Contacts of the strand formed by residues 240 - 247 (chain B) in PDB entry 2P80
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 LYS 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B THR* 3.1 37.3 + - - +
172B TYR* 4.4 0.2 - - - -
173B ASP* 2.9 53.6 + - - +
174B LYS 3.3 3.5 + - - -
238B GLY 4.3 6.1 - - - +
239B GLU* 1.3 74.1 - - - +
241B VAL* 1.3 65.3 + - - +
292B PHE* 2.7 32.8 - - + -
293B TYR 3.8 2.5 - - - -
294B THR* 3.9 10.8 - - + +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 4.6 1.8 - - - -
174B LYS* 2.9 47.8 - - + +
176B TYR* 4.2 11.7 - - + -
235B ALA* 4.2 13.7 - - + -
239B GLU* 4.0 11.2 - - + +
240B LYS* 1.3 78.2 - - - +
242B LEU* 1.3 67.2 + - - +
243B ILE* 3.8 24.4 + - + +
291B ALA 3.6 1.4 - - - +
292B PHE* 3.5 3.2 - - - -
293B TYR* 3.2 33.4 + - - +
295B PHE* 4.4 11.7 - - + -
320B PHE* 5.3 2.9 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B MET* 4.1 11.9 - - - -
162B LEU* 4.4 16.6 - - + -
172B TYR* 4.0 23.0 - - + +
174B LYS 3.1 6.9 + - - -
175B ILE* 3.2 31.9 - - + +
176B TYR 3.1 22.7 + - - -
241B VAL* 1.3 73.7 - - - +
243B ILE* 1.3 59.6 + - - +
244B VAL* 3.9 15.5 - - + -
265B TRP* 3.8 29.6 - - + -
270B PHE* 5.7 0.4 - - + -
290B ALA* 4.1 10.1 - - + -
291B ALA 3.3 15.5 - - - +
292B PHE* 3.8 11.9 - - + +
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Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B TYR* 3.4 12.6 - - + +
178B VAL* 4.4 17.9 - - + -
241B VAL* 4.0 22.0 - - + +
242B LEU* 1.3 74.3 - - - +
244B VAL* 1.3 69.6 + - - +
245B HIS* 3.7 3.6 + - - +
256B LEU* 5.6 8.7 - - + -
290B ALA* 3.7 1.1 - - - -
291B ALA* 2.9 38.2 + - + +
293B TYR* 6.2 3.4 - - + -
295B PHE* 5.6 7.4 - - + -
303B TYR* 4.6 34.8 + - + +
320B PHE* 4.3 24.2 - - + -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 4.5 10.8 - - + -
131B VAL* 3.6 33.7 - - + -
153B ALA* 5.2 0.2 - - + -
155B MET* 4.2 7.0 - - - -
175B ILE* 4.2 10.1 - - + -
176B TYR 3.0 9.6 + - - +
177B TYR* 3.4 20.4 - - + -
178B VAL 2.8 25.6 + - - -
242B LEU* 3.9 24.7 - - + -
243B ILE* 1.3 75.9 - - - +
245B HIS* 1.3 67.3 + - - +
288B ALA* 4.7 3.1 - - + -
289B GLY 3.4 14.6 - - - +
290B ALA* 4.2 3.6 - - + -
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Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B TYR* 4.4 1.1 - - - -
178B VAL* 3.2 20.4 + - + +
180B GLU* 2.9 31.5 + - + +
220B PHE* 3.5 31.2 - + - -
243B ILE* 3.7 4.2 + - + +
244B VAL* 1.3 78.3 - - - +
246B SER* 1.3 89.8 + - - +
252B THR* 4.3 15.4 - - + +
254B PRO* 4.6 3.1 - - + +
283B ILE* 3.7 17.1 - - + +
288B ALA* 3.2 3.2 - - - +
289B GLY 2.9 29.6 + - - -
303B TYR* 3.0 34.1 + + + +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 3.0 31.1 - - - +
151B ASN* 5.3 2.8 + - - +
152B GLY 3.9 0.5 + - - -
153B ALA* 3.8 4.5 - - - -
177B TYR* 2.4 32.3 + - - -
178B VAL 3.4 3.0 + - - -
179B GLY* 3.8 1.9 - - - -
180B GLU 3.0 26.7 + - - +
245B HIS* 1.3 83.6 - - - +
247B GLN* 1.3 60.0 + - - +
248B ALA 4.2 0.4 - - - -
283B ILE* 5.3 0.4 - - - -
287B ALA 3.9 0.4 - - - -
288B ALA* 3.4 13.9 - - - +
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.7 0.9 - - - -
180B GLU* 3.7 44.8 + - + +
181B GLN* 5.0 1.0 + - - -
182B ASP* 2.9 35.8 + - - +
246B SER* 1.3 72.6 - - - +
248B ALA* 1.3 63.0 + - - +
249B ASN* 3.2 9.0 + - - +
250B ARG* 3.0 41.3 - - + +
252B THR* 4.2 15.5 - - + -
283B ILE* 5.0 2.5 - - + +
285B GLY* 3.6 1.6 - - - -
286B GLY 2.7 23.2 + - - -
287B ALA 3.3 15.7 + - - +
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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