Contacts of the helix formed by residues 9 - 19 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 2.3 42.1 + - - +
16F TYR* 3.4 18.8 - - - -
5H HIS* 2.9 16.5 + - - -
6H LEU* 3.3 11.7 - - - -
8H GLY* 1.3 74.2 - - - +
10H HIS* 1.3 61.8 + - - +
12H VAL* 3.2 6.5 - - - +
13H GLU* 3.6 1.4 + - - +
10L HIS* 3.0 33.2 + - - -
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Residues in contact with HIS 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 5.7 1.1 - - + +
5D HIS* 6.0 0.2 - - + -
6D LEU* 3.9 16.1 - - + +
9D SER* 3.0 30.4 + - - -
10D HIS* 3.6 8.1 - + - -
1024D ZN 2.0 34.4 - - - -
1025D CL 3.1 6.9 - - + +
1022G IPH 4.0 19.5 - - + -
6H LEU 3.0 24.0 + - - -
7H CYS 3.0 8.6 + - - +
9H SER* 1.3 76.4 - - - +
11H LEU* 1.3 65.8 + - - +
13H GLU* 3.2 28.0 + - - +
14H ALA* 3.0 22.5 + - - +
10L HIS* 3.3 7.5 + + - -
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Residues in contact with LEU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G ILE* 3.9 33.0 - - + +
3G VAL* 4.3 10.1 - - + +
6G CYS* 3.7 16.6 - - + -
7G CYS* 3.8 26.9 - - - -
16G LEU* 3.7 29.2 - - + -
1022G IPH 4.1 14.3 - - + -
7H CYS* 2.9 13.3 + - - +
8H GLY* 3.0 14.1 + - - +
10H HIS* 1.3 76.5 - - - +
12H VAL* 1.3 54.1 + - + +
14H ALA* 3.2 5.8 + - - +
15H LEU* 2.7 39.5 + - + +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.0 16.3 - - + +
13F GLU* 2.9 41.5 - - - +
16F TYR* 3.8 25.1 - - + -
8H GLY 3.0 12.9 + - - +
9H SER 3.2 4.3 - - - +
11H LEU* 1.3 73.7 - - + +
13H GLU* 1.3 59.1 + - - +
15H LEU* 3.4 2.6 + - + -
16H TYR* 2.8 29.3 + - - +
24H PHE* 3.6 31.7 - - + -
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.6 30.0 - - + +
17B LEU* 4.6 15.1 - - + +
9D SER* 4.6 4.0 + - - -
9F SER* 5.5 9.2 - - - +
12F VAL* 5.1 3.6 - - - -
13F GLU* 3.9 16.2 - - + +
9H SER 3.6 1.1 + - - +
10H HIS* 3.2 38.4 + - - +
11H LEU 3.4 0.6 - - - -
12H VAL* 1.3 79.2 - - - +
14H ALA* 1.3 63.5 + - - +
16H TYR* 3.3 10.6 + - - +
17H LEU* 3.2 29.1 + - + +
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Residues in contact with ALA 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.9 21.5 - - + -
16G LEU* 4.3 14.8 - - + -
1022G IPH 3.9 23.6 - - + -
10H HIS 3.0 13.9 + - - +
11H LEU* 3.4 8.7 - - - +
13H GLU* 1.3 75.4 - - - +
15H LEU* 1.3 65.0 + - - +
17H LEU* 3.4 4.3 + - - +
18H VAL* 3.1 27.0 + - - +
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G ILE* 3.7 29.8 - - + -
16G LEU* 3.3 42.4 - - + +
19G TYR* 4.5 9.2 - - + +
11H LEU* 2.7 25.4 + - + +
12H VAL* 3.7 3.8 - - + +
14H ALA* 1.3 69.8 - - - +
16H TYR* 1.3 67.7 + - - +
18H VAL* 4.5 1.6 - - + +
19H CYS* 2.8 38.0 + - - +
24H PHE* 3.6 42.2 - - + -
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Residues in contact with TYR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL* 6.0 3.0 - - + +
4F GLN 3.8 0.5 + - - -
5F HIS* 2.7 69.0 + + - -
8F GLY* 3.6 16.7 - - - -
9F SER* 3.5 28.3 - - - -
12F VAL* 4.1 22.4 - - + -
12H VAL 2.8 21.4 + - - +
13H GLU* 3.3 9.1 + - - +
15H LEU* 1.3 74.8 - - - +
17H LEU* 1.3 66.6 + - + +
19H CYS* 4.3 0.9 - - - +
20H GLY* 3.7 19.4 + - - +
24H PHE* 3.9 15.2 - + + -
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A CYS 5.9 0.4 - - - +
13A LEU* 4.1 22.9 - - + +
16A LEU* 4.1 16.6 - - + -
1022A IPH 4.4 10.5 - - + -
10B HIS 5.6 0.7 - - - +
13B GLU* 6.0 0.9 - - + -
14B ALA* 3.6 37.7 - - + +
17B LEU* 3.7 29.4 - - + -
18B VAL* 5.3 1.8 - - + -
5F HIS* 5.2 12.2 + - + -
13H GLU* 3.2 16.4 + - + +
14H ALA 3.7 6.7 - - - +
16H TYR* 1.3 85.2 - - + +
18H VAL* 1.3 65.0 + - + +
19H CYS 3.4 0.5 + - - -
20H GLY* 3.6 7.8 + - - -
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Residues in contact with VAL 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 28.1 - - + +
13G LEU* 3.7 39.7 - - + +
16G LEU* 4.4 9.4 - - + -
17G GLU* 3.8 36.3 - - + +
20G CYS* 4.0 5.6 - - - -
14H ALA 3.1 16.6 + - - +
15H LEU* 4.3 1.8 - - + +
17H LEU* 1.3 81.1 - - + +
19H CYS* 1.3 60.5 + - - +
20H GLY 3.4 0.9 + - - -
22H ARG* 3.4 11.4 + - - -
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Residues in contact with CYS 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G CYS* 2.0 53.2 - - + -
15H LEU* 2.8 35.1 + - - +
16H TYR 4.5 1.1 - - - +
18H VAL* 1.3 79.0 - - - +
20H GLY* 1.3 66.0 + - - +
22H ARG* 2.8 31.9 + - - +
23H GLY* 3.1 21.5 - - - +
24H PHE* 3.7 10.8 - - + -
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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