Contacts of the strand formed by residues 257 - 262 (chain O) in PDB entry 2V16
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 ASP 257 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O SER 3.5 1.0 - - - +
199O VAL* 3.8 0.5 - - - -
200O GLY* 3.0 29.7 + - - +
255O LEU 3.6 5.9 - - - +
256O PRO* 1.3 82.5 - - - +
258O ILE* 1.3 63.9 + - - +
259O SER* 4.2 5.4 - - - +
268O THR* 4.4 12.5 - - + +
269O LEU 3.4 11.7 - - - +
270O THR* 3.2 29.8 - - - +
271O SER* 4.1 0.7 + - - -
274O TYR* 4.4 1.3 - - - -
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Residues in contact with ILE 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197O VAL* 3.1 36.1 - - + -
198O SER 3.2 8.1 - - - +
199O VAL* 4.0 22.7 - - + -
231O LEU* 4.5 12.6 - - + -
235O LEU* 4.0 15.3 - - + -
257O ASP* 1.3 76.2 - - - +
259O SER* 1.2 65.5 + - - +
260O PHE* 3.8 24.5 - - + -
268O THR* 3.6 0.2 - - - -
269O LEU* 2.8 30.4 + - + +
274O TYR* 4.1 26.5 - - + +
286O ILE* 4.8 13.0 - - + -
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Residues in contact with SER 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196O GLY 3.8 0.5 - - - +
197O VAL* 3.6 3.3 - - - -
198O SER* 3.0 34.3 + - - -
200O GLY 4.9 4.5 + - - -
257O ASP* 4.2 5.0 - - - +
258O ILE* 1.2 82.3 + - - +
260O PHE* 1.3 64.6 + - - +
261O HIS 3.4 5.0 + - - -
266O GLU* 3.4 21.7 - - - +
267O TYR 3.2 8.3 - - - -
268O THR* 2.7 27.0 + - - +
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Residues in contact with PHE 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O MET* 3.0 33.2 - - + -
196O GLY 4.3 2.2 - - - -
197O VAL* 3.9 13.5 - - + -
221O ILE* 3.8 38.8 - - + -
258O ILE* 3.8 22.2 - - + -
259O SER* 1.3 75.3 - - - +
261O HIS* 1.4 57.7 + - - +
262O LEU* 3.1 21.2 + - + +
267O TYR 2.5 41.4 + - - +
269O LEU* 3.9 26.5 - - + -
286O ILE* 5.8 1.8 - - + -
299O TRP* 4.3 5.6 - + - -
301O LEU* 4.4 10.3 - - + -
305O PHE* 3.6 24.0 - + + -
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Residues in contact with HIS 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O MET* 3.7 1.8 - - - +
195O LYS* 3.0 46.9 + - + +
196O GLY* 3.3 26.9 + - - +
259O SER 3.4 2.4 + - - -
260O PHE* 1.4 65.6 - - - +
262O LEU* 1.3 71.3 + - - +
264O GLY* 3.3 35.1 + - - -
265O LYS 3.2 11.4 - - - -
266O GLU* 2.9 40.3 + - + +
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Residues in contact with LEU 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O ILE* 3.7 5.3 - - + +
192O ILE* 3.7 27.8 - - + -
193O GLN 4.4 2.9 - - - +
194O MET* 4.0 34.3 - - + -
195O LYS* 4.1 0.4 - - - -
212O ALA* 5.0 0.2 - - + -
260O PHE* 3.1 21.4 + - + +
261O HIS* 1.3 81.8 - - - +
263O GLY* 1.4 67.3 - - - +
264O GLY 3.0 0.4 - - - -
265O LYS 2.5 22.7 + - - +
267O TYR* 2.9 58.6 - - + -
301O LEU* 4.2 15.0 - - + -
305O PHE* 4.5 5.4 - - + -
322O PHE* 4.9 4.5 - - + -
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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