Contacts of the strand formed by residues 264 - 268 (chain D) in PDB entry 1O04
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 ARG 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467C GLY 2.8 28.7 + - - -
468C TYR* 3.7 8.3 - - - +
469C LYS* 3.4 18.1 + - - +
472C GLY 2.9 19.5 + - - -
473C SER* 3.8 22.5 - - - +
474C GLY 5.6 1.1 - - - +
159D VAL* 3.8 12.8 - - + +
239D ASP* 3.0 21.1 + - - -
240D LYS* 3.2 16.3 - - + +
241D VAL* 2.8 31.2 + - - +
262D LEU 3.7 15.9 + - - -
263D LYS* 1.3 73.9 - - - +
265D VAL* 1.3 56.2 + - - +
484D ALA 5.3 3.1 - - - +
487D GLU* 2.8 33.5 + - - -
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Residues in contact with VAL 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLN* 3.8 8.3 - - - +
240D LYS* 4.0 1.1 - - - -
241D VAL* 3.4 19.1 - - + -
253D ILE* 4.4 3.6 - - + -
254D GLN* 4.8 15.5 - - + -
257D ALA* 3.4 32.3 - - + -
263D LYS 3.7 3.4 - - - +
264D ARG* 1.3 78.4 - - - +
266D THR* 1.3 71.9 + - - +
267D LEU* 3.6 35.4 - - + -
473D SER* 4.5 6.4 + - - +
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Residues in contact with THR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D LYS* 2.9 26.0 + - - +
241D VAL 3.1 6.6 + - - +
242D ALA* 3.5 13.0 - - - +
243D PHE 3.0 25.4 + - - -
265D VAL* 1.3 77.3 - - - +
267D LEU* 1.3 69.5 + - - +
268D GLU* 5.8 2.2 - - - -
473D SER* 3.6 15.9 - - - +
474D GLY* 4.3 13.7 - - - -
475D ARG 5.3 2.0 - - - +
476D GLU* 4.9 7.0 + - - +
484D ALA* 3.6 21.9 - - + +
485D TYR* 5.8 0.9 - - - -
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 3.9 30.5 - - + +
243D PHE* 3.4 26.5 - - + -
250D GLY* 3.9 13.0 - - - +
253D ILE* 4.0 10.5 - - + -
254D GLN* 4.0 10.5 - - + +
265D VAL* 3.6 21.3 - - + -
266D THR* 1.3 83.7 - - - +
268D GLU* 1.3 67.4 + - - +
269D LEU* 3.9 21.1 - - + -
467D GLY 5.3 0.5 + - - -
472D GLY* 3.1 4.2 - - - -
473D SER* 2.9 47.9 + - - +
474D GLY 4.8 0.3 - - - +
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Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D PHE 2.9 8.4 + - - +
244D THR* 3.2 17.2 - - - +
245D GLY 3.0 25.6 + - - +
266D THR* 5.8 2.2 - - - -
267D LEU* 1.3 76.6 - - - +
269D LEU* 1.3 59.6 + - - +
427D LEU* 4.3 0.3 - - - +
465D PHE* 2.8 29.8 - - - +
466D GLY* 3.3 22.6 - - - -
467D GLY 4.4 0.3 + - - -
471D SER 4.1 1.3 - - - -
473D SER 5.5 0.7 - - - +
474D GLY 4.0 3.4 - - - +
475D ARG 4.0 2.1 - - - -
476D GLU* 3.4 41.4 + - + +
6504D NAD 3.1 35.0 + - - +
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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