Contacts of the helix formed by residues 9 - 19 (chain L) in PDB entry 2WS7
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 9 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D HIS* 3.3 26.5 + - - -
13J GLU* 4.8 16.7 + - - +
16J TYR* 3.3 27.7 - - - -
5L HIS 4.3 0.4 - - - -
6L LEU* 3.0 16.8 + - - -
8L GLY* 1.3 73.4 - - - +
10L HIS* 1.3 61.9 + - - +
12L VAL* 3.1 20.5 + - - +
13L GLU* 3.4 12.7 + - - +
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Residues in contact with HIS 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D HIS* 3.3 6.2 + + - -
1024D ZN 2.0 37.7 - - - -
1025D CL 3.3 1.9 - - + +
5H HIS* 5.5 2.4 + - + +
6H LEU* 3.4 22.8 - - + +
9H SER* 3.0 34.9 + - - -
10H HIS* 3.6 8.1 - + - -
1021K IPH 3.8 19.0 - - + -
6L LEU 3.4 12.6 - - - -
7L CYS 2.8 12.1 + - - +
9L SER* 1.3 73.7 - - - +
11L LEU* 1.3 54.5 + - - +
13L GLU* 3.3 8.3 + - - +
14L ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K ILE* 3.7 39.7 - - + +
3K VAL* 3.9 21.3 - - + +
6K CYS* 4.1 15.9 - - + -
7K CYS* 4.8 2.7 - - - -
16K LEU* 3.4 35.7 - - + -
1021K IPH 3.9 15.4 - - + -
7L CYS 2.9 6.7 + - - +
8L GLY* 3.0 18.4 + - - +
10L HIS* 1.3 77.2 - - - +
12L VAL* 1.3 57.2 + - + +
14L ALA* 3.5 1.3 + - - +
15L LEU* 2.9 31.4 + - + +
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Residues in contact with VAL 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL* 3.9 26.8 - - + +
13J GLU* 4.8 3.4 - - - -
16J TYR* 3.9 34.3 - - + -
8L GLY 3.0 12.8 + - - +
9L SER* 3.1 21.1 - - - +
11L LEU* 1.3 73.6 - - + +
13L GLU* 1.3 60.6 + - + +
15L LEU* 3.7 11.6 - - + +
16L TYR* 2.8 31.9 + - - +
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Residues in contact with GLU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J SER* 2.6 48.1 + - - +
12J VAL* 3.5 10.5 - - + +
13J GLU* 3.5 23.6 - - + +
9L SER* 3.4 14.0 + - - +
10L HIS* 3.3 10.4 + - - +
12L VAL* 1.3 76.9 - - + +
14L ALA* 1.3 64.0 + - - +
16L TYR* 3.4 7.7 + - - +
17L LEU* 3.3 34.5 + - + +
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Residues in contact with ALA 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 3.9 24.2 - - + -
16K LEU* 3.7 14.6 - - + -
1021K IPH 3.6 25.6 - - + -
10L HIS 2.9 17.1 + - - +
11L LEU 3.7 4.3 - - - +
13L GLU* 1.3 77.2 - - - +
15L LEU* 1.3 56.0 + - - +
17L LEU* 3.6 1.6 + - - +
18L VAL* 3.1 34.7 + - - +
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Residues in contact with LEU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ILE* 3.7 26.0 - - + -
16K LEU* 3.2 44.6 - - + +
19K TYR* 3.8 16.8 - - + +
11L LEU* 2.9 27.1 + - + +
12L VAL* 3.2 12.5 + - + +
14L ALA* 1.3 74.6 - - - +
16L TYR* 1.3 59.8 + - - +
18L VAL* 4.6 1.3 - - + +
19L CYS* 2.9 51.0 + - - +
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Residues in contact with TYR 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J GLN 3.8 0.9 + - - -
5J HIS* 2.7 69.7 + + - -
8J GLY* 3.5 16.1 - - - -
9J SER* 3.7 23.1 - - - -
12J VAL* 3.7 25.8 - - + -
12L VAL 2.8 20.4 + - - +
13L GLU* 3.7 8.3 - - - +
15L LEU* 1.3 73.2 - - - +
17L LEU* 1.3 61.2 + - + +
19L CYS* 5.0 0.2 - - - -
20L GLY* 2.8 52.3 + - - +
21L GLU* 4.6 13.5 - - + +
22L ARG 6.0 0.4 - - - -
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Residues in contact with LEU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 3.4 42.8 - - + +
1021E IPH 5.6 4.5 - - + -
10F HIS 5.8 0.4 - - - +
13F GLU* 5.3 1.3 - - + +
14F ALA* 4.3 26.2 - - + +
17F LEU* 3.4 31.9 - - + -
5J HIS* 4.6 20.9 - - + +
13L GLU* 3.3 23.3 + - + +
14L ALA 3.8 0.4 - - - +
16L TYR* 1.3 81.2 - - + +
18L VAL* 1.3 67.2 + - + +
20L GLY* 4.3 3.7 + - - +
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Residues in contact with VAL 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 3.7 20.6 - - + +
13K LEU* 3.8 49.6 - - + +
16K LEU* 4.6 7.0 - - + -
17K GLU* 4.2 33.0 - - + +
20K CYS* 4.1 4.9 - - - -
14L ALA 3.1 20.6 + - - +
15L LEU* 4.4 3.4 - - - +
17L LEU* 1.3 81.7 - - + +
19L CYS* 1.3 62.0 + - - +
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Residues in contact with CYS 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR 4.3 1.1 - - - -
20K CYS* 2.0 58.2 - - + +
15L LEU* 2.9 43.4 + - - +
16L TYR* 4.4 0.4 - - - +
18L VAL* 1.3 81.0 - - - +
20L GLY* 1.3 59.1 + - - +
21L GLU 4.3 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