Contacts of the helix formed by residues 11 - 17 (chain H) in PDB entry 2W3S
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 11 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H HIS* 2.9 11.3 + - - -
10H ASP* 1.3 93.0 + - - +
12H ALA* 1.3 55.5 + - - +
13H ARG 3.2 2.7 - - - -
14H ALA* 2.8 12.8 + - - -
15H HIS* 2.7 55.0 + - - -
222H ARG* 3.7 2.3 + - - -
223H ARG* 2.8 32.3 + - - -
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Residues in contact with ALA 12 (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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96G ILE* 3.9 31.8 - - + +
101G SER* 4.5 7.2 + - - +
8H PRO* 4.5 9.2 - - + -
9H HIS* 2.9 23.3 + - + +
10H ASP 3.6 0.4 - - - -
11H SER* 1.3 75.5 - - - +
13H ARG* 1.3 64.6 + - - +
15H HIS* 3.2 11.6 + - - +
16H VAL* 2.9 25.1 + - - +
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Residues in contact with ARG 13 (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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86G GLY 3.7 16.6 + - - -
87G ARG* 5.3 0.6 - - - +
88G LEU* 3.4 38.4 - - + +
96G ILE* 3.7 22.0 - - + +
11H SER 3.1 1.2 + - - -
12H ALA* 1.3 76.9 - - - +
14H ALA* 1.3 58.1 + - - +
16H VAL* 3.2 3.2 + - - +
17H THR* 2.9 47.5 + - + +
19H GLN* 5.0 11.1 + - - +
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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
----------------------------------------------------------
187F GLU* 5.6 7.2 - - + -
11H SER* 2.8 16.2 + - - +
13H ARG* 1.3 73.3 - - - +
15H HIS* 1.3 57.9 + - - +
17H THR* 3.8 6.3 - - - -
18H GLY* 2.8 29.5 + - - -
19H GLN* 2.9 18.4 + - + +
20H ALA* 3.2 28.1 + - + +
223H ARG* 4.8 3.1 - - - +
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Residues in contact with HIS 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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101G SER* 2.9 30.8 + - - +
102G GLN 2.8 29.8 - - - -
103G CYS 3.2 19.9 + - - -
104G GLY* 3.5 12.0 - - - -
107G THR* 4.0 8.6 - - + +
108G PRO* 4.5 9.0 - - - +
9H HIS* 3.6 19.5 - + - -
11H SER* 2.7 37.2 + - - -
12H ALA* 3.2 9.1 - - - +
14H ALA* 1.3 76.3 - - - +
16H VAL* 1.3 59.2 + - + +
18H GLY* 3.0 15.2 + - - -
20H ALA* 4.0 10.8 - - + -
22H TYR* 4.0 8.7 + - - -
223H ARG* 4.6 4.8 + - - -
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Residues in contact with VAL 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 3.4 14.3 - - - +
88G LEU* 4.6 1.6 - - + -
92G GLN* 3.0 53.3 + - + +
95G MET* 3.6 13.0 - - + -
96G ILE* 4.3 10.1 - - + +
101G SER* 6.0 1.3 - - - +
107G THR* 3.8 11.9 - - + -
111G ILE* 3.4 33.3 - - + +
12H ALA 2.9 14.6 + - - +
13H ARG* 3.4 14.1 - - - +
15H HIS* 1.3 76.5 - - + +
17H THR* 1.3 67.9 + - + +
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Residues in contact with THR 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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78G ILE* 3.9 19.1 - - - +
79G GLU* 4.4 6.9 - - - +
82G ALA* 5.5 3.1 - - + -
88G LEU* 3.8 29.4 - - + -
92G GLN* 3.9 10.3 - - - +
13H ARG* 2.9 34.8 + - + +
14H ALA 3.5 3.8 + - - -
16H VAL* 1.3 81.9 - - + +
18H GLY* 1.3 61.0 + - - +
19H GLN* 3.1 36.6 + - - +
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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