Contacts of the helix formed by residues 105 - 114 (chain D) 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 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D HIS* 3.4 14.0 - - - +
103D ALA* 3.2 2.0 - - - +
104D THR* 1.3 81.9 + - - +
106D HIS* 1.3 64.6 + - - +
107D ARG* 3.7 8.0 + - - +
108D ALA* 3.1 24.9 + - - +
109D ALA* 3.1 22.2 + - - +
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Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D HIS* 3.4 27.6 + - + +
35D LEU 4.7 9.8 + - - -
36D ALA* 6.4 0.9 - - + +
105D SER* 1.3 71.0 - - - +
107D ARG* 1.3 67.3 + - - +
109D ALA* 3.0 7.3 + - - +
110D ARG* 2.9 41.6 + - + +
255D MET* 5.8 0.2 - - - -
256D ARG* 3.0 73.7 + - + +
258D ASP* 3.5 26.7 - - - -
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR* 6.0 3.2 - - - +
25C GLU* 5.2 13.2 + - - +
212C VAL* 3.2 38.7 + - - +
213C THR* 4.7 3.2 - - - +
216C LEU* 3.2 29.7 - - - +
217C ARG 4.6 11.3 + - - -
105D SER* 3.3 8.4 + - - +
106D HIS* 1.3 82.4 + - - +
108D ALA* 1.3 63.2 + - - +
110D ARG* 3.2 5.7 + - - +
111D ILE* 2.9 47.1 + - + +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D SER* 4.9 0.5 + - - -
59D PRO 3.7 19.3 - - - +
60D GLY* 4.5 5.4 - - - -
103D ALA* 3.7 15.9 - - + -
104D THR* 4.8 1.1 - - - +
105D SER* 3.1 24.5 + - - +
107D ARG* 1.3 76.1 - - - +
109D ALA* 1.3 52.6 + - - +
111D ILE* 3.2 8.7 + - - +
112D ALA* 2.7 38.8 + - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D HIS 3.6 24.5 - - - +
35D LEU 4.0 2.2 - - - -
36D ALA* 3.7 24.0 - - + +
101D VAL* 4.1 12.8 - - + +
103D ALA* 3.6 9.5 - - + +
105D SER 3.1 8.0 + - - +
106D HIS* 3.0 10.4 + - + +
108D ALA* 1.3 73.6 - - - +
110D ARG* 1.3 59.0 + - - +
112D ALA* 3.3 1.9 + - - +
113D ALA* 2.8 30.8 + - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C THR 5.2 5.5 + - - -
214C LYS* 4.5 5.5 + - - +
216C LEU* 3.8 20.5 - - + +
36D ALA* 4.2 13.2 - - + -
106D HIS* 2.9 35.3 + - + +
107D ARG* 3.5 9.4 - - - +
109D ALA* 1.3 72.9 - - - +
111D ILE* 1.3 66.9 + - - +
113D ALA* 3.1 16.7 + - - +
114D ARG* 3.5 44.7 + - - +
258D ASP* 3.0 44.2 + - - +
260D ASP* 3.1 16.2 + - - +
261D ASP* 3.5 30.0 + - - -
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU* 3.6 33.4 - - + +
58D SER* 4.2 4.9 - - - +
59D PRO* 6.0 1.1 - - + -
107D ARG* 2.9 53.2 + - + +
108D ALA* 3.7 5.4 - - - +
110D ARG* 1.3 74.4 - - - +
112D ALA* 1.3 63.5 + - - +
114D ARG* 3.3 18.4 + - - +
115D LYS* 3.7 31.2 - - - +
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 3.5 21.3 - - + +
58D SER* 3.7 17.7 - - - -
61D VAL* 3.6 30.1 - - + -
101D VAL* 3.8 10.5 - - + -
108D ALA 2.7 21.8 + - - +
109D ALA 3.7 4.0 - - - +
111D ILE* 1.3 75.3 - - - +
113D ALA* 1.3 60.9 - - - +
114D ARG 3.1 1.0 + - - -
115D LYS* 3.2 13.8 + - - +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA* 4.2 4.9 - - + -
37D PHE 3.4 30.5 - - - +
38D GLY* 4.2 4.7 - - - -
99D PHE* 3.3 21.2 - - - -
101D VAL* 3.9 13.9 - - + +
109D ALA 2.8 17.7 + - - +
110D ARG* 3.1 8.9 + - - +
112D ALA* 1.3 77.9 - - - +
114D ARG* 1.3 58.8 + - + +
115D LYS 3.2 4.6 + - - -
116D ALA* 4.2 1.2 + - - +
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LYS* 3.3 20.4 + - - +
215C ALA* 4.2 4.6 + - - -
216C LEU* 2.7 48.1 - - - +
110D ARG* 3.5 38.3 + - - +
111D ILE* 3.6 9.6 - - - +
112D ALA 3.1 1.4 - - - -
113D ALA* 1.3 78.1 - - + +
115D LYS* 1.3 61.3 + - + +
116D ALA 3.7 3.0 + - - +
260D ASP* 5.3 2.2 + - - -
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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