Contacts of the strand formed by residues 234 - 244 (chain E) in PDB entry 1PWY
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 ARG 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E ASP* 2.8 39.4 + - - +
110E THR* 3.0 28.3 + - + +
111E LEU 2.9 26.7 + - - +
167E ASP* 3.8 24.9 - - + +
169E THR* 6.0 0.2 - - - -
170E MET* 3.8 24.9 - - + -
229E ARG* 4.1 6.7 - - - +
232E GLY 3.3 2.2 + - - -
233E LEU* 1.3 69.6 - - - +
235E VAL* 1.3 60.6 + - - +
236E PHE* 5.0 0.7 - - + -
283E PRO* 3.5 46.4 + - - +
284E LEU 5.4 0.4 + - - -
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E LEU* 3.6 13.0 - - + +
113E VAL* 4.6 4.0 - - + -
165E ALA 3.7 9.2 - - - +
166E TYR* 3.0 11.9 - - + -
167E ASP* 2.6 34.4 + - - +
225E VAL* 4.0 33.0 - - + +
228E ALA* 3.4 28.5 - - + -
229E ARG* 3.7 15.7 - - - +
233E LEU* 3.0 18.5 + - + +
234E ARG* 1.3 76.8 - - - +
236E PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E THR* 3.7 15.9 - - + -
111E LEU 3.2 1.1 + - - +
112E VAL* 2.9 49.0 - - + -
113E VAL* 3.1 7.3 + - - +
131E LEU* 5.4 2.9 - - + -
132E ILE 5.6 0.4 - - - -
166E TYR* 4.6 7.9 - - - +
167E ASP 4.7 5.6 - - - +
170E MET* 3.8 50.5 - - + -
171E ARG* 5.0 7.4 - - + -
234E ARG* 5.0 0.7 - - + -
235E VAL* 1.3 78.9 - - - +
237E GLY* 1.3 60.0 + - - +
238E PHE* 3.9 30.1 - + - -
275E VAL* 5.8 1.1 - - + -
278E LEU* 4.5 13.7 - - + -
279E MET* 4.9 2.5 - - + -
282E ILE* 3.7 33.2 - - + -
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Residues in contact with GLY 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E VAL* 4.7 1.6 - - - -
113E VAL* 2.9 25.0 - - - +
131E LEU* 3.8 6.9 - - - +
132E ILE* 3.0 29.7 + - - +
166E TYR* 4.6 4.9 - - - -
236E PHE* 1.3 78.9 - - - +
238E PHE* 1.3 71.9 + - - -
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Residues in contact with PHE 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E VAL* 5.3 1.8 - - + -
113E VAL 3.1 11.3 + - - +
114E THR* 4.5 6.4 - - + +
115E ASN* 3.6 12.1 + - - -
129E ILE* 3.9 11.4 - - + -
130E MET 3.2 8.3 - - - +
131E LEU* 3.6 40.4 - - + -
132E ILE* 3.5 14.0 - - - +
174E ALA* 4.6 2.9 - - + -
187E LEU* 3.8 2.2 - - + -
236E PHE* 3.9 24.5 - + - -
237E GLY* 1.3 75.8 - - - -
239E SER* 1.3 61.2 + - - +
240E LEU 4.3 0.7 - - - -
271E LEU* 3.6 31.0 - - + -
274E PHE* 3.3 27.1 - + - -
275E VAL* 4.2 14.6 - - + -
278E LEU* 3.3 32.5 - - + -
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ASN* 2.5 26.0 + - - -
117E ALA* 3.4 17.2 - - - +
129E ILE* 4.5 0.9 - - - -
130E MET* 2.7 62.1 + - - +
132E ILE* 4.3 4.0 - - - -
192E TYR* 3.5 7.3 - - - -
216E ALA* 4.5 0.3 - - - +
238E PHE* 1.3 76.7 - - - +
240E LEU* 1.3 59.3 + - - +
241E ILE* 3.3 10.0 + - - +
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Residues in contact with LEU 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.8 16.8 - - + -
115E ASN 2.9 13.7 + - - +
116E ALA* 3.5 2.2 - - + -
117E ALA 3.3 10.5 + - - -
127E GLY 3.4 13.0 - - - +
128E ASP 3.4 16.8 - - - +
129E ILE* 3.4 17.5 - - + +
238E PHE 4.3 0.2 - - - -
239E SER* 1.3 69.8 - - - +
241E ILE* 1.3 59.4 + - - +
242E THR* 2.8 22.4 + - + +
262E ALA* 4.5 0.4 - - + -
263E ALA* 3.7 37.0 - - + +
267E ALA* 4.0 17.5 - - + +
268E ALA 3.8 13.2 - - - +
271E LEU* 4.0 15.7 - - + +
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Residues in contact with ILE 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ALA* 3.4 6.3 - - + +
118E GLY 4.5 6.7 - - - +
119E GLY* 4.4 7.0 - - - -
124E PHE* 3.3 39.0 - - + -
125E GLU 3.9 9.2 - - - +
126E VAL* 3.7 21.8 - - - +
127E GLY* 2.7 33.3 + - - -
128E ASP* 3.0 16.0 + - + +
130E MET* 4.0 13.2 - - + +
216E ALA* 4.2 14.1 - - + -
239E SER* 3.4 18.2 - - - +
240E LEU* 1.3 66.6 - - - +
242E THR* 1.3 58.2 + - - +
243E ASN 4.0 16.2 - - - +
244E LYS* 4.8 2.0 - - + +
262E ALA* 4.3 0.7 - - - +
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Residues in contact with THR 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ALA* 3.4 19.7 - - + -
117E ALA 2.9 3.3 + - - -
126E VAL* 3.6 14.2 - - - +
240E LEU* 2.8 20.9 + - + +
241E ILE* 1.3 74.3 - - - +
243E ASN* 1.3 66.8 + - - +
259E GLU* 3.8 9.7 - - - +
260E VAL* 4.6 9.2 - - + +
261E LEU* 5.3 1.0 - - - +
262E ALA* 3.6 19.5 - - + +
263E ALA* 3.9 22.4 - - + +
290E AC2 2.9 36.7 + - - -
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Residues in contact with ASN 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ALA 3.8 0.2 + - - -
118E GLY* 3.2 1.7 - - - -
119E GLY 2.8 21.5 + - - -
126E VAL* 4.2 8.1 - - + -
241E ILE* 3.4 4.8 + - - +
242E THR* 1.3 83.7 + - - +
244E LYS* 1.3 61.8 + - - +
254E LYS 4.4 1.6 - - - +
255E ALA* 3.1 32.2 + - - +
256E ASN 3.2 13.3 - - - +
259E GLU* 3.1 17.4 - - - +
290E AC2 2.7 49.2 + - - -
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Residues in contact with LYS 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLY* 3.8 18.8 + - - +
121E ASN 3.1 19.9 + - - -
122E PRO* 3.9 14.4 - - - -
124E PHE* 3.0 35.8 + - - +
125E GLU* 4.4 1.6 - - - -
126E VAL* 4.0 28.4 - - + +
241E ILE* 4.9 1.6 - - + -
243E ASN* 1.3 74.1 - - - +
245E VAL* 1.3 66.5 + - - +
246E ILE* 3.7 3.3 + - - +
253E GLU* 4.3 7.0 - - - +
254E LYS 3.9 7.6 + - - +
255E ALA* 3.3 16.6 - - - +
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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