Contacts of the helix formed by residues 107 - 124 (chain D) in PDB entry 2WWR
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 LEU 107 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D VAL* 3.7 37.7 - - + +
103D THR 3.4 24.0 - - - +
105D ASP 4.6 6.7 - - - +
106D VAL* 1.3 81.5 - - + +
108D THR* 1.3 68.4 + - - +
109D ASP 3.6 1.1 - - - -
110D THR* 3.4 6.7 + - - -
111D THR* 3.0 32.8 + - + +
164D ILE* 6.4 0.4 - - + -
296D SER* 4.1 11.9 - - - -
301D THR* 4.0 20.0 - - + -
305D MET* 3.9 25.4 - - + -
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASP* 3.2 31.3 + - - -
106D VAL 3.6 0.8 - - - -
107D LEU* 1.3 84.2 - - - +
109D ASP* 1.3 66.3 + - - +
110D THR 3.2 0.3 + - - -
111D THR 3.3 0.2 + - - -
112D ALA* 3.0 23.6 + - - +
163D ARG* 3.4 56.2 + - - +
164D ILE* 3.7 12.7 + - - +
167D ALA* 4.0 11.9 - - + -
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Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 3.8 28.9 - - + +
176C GLY* 5.9 1.6 - - - -
105D ASP 4.6 4.2 - - - +
106D VAL 6.0 0.2 - - - -
107D LEU 3.6 0.2 - - - -
108D THR* 1.3 82.2 - - - +
110D THR* 1.3 58.3 + - - +
112D ALA* 4.7 1.6 - - - -
113D GLU* 3.0 30.2 + - - +
163D ARG* 4.6 6.0 + - - -
167D ALA* 5.1 1.7 - - - +
171D ARG* 3.4 33.8 + - - +
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG* 2.9 35.9 + - - +
150C GLY* 6.1 0.2 - - - -
152C THR* 5.2 3.4 + - - -
106D VAL 4.9 0.9 + - - -
107D LEU* 3.4 10.1 + - - -
108D THR 3.1 0.6 - - - -
109D ASP* 1.3 78.0 - - - +
111D THR* 1.3 59.8 + - - +
113D GLU* 3.3 8.4 + - - +
114D LEU 2.8 23.2 + - - -
295D GLY 3.2 11.2 - - - +
296D SER* 3.8 11.2 - - - -
298D THR* 3.7 22.6 + - + +
301D THR* 2.6 23.8 + - - +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 3.0 28.5 + - - +
110D THR* 1.3 72.6 - - - +
112D ALA* 1.3 55.7 + - - +
114D LEU* 3.0 3.5 + - + +
115D ALA* 2.7 34.0 + - - +
164D ILE* 3.7 21.1 - - + -
243D ILE* 3.9 21.5 - - + +
269D ASP* 5.8 0.4 - - - +
295D GLY* 3.2 29.0 + - - -
296D SER* 4.2 4.9 + - - -
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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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108D THR 3.0 12.9 + - - +
109D ASP 4.2 2.7 - - - +
111D THR* 1.3 76.0 - - - +
113D GLU* 1.3 61.8 + - - +
115D ALA* 3.6 2.9 - - - +
116D VAL* 3.2 30.3 + - - +
164D ILE* 3.4 17.5 - - + +
167D ALA* 3.4 37.9 - - + +
168D ILE* 3.7 12.5 - - + +
171D ARG* 4.2 3.8 - - - +
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Residues in contact with GLU 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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120C LEU* 4.1 14.8 - - + +
123C CYS* 4.5 1.6 - - - -
124C ARG* 3.3 38.4 + - + +
149C TYR 4.5 1.0 - - - +
150C GLY* 3.6 11.8 - - - -
151C LEU* 3.3 26.3 + - - +
152C THR* 4.4 7.8 + - - -
175C PHE* 4.0 19.5 - - + +
109D ASP 3.0 22.4 + - - +
110D THR* 3.3 7.1 - - - +
111D THR 3.2 0.2 - - - -
112D ALA* 1.3 77.4 - - - +
114D LEU* 1.3 57.7 + - - +
116D VAL* 3.4 3.6 + - - +
117D SER* 2.8 27.9 + - - -
171D ARG* 4.1 13.7 + - - +
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Residues in contact with LEU 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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124C ARG* 3.5 34.3 - - + +
126C LEU* 4.0 16.4 - - + -
110D THR 2.8 15.0 + - - +
111D THR* 3.0 6.7 + - + +
113D GLU* 1.3 73.6 - - - +
115D ALA* 1.3 57.5 + - - +
117D SER* 3.1 4.6 + - - -
118D LEU* 2.7 34.5 + - + +
243D ILE* 5.3 2.7 - - + -
269D ASP* 3.5 24.9 - - + +
291D LEU* 4.0 8.1 - - + -
294D ILE* 3.6 26.0 - - + -
295D GLY* 3.4 29.2 - - - +
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Residues in contact with ALA 115 (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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111D THR 2.7 18.6 + - - +
112D ALA 3.6 6.1 - - - +
114D LEU* 1.3 72.8 - - - +
116D VAL* 1.3 57.4 + - - +
118D LEU* 3.3 4.5 + - - +
119D LEU* 2.9 29.4 + - - +
168D ILE* 3.7 26.9 - - + -
213D VAL* 4.7 7.0 - - + -
241D ILE* 4.3 4.5 - - - +
243D ILE* 3.8 29.1 - - + +
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Residues in contact with VAL 116 (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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120C LEU* 4.4 0.2 - - + -
175C PHE* 4.0 20.0 - - + -
112D ALA 3.2 18.0 + - - +
113D GLU 3.8 3.6 - - - +
115D ALA* 1.3 73.6 - - - +
117D SER* 1.3 60.6 + - - +
119D LEU* 3.6 6.6 - - - +
120D LEU* 2.8 48.4 + - + +
168D ILE* 4.2 19.3 - - + +
171D ARG* 3.9 22.7 - - + -
172D LEU* 3.8 26.0 - - + -
175D PHE* 4.8 4.0 - - + -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 5.6 0.9 - - - +
120C LEU* 3.2 50.4 + - - +
121C THR* 5.4 0.7 - - - -
124C ARG* 5.0 3.1 - - - -
126C LEU* 3.5 17.7 - - - +
113D GLU 2.8 18.0 + - - -
114D LEU* 3.1 11.0 + - - -
116D VAL* 1.3 78.0 - - - +
118D LEU* 1.3 56.0 + - - +
120D LEU* 4.0 1.9 - - - +
121D THR* 3.1 30.5 + - - -
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 4.3 3.5 - - - +
114D LEU* 2.7 19.9 + - + +
115D ALA* 3.6 4.7 - - - +
117D SER* 1.3 72.0 - - - +
119D LEU* 1.3 63.7 + - - +
121D THR* 3.3 7.6 - - + +
122D THR* 2.9 34.2 + - - +
241D ILE* 4.1 12.6 - - + -
243D ILE* 4.5 4.7 - - + -
267D GLY* 3.6 32.8 - - - +
268D LEU 3.8 2.0 - - - +
269D ASP* 3.6 25.1 - - + +
289D VAL* 3.7 30.5 - - + -
291D LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 119 (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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115D ALA 2.9 17.0 + - - +
116D VAL* 3.6 7.4 - - - +
118D LEU* 1.3 76.2 - - - +
120D LEU* 1.3 66.7 + - + +
122D THR* 3.3 2.4 + - - -
123D CYS* 3.1 24.1 + - - -
151D LEU* 3.8 35.4 - - + -
172D LEU* 4.2 17.3 - - + -
211D PHE* 3.4 36.6 - - + -
213D VAL* 5.1 8.7 - - + -
239D VAL* 4.3 4.3 - - + -
241D ILE* 3.6 35.1 - - + +
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Residues in contact with LEU 120 (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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113C GLU* 4.2 11.0 - - + +
116C VAL* 4.3 2.7 - - + -
117C SER* 3.4 34.0 - - - +
120C LEU* 3.7 28.0 - - + -
116D VAL* 2.8 31.7 + - + +
117D SER* 4.0 4.0 - - - +
119D LEU* 1.3 74.5 - - + +
121D THR* 1.3 57.9 + - - +
123D CYS* 3.6 8.4 - - - -
124D ARG* 3.0 37.0 + - + +
151D LEU* 3.9 24.9 - - + -
175D PHE* 4.0 25.1 - - + -
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Residues in contact with THR 121 (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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117C SER* 5.2 0.8 + - - -
121C THR* 3.0 21.8 + - - -
126C LEU* 3.8 20.7 - - + +
130C ILE* 5.3 1.5 - - + +
117D SER 3.1 14.3 + - - -
118D LEU* 3.3 13.5 - - - +
120D LEU* 1.3 76.1 - - - +
122D THR* 1.3 68.8 + - - +
125D ARG 3.3 1.0 + - - -
126D LEU* 3.0 52.0 + - - +
127D PRO* 3.5 11.1 - - + +
289D VAL* 4.3 19.3 - - + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 2.9 18.8 + - - +
119D LEU 3.7 4.0 - - - -
120D LEU 3.2 0.2 - - - -
121D THR* 1.3 78.5 - - - +
123D CYS* 1.3 64.1 + - - +
125D ARG* 3.1 18.8 + - - +
239D VAL* 3.9 14.6 - - + -
241D ILE* 4.6 2.5 - - - -
265D ALA* 3.8 29.6 - - + +
266D ALA 3.8 17.9 - - - +
267D GLY* 3.9 8.5 - - - +
287D ASN 5.3 0.9 - - - +
289D VAL* 3.5 27.6 - - + +
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Residues in contact with CYS 123 (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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113C GLU* 5.7 0.7 - - - -
119D LEU* 3.1 25.1 + - - +
120D LEU* 3.6 15.7 - - - -
122D THR* 1.3 78.1 - - - +
124D ARG* 1.3 70.2 + - - +
125D ARG* 3.2 4.0 + - - +
148D GLY* 3.2 7.8 - - - -
149D TYR* 3.2 47.8 + - + +
150D GLY* 5.5 0.4 - - - -
151D LEU* 5.2 2.9 - - - -
211D PHE* 3.7 26.9 - - + -
239D VAL* 4.2 15.0 - - + -
265D ALA* 5.9 0.4 - - - -
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Residues in contact with ARG 124 (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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110C THR* 3.0 29.5 + - - +
113C GLU* 3.1 28.5 + - - +
114C LEU* 3.5 15.3 - - + +
117C SER* 4.0 14.6 - - - +
294C ILE* 2.8 40.3 + - - +
295C GLY 2.9 13.3 + - - -
297C ALA 3.6 16.6 + - - +
298C THR* 3.7 19.9 - - - +
120D LEU* 3.0 21.2 + - + +
121D THR 4.0 0.2 - - - -
123D CYS* 1.3 85.1 - - - +
125D ARG* 1.3 69.2 + - - +
126D LEU* 3.2 23.7 + - + +
146D LEU 5.0 3.5 - - - +
148D GLY* 4.6 4.2 - - - -
149D TYR 4.2 7.2 - - - -
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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
------------------------------------------------------------
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