Contacts of the strand formed by residues 240 - 247 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C THR* 2.7 39.8 + - - +
172C TYR* 4.3 1.6 - - - -
173C ASP* 2.7 59.6 + - - +
174C LYS 3.2 2.8 + - - -
238C GLY 3.9 3.6 + - - +
239C GLU* 1.3 72.2 - - - +
241C VAL* 1.3 67.9 + - - +
292C PHE* 2.8 29.4 - - + -
293C TYR 3.7 5.4 - - - -
294C THR* 3.9 7.2 - - + +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 4.4 2.5 - - - -
174C LYS* 3.0 35.4 - - + +
176C TYR* 3.9 22.2 - - + -
234C THR 5.1 0.2 - - - +
235C ALA* 4.2 24.7 - - + -
239C GLU* 4.5 3.8 - - + +
240C LYS* 1.3 85.4 - - - +
242C LEU* 1.3 65.6 + - - +
243C ILE* 3.9 15.8 + - + +
291C ALA 3.6 1.4 - - - +
292C PHE* 3.4 3.9 - - - -
293C TYR* 3.1 32.3 + - - +
295C PHE* 4.2 13.9 - - + -
320C PHE* 5.6 2.7 - - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C MET* 3.9 17.0 - - - -
162C LEU* 4.5 10.1 - - + -
172C TYR* 4.0 30.1 - - + +
174C LYS 2.9 6.9 + - - -
175C ILE* 3.2 18.5 - - + +
176C TYR 3.1 23.0 + - - -
241C VAL* 1.3 72.2 - - - +
243C ILE* 1.3 62.6 + - - +
244C VAL* 3.9 22.2 - - + -
265C TRP* 3.8 20.2 - - + -
270C PHE* 5.7 0.9 - - + -
290C ALA* 4.1 13.2 - - + -
291C ALA 3.4 14.1 - - - +
292C PHE* 3.7 19.7 - - + +
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Residues in contact with ILE 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C TYR* 3.4 11.7 - - + +
178C VAL* 4.5 17.5 - - + -
241C VAL* 4.1 19.5 - - + +
242C LEU* 1.3 75.6 - - - +
244C VAL* 1.3 69.2 + - - +
245C HIS* 3.7 3.7 + - + +
256C LEU* 5.4 12.8 - - + -
290C ALA* 3.8 1.2 - - - -
291C ALA* 2.9 37.8 + - + +
293C TYR* 6.2 4.3 - - + -
295C PHE* 5.6 5.6 - - + -
303C TYR* 4.5 32.4 + - + +
320C PHE* 4.4 28.3 - - + -
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 4.4 13.2 - - + -
131C VAL* 3.7 33.2 - - + -
153C ALA* 5.1 0.2 - - + -
155C MET* 3.9 17.3 - - - -
175C ILE* 4.5 8.1 - - + -
176C TYR 3.0 9.7 + - - +
177C TYR* 3.4 21.2 - - + -
178C VAL* 2.9 27.0 + - - +
242C LEU* 3.8 15.7 + - + -
243C ILE* 1.3 74.6 - - - +
245C HIS* 1.3 66.2 + - - +
288C ALA* 4.8 3.4 - - + -
289C GLY 3.5 13.0 - - - +
290C ALA* 4.1 3.8 - - + +
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Residues in contact with HIS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 4.4 0.9 - - - -
178C VAL* 3.2 23.3 + - + +
180C GLU* 2.9 31.6 + - + +
220C PHE* 3.6 28.3 - + - -
243C ILE* 3.7 4.8 + - + +
244C VAL* 1.3 77.6 - - - +
246C SER* 1.3 90.9 + - - +
252C THR* 4.3 15.4 - - + +
254C PRO* 4.8 3.1 - - + +
283C ILE* 3.7 16.6 - - + +
288C ALA* 3.2 3.4 - - - +
289C GLY 2.9 30.1 + - - -
303C TYR* 3.1 34.8 + + - +
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Residues in contact with SER 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 3.0 31.1 - - - +
151C ASN* 4.7 5.8 + - - +
152C GLY* 3.6 2.3 + - - -
153C ALA* 3.8 4.9 - - - -
177C TYR* 2.7 29.0 + - - -
178C VAL 3.4 4.2 + - - -
179C GLY* 4.2 0.9 - - - -
180C GLU 3.0 25.8 + - - +
245C HIS* 1.3 83.2 - - - +
247C GLN* 1.3 59.5 + - - +
283C ILE* 5.2 0.7 - - - -
287C ALA 3.9 0.4 - - - -
288C ALA* 3.3 13.7 - - - +
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Residues in contact with GLN 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 4.7 1.1 - - - -
180C GLU* 3.7 44.1 + - + +
182C ASP* 2.9 35.7 + - - +
246C SER* 1.3 72.3 - - - +
248C ALA* 1.3 59.6 + - - +
249C ASN* 2.9 5.7 + - - +
250C ARG* 2.6 56.6 + - - +
252C THR* 4.2 15.0 - - + -
283C ILE* 5.0 2.4 - - + +
285C GLY* 3.6 1.3 - - - -
286C GLY 2.8 21.0 + - - -
287C ALA 3.3 16.4 + - - +
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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