Contacts of the helix formed by residues 10 - 20 (chain K) in PDB entry 2WSC
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 ILE 10 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A PHE* 4.9 11.8 - - + -
270A PHE 4.6 5.2 - - - +
271A THR* 3.7 24.9 - - + +
6K SER 2.8 25.4 - - - +
7K THR* 2.9 23.5 + - + +
9K LEU* 1.3 81.1 - - + +
11K MET* 1.3 62.8 + - - +
12K VAL 3.1 1.1 - - - -
13K THR* 2.6 45.1 + - + +
14K THR* 3.6 8.0 + - - +
63K CYS* 3.5 28.3 - - - -
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Residues in contact with MET 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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269A PHE* 5.2 8.3 - - + -
7K THR 3.4 6.0 + - - +
8K ASN* 3.4 17.9 - - - +
10K ILE* 1.3 76.3 - - - +
12K VAL* 1.3 59.1 + - + +
14K THR* 3.4 6.8 - - - +
15K THR* 2.4 80.7 + - + -
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Residues in contact with VAL 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ASN 5.2 0.7 - - - +
9K LEU* 3.1 24.9 - - + +
11K MET* 1.3 87.9 - - + +
13K THR* 1.3 59.4 + - + +
15K THR* 3.9 0.7 - - - -
16K THR* 3.0 57.2 + - + +
17K LEU* 3.2 3.6 + - - +
59K ASP* 6.1 0.9 - - - +
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Residues in contact with THR 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU 4.3 3.1 - - - +
10K ILE* 2.6 58.4 + - + +
12K VAL* 1.3 76.1 - - + +
14K THR* 1.3 58.1 + - - +
17K LEU* 3.1 27.0 - - - +
59K ASP* 4.7 16.6 - - - +
60K THR* 4.7 6.9 + - - +
63K CYS* 3.9 21.3 - - + -
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Residues in contact with THR 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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269A PHE* 2.6 48.0 - - + -
1797A CLA 5.4 10.4 - - - -
10K ILE 3.8 6.5 - - - +
11K MET 3.4 9.4 - - - +
13K THR* 1.3 79.3 + - - +
15K THR* 1.3 63.9 + - + +
16K THR 3.3 1.8 - - - -
17K LEU* 3.0 7.8 + - - +
18K MET* 2.6 54.2 + - - +
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Residues in contact with THR 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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269A PHE* 4.8 8.3 - - + -
11K MET* 2.4 66.9 + - + +
12K VAL* 3.8 1.2 + - - -
14K THR* 1.3 79.5 - - + +
16K THR* 1.3 54.4 + - - +
18K MET* 3.3 7.3 + - - +
19K LEU* 2.7 41.4 + - - +
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Residues in contact with THR 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 VAL* 3.0 43.1 + - + +
15K THR* 1.3 76.1 + - - +
17K LEU* 1.3 63.6 + - - +
18K MET 3.2 1.1 - - - -
19K LEU* 4.4 1.8 - - - +
20K PHE* 2.9 52.6 + - + +
56K THR* 4.7 0.2 - - - -
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Residues in contact with LEU 17 (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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1797A CLA 6.2 3.6 - - - -
12K VAL 3.2 5.9 + - - -
13K THR* 3.1 25.6 - - - +
14K THR* 3.0 12.5 + - - +
16K THR* 1.3 76.7 - - - +
18K MET* 1.3 80.3 + - + +
21K ALA* 3.0 27.5 - - - +
56K THR* 3.2 37.7 - - + +
57K LEU* 4.9 14.8 - - + -
59K ASP* 6.0 2.0 - - + +
60K THR* 3.4 26.7 - - - +
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Residues in contact with MET 18 (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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1772A CLA 3.2 38.1 - - + -
1797A CLA 6.1 2.9 - - - +
14K THR* 2.6 44.2 + - - +
15K THR* 3.5 6.7 - - + +
16K THR 3.2 0.2 - - - -
17K LEU* 1.3 89.4 - - + +
19K LEU* 1.3 60.2 + - + +
21K ALA* 3.2 8.9 + - - +
22K GLY* 3.0 20.6 + - - -
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Residues in contact with LEU 19 (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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15K THR* 2.7 23.2 + - - +
16K THR* 5.0 1.1 - - - -
18K MET* 1.3 69.4 - - + +
20K PHE* 1.3 58.3 + - - +
22K GLY* 3.0 23.3 + - - +
23K ARG* 4.0 4.4 + - - +
3009K CLA 4.8 34.3 - - + -
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Residues in contact with PHE 20 (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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16K THR* 2.9 38.1 + - + +
19K LEU* 1.3 75.0 - - - +
21K ALA* 1.3 59.8 + - - +
22K GLY 2.9 6.9 + - - -
23K ARG* 4.7 3.3 + - - +
24K PHE* 5.4 1.0 + - - +
51K ASP* 4.6 19.5 - - - -
52K PRO* 4.5 12.9 - - + +
55K PHE* 5.0 8.1 - + + -
56K THR* 3.8 33.9 - - + -
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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