Contacts of the helix formed by residues 4 - 16 (chain K) in PDB entry 6C0W
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 THR 4 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ARG* 4.1 23.8 - - - +
81A GLY* 5.2 4.7 - - - +
2K ASP* 3.4 12.3 + - + +
3K GLU* 1.3 84.9 - - - +
5K VAL* 1.3 77.8 + - - +
6K ALA 3.2 2.7 + - - -
7K GLU* 3.4 14.4 + - - +
8K PHE* 3.5 9.5 + - - +
143K LYS* 5.9 9.2 - - + -
147K TYR* 5.1 1.0 + - - -
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Residues in contact with VAL 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 4.5 17.3 - - + -
2K ASP* 4.2 19.1 - - + +
4K THR* 1.3 87.3 + - - +
6K ALA* 1.3 63.3 + - - +
8K PHE* 3.2 8.9 + - - +
9K ILE* 3.0 38.3 + - + +
61K ALA* 4.8 5.8 - - + -
62K SER* 3.5 31.2 - - - +
63K ILE* 3.8 27.1 - - + +
66K ALA* 5.1 2.5 - - + -
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Residues in contact with ALA 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 4.4 12.6 - - + -
2K ASP 5.1 1.3 + - - +
3K GLU* 5.3 14.4 - - + +
4K THR 3.2 1.6 - - - +
5K VAL* 1.3 81.0 - - - +
7K GLU* 1.3 56.8 + - - +
9K ILE* 3.4 3.2 + - - -
10K LYS* 2.9 31.3 + - - +
53K ILE* 3.8 22.0 - - + +
57K GLU* 4.2 18.6 - - - +
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Residues in contact with GLU 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR 4.4 1.8 - - - +
80A ARG* 2.8 52.7 + - + +
82A VAL* 3.8 25.4 - - + -
74B GLU* 4.9 4.4 - - - +
3K GLU 5.6 0.6 + - - +
4K THR* 3.4 10.6 + - - +
5K VAL 3.3 0.4 - - - -
6K ALA* 1.3 78.1 - - - +
8K PHE* 1.3 57.5 + - - +
10K LYS* 3.2 29.4 + - - +
11K ARG* 2.8 59.9 + - - +
147K TYR* 4.1 1.6 - - - +
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Residues in contact with PHE 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K THR 3.5 6.6 + - - +
5K VAL* 3.2 14.2 + - - +
7K GLU* 1.3 78.8 - - - +
9K ILE* 1.3 55.4 + - - +
11K ARG* 3.4 2.6 + - - +
12K THR* 2.7 51.1 + - - -
63K ILE* 5.3 6.1 - - + -
66K ALA* 3.4 46.2 - - + -
67K ALA* 4.4 1.3 - - - -
69K LEU* 6.4 0.7 - - + -
70K ASP* 3.8 30.1 - - + -
134K ARG* 4.0 11.9 - - - -
146K GLN* 4.2 29.4 - - + -
147K TYR* 3.7 36.5 + + + +
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Residues in contact with ILE 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K VAL* 3.0 25.7 + - + +
6K ALA* 5.0 1.1 - - - -
8K PHE* 1.3 74.7 - - + +
10K LYS* 1.3 58.2 + - - +
12K THR* 3.4 5.0 + - - -
13K ILE* 3.0 49.6 + - + +
28K TRP* 5.1 14.1 - - + -
53K ILE* 3.8 21.1 - - + -
56K CYS* 5.6 11.4 - - + -
61K ALA* 5.2 10.3 - - + -
62K SER 5.1 3.1 - - - +
66K ALA* 3.7 32.3 - - + +
69K LEU* 4.1 14.8 - - + -
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Residues in contact with LYS 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 4.2 8.3 - - - +
74B GLU* 5.1 4.8 + - - -
6K ALA 2.9 18.2 + - - +
7K GLU* 3.2 37.0 + - - +
9K ILE* 1.3 78.3 - - - +
11K ARG* 1.3 56.7 + - - +
13K ILE* 3.8 4.3 - - - +
14K LEU* 2.9 45.2 + - + +
49K VAL* 4.1 26.5 - - + +
50K GLN* 5.5 8.1 - - + -
53K ILE* 4.2 18.7 - - + +
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Residues in contact with ARG 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 5.8 1.0 + - - -
82A VAL* 4.1 26.7 - - - +
84A PHE* 5.8 4.6 - - - -
74B GLU* 5.7 7.3 + - - +
79B LYS* 3.3 43.1 - - - +
7K GLU* 2.8 47.0 + - - +
8K PHE* 3.8 5.6 - - - +
10K LYS* 1.3 77.7 - - - +
12K THR* 1.3 57.7 + - - +
14K LEU* 3.4 18.1 + - - +
15K LYS* 3.0 38.9 + - + +
147K TYR* 4.6 16.4 - - + -
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Residues in contact with THR 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K PHE* 2.7 43.4 + - + -
9K ILE* 3.8 6.1 - - - -
11K ARG* 1.3 77.7 - - - +
13K ILE* 1.3 62.2 + - - +
15K LYS* 3.2 20.3 + - + +
16K ILE* 3.3 18.3 + - + +
69K LEU* 4.3 22.9 - - + -
70K ASP* 4.6 12.7 + - - +
73K TYR* 4.3 28.0 - - + -
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Residues in contact with ILE 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ILE* 3.0 35.7 + - + +
10K LYS* 4.2 1.3 - - - +
12K THR* 1.3 75.1 - - - +
14K LEU* 1.3 65.2 + - - +
16K ILE* 3.0 32.8 + - + +
21K LEU* 3.8 26.0 - - + +
25K LEU* 4.8 13.9 - - + -
28K TRP* 5.8 2.2 - - + -
45K LYS* 4.3 2.3 + - - -
49K VAL* 3.7 25.6 - - + +
52K LEU* 4.6 24.0 - - + -
53K ILE* 5.6 3.1 - - + -
69K LEU* 4.2 16.8 - - + -
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Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K LYS* 2.9 36.7 + - + +
11K ARG* 3.6 19.3 - - - +
13K ILE* 1.3 77.4 - - - +
15K LYS* 1.3 59.5 + - + +
16K ILE 3.4 5.2 + - - +
45K LYS* 4.0 40.7 - - + +
46K GLU* 5.0 9.0 - - + -
49K VAL* 4.1 13.4 - - + +
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Residues in contact with LYS 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 5.5 6.7 - - - +
11K ARG* 3.0 29.6 + - + +
12K THR* 3.2 13.9 + - - +
14K LEU* 1.3 77.4 - - + +
16K ILE* 1.3 61.6 + - - +
17K PRO* 3.5 8.1 - - - +
73K TYR* 3.3 46.0 + - + +
74K MET* 5.9 3.4 - - - +
77K HIS* 5.5 0.3 - - - -
80K GLN* 5.0 7.6 + - - +
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Residues in contact with ILE 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K THR* 3.3 21.1 - - + +
13K ILE* 3.0 31.3 + - + +
14K LEU 3.8 0.6 - - - +
15K LYS* 1.3 76.2 - - - +
17K PRO* 1.3 81.2 - - + +
20K GLU* 4.7 2.5 - - + -
21K LEU* 3.9 24.0 - - + +
24K ILE* 3.8 36.3 - - + -
25K LEU* 6.0 1.1 - - + -
45K LYS* 2.8 28.1 + - - -
69K LEU* 5.1 3.1 - - + -
73K TYR* 3.6 22.2 - - + -
77K HIS* 5.9 0.7 - - - +
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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