Contacts of the strand formed by residues 309 - 316 (chain P) in PDB entry 2D2I
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 309 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175O LYS* 3.8 24.9 - - + -
176O GLY* 4.8 6.7 - - - -
177O THR* 4.2 19.5 - - + -
248O VAL* 5.5 1.3 - - + +
250O GLN* 5.7 4.0 - - + +
309O LEU* 4.8 13.7 - - + -
248P VAL* 3.8 29.4 - - + -
249P VAL 3.7 16.4 - - - +
250P GLN* 4.0 10.5 - - + +
303P LEU* 3.5 2.7 - - + +
304P VAL* 3.5 1.2 - - - -
305P MET* 2.8 48.8 + - + +
307P GLY 3.9 1.2 - - - -
308P ASP* 1.3 77.3 - - - +
310P VAL* 1.3 60.9 + - - +
311P LYS* 5.7 0.4 - - + -
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Residues in contact with VAL 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P LEU* 4.2 15.0 - - + -
171P PHE* 5.8 2.0 - - + -
247P LEU 3.4 1.8 - - - +
248P VAL* 3.2 5.4 - - - +
249P VAL* 2.7 73.7 + - + +
251P VAL* 4.0 15.0 - - + -
255P THR* 4.1 16.2 - - + -
260P VAL* 4.4 8.3 - - + -
302P THR* 6.1 0.2 - - + -
303P LEU 3.6 2.9 - - - -
304P VAL* 3.5 31.9 - - + -
309P LEU* 1.3 79.0 - - - +
311P LYS* 1.3 60.9 + - - +
312P VAL* 5.2 3.6 - - + -
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Residues in contact with LYS 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O THR* 3.2 40.0 + - - +
178O MET* 4.0 8.6 + - - +
179O THR* 3.0 26.0 + - - +
232O GLY* 5.6 1.3 - - - -
233O ILE* 4.1 23.1 - - + +
246O ASP 5.5 0.4 + - - -
248O VAL* 6.0 0.4 - - - +
246P ASP* 3.1 30.7 + - - +
247P LEU 3.1 5.2 - - - +
248P VAL* 3.7 10.0 - - + +
301P LEU 5.0 3.6 - - - +
302P THR* 3.5 6.3 - - - +
303P LEU* 3.0 48.6 + - + +
309P LEU* 5.4 1.1 - - + +
310P VAL* 1.3 74.8 - - - +
312P VAL* 1.3 67.4 + - - +
313P ILE* 4.5 5.4 - - + -
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Residues in contact with VAL 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P VAL* 4.1 22.4 - - + -
167P LEU* 4.1 23.3 - - + -
245P VAL* 3.5 2.1 - - - +
247P LEU* 2.9 38.6 + - + +
260P VAL* 4.5 11.4 - - + -
264P LEU* 4.1 26.9 - - + -
297P VAL* 4.4 11.2 - - + -
302P THR* 4.8 6.3 - - + +
310P VAL* 5.2 2.7 - - + -
311P LYS* 1.3 81.8 - - - +
313P ILE* 1.3 79.3 + - - +
314P ALA* 4.9 2.5 - - + -
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Residues in contact with ILE 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233O ILE* 3.6 24.0 - - + -
235O LEU* 5.4 8.5 - - + -
244P VAL* 3.4 23.6 - - + -
245P VAL 3.3 1.8 - - - +
246P ASP* 3.4 35.2 - - + +
297P VAL* 3.6 3.1 - - - -
298P ASP* 2.8 31.5 + - + +
301P LEU* 3.7 48.4 + - + +
302P THR* 5.3 0.8 + - - -
311P LYS* 4.3 4.5 - - + -
312P VAL* 1.3 80.2 - - - +
314P ALA* 1.3 66.9 + - - +
315P TRP* 5.2 2.5 - - + +
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Residues in contact with ALA 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P CYS* 3.5 13.2 - - - -
163P VAL* 4.4 12.6 - - + -
244P VAL* 3.5 4.7 - - - -
245P VAL* 3.0 50.7 + - + +
295P SER* 4.3 4.7 - - - -
296P ILE 3.1 18.8 - - - +
297P VAL* 4.1 4.0 - - + -
298P ASP 4.4 0.2 - - - +
312P VAL* 4.9 2.9 - - + -
313P ILE* 1.3 77.5 - - - +
315P TRP* 1.3 63.3 + - - +
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Residues in contact with TRP 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O ILE* 3.4 43.1 - - + -
210O PRO* 3.4 29.8 - - + -
235O LEU* 5.2 1.3 - - + -
242P VAL* 4.2 4.3 - - + -
243P SER 3.3 13.2 - - - -
244P VAL* 3.6 27.8 - - + -
283P LEU 4.3 4.0 - - - -
285P SER* 3.6 32.1 - - - -
288P PHE* 3.3 41.2 - + + -
295P SER* 3.4 1.4 - - - -
296P ILE* 2.7 57.2 + - + +
298P ASP* 3.1 30.8 + - + +
301P LEU* 5.6 0.4 - - + -
313P ILE* 5.2 0.9 - - + +
314P ALA* 1.3 74.0 - - - +
316P TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155P CYS* 3.6 31.4 - - + -
156P THR* 2.9 21.5 + - - +
159P CYS* 3.6 12.8 - - + -
180P THR* 2.7 24.1 + - - -
182P HIS* 3.4 6.5 - - - -
242P VAL* 3.4 5.5 - - - +
243P SER* 2.8 52.6 + - - -
244P VAL* 3.5 19.1 - - - -
245P VAL* 3.7 17.7 - - + -
288P PHE 5.5 0.2 - - - -
293P GLU 5.1 1.6 - - - +
294P SER* 3.3 24.2 - - - +
296P ILE* 4.3 7.0 - - - -
314P ALA 3.7 1.1 - - - -
315P TRP* 1.3 78.7 - - - +
317P ASP* 1.3 62.0 + - - +
318P ASN* 3.1 23.7 + - + -
321P GLY* 6.4 0.2 - - - -
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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