Contacts of the strand formed by residues 295 - 298 (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 SER 295 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159P CYS* 3.1 38.8 + - - -
162P PRO* 4.0 6.2 - - - +
163P VAL* 3.9 11.7 - - - +
275P ILE 3.1 7.8 + - - +
276P ILE* 3.2 21.9 - - - +
277P LYS 2.8 31.2 + - - +
293P GLU* 3.4 0.9 - - - +
294P SER* 1.3 77.6 - - - +
296P ILE* 1.3 58.0 + - - +
297P VAL 3.9 0.4 - - - -
314P ALA* 4.3 1.3 - - - -
315P TRP 3.4 5.6 - - - -
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Residues in contact with ILE 296 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P LYS* 3.3 30.1 - - + +
279P SER* 3.8 15.3 - - - -
288P PHE* 3.6 43.3 - - + -
291P THR* 3.4 35.7 - - + -
293P GLU* 4.8 4.3 - - + +
295P SER* 1.3 76.4 - - - +
297P VAL* 1.3 64.7 + - - +
298P ASP 3.3 1.2 + - - -
314P ALA* 3.1 3.2 - - - -
315P TRP* 2.7 54.9 + - + +
316P TYR* 4.3 6.7 - - - +
317P ASP 5.0 0.4 - - - +
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Residues in contact with VAL 297 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P VAL* 4.3 15.7 - - + -
261P ASN* 4.4 8.1 - - - +
264P LEU* 4.0 37.5 - - + -
276P ILE* 3.8 23.6 - - + -
277P LYS 2.8 11.4 + - - +
278P TYR* 4.3 17.0 - - + -
279P SER* 2.9 29.6 + - - +
295P SER 3.9 0.6 - - - +
296P ILE* 1.3 70.0 - - - +
298P ASP* 1.3 61.7 + - - +
299P SER 3.1 12.1 + - - +
302P THR* 4.6 0.9 - - - +
312P VAL* 4.4 8.1 - - + -
313P ILE 3.6 8.7 - - - +
314P ALA* 4.1 0.4 - - + -
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Residues in contact with ASP 298 (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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199O ARG* 2.8 41.2 + - - -
279P SER* 3.6 9.7 + - - +
281P LEU 4.4 4.9 - - - +
283P LEU 4.6 0.5 + - - +
288P PHE* 5.0 3.3 - - - -
296P ILE 3.3 2.2 + - - -
297P VAL* 1.3 71.5 - - - +
299P SER* 1.3 62.1 + - - +
300P SER* 3.8 5.2 + - - -
301P LEU* 3.1 41.5 + - + +
302P THR* 3.7 6.8 + - - -
313P ILE* 2.8 22.5 + - + +
315P TRP* 3.1 26.7 + - + +
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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