6 - - - +
14A ILE* 1.3 56.8 + - + +
16A HIS* 4.7 1.8 - - - -
17A ASP* 2.8 58.3 + - + +
133A ILE* 2.7 37.9 + - + +
134A ASN* 4.5 2.2 + - - +
135A ILE* 3.4 27.5 - - + +
181A ALA 5.5 1.2 + - - -
182A THR* 4.2 18.9 + - + +
2B LYS* 5.2 5.3 - - - +
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Residues in contact with ILE 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 VAL* 3.2 35.8 + - + +
11A GLY* 4.3 2.5 - - - +
13A LYS* 1.3 72.8 - - - +
15A MET* 1.3 64.3 + - + +
18A VAL* 3.0 39.1 + - + -
19A ILE* 3.1 13.8 + - + +
40A MET* 4.3 25.6 - - + -
41A LEU* 4.0 28.3 - - + -
44A CYS* 4.3 10.8 - - - -
45A CYS* 5.8 0.7 - - - -
76A LEU* 4.5 12.6 - - + -
133A ILE* 4.6 15.3 - - + -
135A ILE* 4.8 5.6 - - + -
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Residues in contact with MET 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 GLY 3.2 20.8 + - - +
12A GLU* 3.7 5.2 - - - +
14A ILE* 1.3 78.7 - - - +
16A HIS* 1.3 58.1 + - - +
19A ILE* 3.8 24.4 - - + +
20A LYS* 2.9 49.5 + - + +
41A LEU* 5.9 0.2 - - - -
45A CYS* 3.6 29.2 - - - -
49A ASP* 4.0 15.0 - - + +
50A ILE* 4.4 7.9 - - - -
53A GLU* 3.7 30.7 - - + -
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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 GLU 2.8 22.1 + - - +
13A LYS* 4.4 2.2 - - - +
15A MET* 1.3 77.3 - - - +
17A ASP* 1.3 83.1 + - - +
18A VAL 3.6 0.5 + - - -
20A LYS* 4.2 17.3 - - + +
21A LYS* 3.8 17.2 + - - +
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Residues in contact with ASP 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 50.5 + - + +
16A HIS* 1.3 98.1 + - - +
18A VAL* 1.3 63.1 + - + +
21A LYS* 3.3 18.3 + - - +
105A PHE* 3.3 18.2 - - - -
133A ILE* 4.7 10.0 - - + +
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Residues in contact with VAL 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 ILE* 3.0 30.5 + - + +
16A HIS 3.4 0.6 - - - -
17A ASP* 1.3 83.4 - - - +
19A ILE* 1.3 77.2 + - + +
20A LYS 3.6 0.9 - - - -
21A LYS* 3.5 3.4 + - - +
22A VAL* 3.4 24.8 + - - +
31A LEU* 5.5 0.7 - - + -
74A VAL* 4.1 13.2 - - + -
76A LEU* 4.4 16.2 - - + -
105A PHE* 3.6 45.3 - - + -
133A ILE* 4.0 16.2 - - + -
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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