Contacts of the helix formed by residues 6 - 19 (chain A) in PDB entry 3S1K
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 LYS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 1.3 76.1 + - - +
8A MET* 3.3 8.2 + - + +
9A HIS* 3.2 45.5 + - + +
10A ASN* 3.4 19.6 + - - +
16W LYS* 4.3 13.6 - - - +
18W MET* 5.2 1.4 - - - +
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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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6A LYS* 1.3 82.4 - - - +
8A MET* 1.3 58.3 + - + +
10A ASN* 3.5 4.8 + - - +
11A ALA* 3.0 27.4 + - - +
16W LYS* 4.0 25.1 + - + +
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Residues in contact with MET 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 LYS* 3.2 7.2 - - + +
7A GLU* 1.3 76.9 - - + +
9A HIS* 1.3 73.1 + - + +
11A ALA* 3.1 11.8 + - + +
12A TYR* 3.1 56.5 + - + -
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Residues in contact with HIS 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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6A LYS* 3.2 47.9 + - + +
7A GLU 3.4 0.4 - - - -
8A MET* 1.3 82.3 - - + +
10A ASN* 1.3 57.5 + - - +
12A TYR* 3.4 6.2 + + - +
13A ALA* 3.1 21.8 + - - +
34A LEU* 3.8 6.0 - - + +
38A PRO* 3.6 47.1 + - + +
39A SER* 5.5 0.6 - - - -
41A SER* 3.8 10.8 - - - +
18W MET* 3.6 23.2 - - + +
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Residues in contact with ASN 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 LYS 3.4 5.5 + - - +
7A GLU 3.5 5.7 + - - +
8A MET 3.2 0.4 - - - -
9A HIS* 1.3 76.2 - - - +
11A ALA* 1.3 61.3 + - - +
13A ALA* 3.3 1.9 + - - +
14A ILE* 3.0 45.4 + - - +
79V GLN* 3.0 24.7 + - - +
16W LYS* 3.4 32.7 - - + +
17W PHE* 3.1 8.8 + - - +
18W MET* 3.0 43.8 + - + +
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Residues in contact with ALA 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 GLU 3.0 15.4 + - - +
8A MET* 3.1 19.7 + - + +
10A ASN* 1.3 77.3 - - - +
12A TYR* 1.3 61.7 + - + +
14A ILE* 3.5 10.2 + - - +
15A GLU* 3.1 30.7 + - - +
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Residues in contact with TYR 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 MET* 3.1 54.5 + - + -
9A HIS* 3.6 7.6 - + - +
11A ALA* 1.3 75.2 - - + +
13A ALA* 1.3 64.8 + - - +
15A GLU* 3.3 11.0 + - - +
16A ILE* 3.1 26.9 + - - +
34A LEU* 4.0 7.9 - - + -
41A SER* 3.6 36.3 - - - +
42A ALA* 3.5 33.2 - - + +
45A LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 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 HIS 3.1 14.2 + - - +
10A ASN 3.3 8.3 + - - +
12A TYR* 1.3 76.1 - - - +
14A ILE* 1.3 62.3 + - - +
16A ILE* 3.4 4.3 + - - +
17A ALA* 3.0 23.6 + - - +
31A ILE* 3.8 13.4 - - + +
34A LEU* 3.7 16.5 - - + +
17W PHE* 4.3 11.4 - - + -
18W MET* 3.8 27.6 - - + -
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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 ASN* 3.0 42.5 + - - +
11A ALA* 3.8 8.3 - - - +
13A ALA* 1.3 75.2 - - - +
15A GLU* 1.3 58.8 + - + +
17A ALA* 3.3 4.4 + - - +
18A LEU* 3.0 41.8 + - + +
79V GLN* 3.7 19.3 - - - +
91V ILE* 3.5 31.4 - - + +
17W PHE* 4.0 24.2 - - + -
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Residues in contact with GLU 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 ALA* 3.1 20.7 + - - +
12A TYR* 3.3 13.7 + - - +
14A ILE* 1.3 77.9 - - + +
16A ILE* 1.3 62.4 + - - +
18A LEU* 3.1 20.7 + - + +
19A LEU* 3.5 14.7 + - - +
45A LEU* 3.4 34.9 - - + +
49A LYS* 4.2 12.5 + - - -
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Residues in contact with ILE 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 TYR 3.1 16.1 + - - +
13A ALA 3.7 3.6 - - - +
15A GLU* 1.3 75.5 - - - +
17A ALA* 1.3 63.7 + - - +
18A LEU 3.3 0.9 + - - -
19A LEU* 3.4 25.3 + - + +
22A LEU* 4.2 7.8 - - + +
27A PHE* 4.8 3.2 - - - +
30A PHE* 3.6 35.4 - - + +
31A ILE* 4.0 13.0 - - + -
34A LEU* 3.9 24.9 - - + -
41A SER 4.7 0.4 - - - +
44A LEU* 3.8 31.9 - - + +
45A LEU* 3.7 22.4 - - + +
48A ALA* 4.4 8.1 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.5 + - - +
14A ILE* 3.6 5.6 - - - +
15A GLU 3.2 0.4 - - - -
16A ILE* 1.3 76.6 - - - +
18A LEU* 1.3 50.6 + - - +
19A LEU 3.4 2.5 + - - +
27A PHE* 3.4 37.6 - - + -
31A ILE* 3.9 3.1 - - + -
81V MET* 3.4 14.7 - - + +
89V GLN* 2.7 28.1 + - - -
91V ILE* 6.0 0.4 - - + -
17W PHE* 3.7 18.8 - - + -
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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 ILE* 3.0 32.7 + - + +
15A GLU* 3.1 13.6 + - + +
17A ALA* 1.3 75.9 - - - +
19A LEU* 1.3 64.2 + - - +
20A PRO* 3.1 8.8 - - - +
81V MET* 3.6 23.1 - - + -
89V GLN* 3.3 40.8 + - + +
90V HIS* 3.8 6.5 - - + -
91V ILE* 4.3 3.6 - - + +
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Residues in contact with LEU 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 GLU 3.7 6.7 - - - +
16A ILE* 3.4 25.8 - - - +
17A ALA 3.4 3.2 - - - +
18A LEU* 1.3 76.3 - - - +
20A PRO* 1.3 69.0 - - + +
21A ASN 3.7 0.2 + - - -
22A LEU* 4.0 17.8 + - + +
27A PHE* 5.5 2.4 - - - -
45A LEU* 4.7 6.7 - - + -
48A ALA* 3.6 38.4 - - + +
49A LYS* 4.2 22.0 - - + +
52A ASN* 3.3 32.0 - - + +
89V GLN* 3.7 6.8 + - - -
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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