Contacts of the strand formed by residues 262 - 268 (chain A) in PDB entry 3H8E
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 PHE 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS 4.4 3.6 - - - -
261A PRO* 1.3 74.8 - - - +
263A VAL* 1.3 60.5 + - - +
264A LEU* 5.8 2.5 - - + -
311A VAL* 4.1 28.5 - - + -
312A ASN 2.9 17.0 + - - +
313A LEU* 3.3 11.2 - - + +
314A VAL 2.9 24.4 + - - -
369A GLN* 2.1 38.6 - - + -
370A ALA* 3.6 12.6 - - + +
372A ILE* 6.3 0.7 - - + -
490A TYR* 3.3 34.3 - + + -
491A LEU* 4.0 20.4 - - + -
494A ARG* 3.6 32.3 - - + -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO* 4.7 2.2 - - + -
262A PHE* 1.3 76.2 - - - +
264A LEU* 1.3 67.1 + - - +
265A VAL* 3.9 13.0 - - + -
314A VAL* 3.1 23.1 - - + +
316A LEU* 3.8 29.8 - - + -
363A ALA* 4.2 7.4 - - + +
366A PHE* 4.4 14.6 - - + -
368A PRO* 3.6 26.5 - - + -
370A ALA 2.8 12.9 + - - +
371A VAL* 3.3 8.5 - - + -
372A ILE* 2.9 27.5 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A PHE* 5.7 1.3 - - + -
263A VAL* 1.3 78.8 - - - +
265A VAL* 1.4 55.8 + - - +
266A GLY 4.1 0.2 - - - -
297A VAL* 3.9 30.2 - - + +
300A THR* 3.9 31.9 - - + +
313A LEU* 3.9 29.2 - - + -
314A VAL 2.9 8.8 + - - +
315A CYS* 3.4 3.6 - - - +
316A LEU* 2.8 31.9 + - - +
372A ILE* 3.4 32.1 - - + +
374A ILE* 4.3 2.2 - - + -
487A LEU* 4.3 18.2 - - + -
490A TYR* 5.7 3.4 - - + -
491A LEU* 4.6 6.1 - - + -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 3.9 18.8 - - + -
264A LEU* 1.4 77.2 - - - +
266A GLY* 1.3 61.4 + - - +
267A LYS 4.2 0.3 + - - -
297A VAL* 4.3 2.0 - - - -
316A LEU* 3.3 16.6 - - + +
318A ALA* 5.3 0.4 - - + -
356A LEU* 3.6 24.7 - - + +
359A THR* 3.7 27.1 - - + -
360A LEU* 4.3 10.3 - - + -
363A ALA* 4.8 2.0 - - + -
371A VAL* 4.0 17.9 - - + -
372A ILE 2.8 7.5 + - - +
373A ASP* 3.1 13.5 - - + +
374A ILE* 2.8 28.2 + - - +
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 1.3 75.4 - - - +
267A LYS* 1.3 65.8 + - - -
268A GLY 3.4 0.2 + - - -
293A GLY 3.8 5.6 - - - -
294A ALA* 3.6 19.3 - - - +
297A VAL* 4.0 6.6 - - - +
316A LEU 2.9 10.7 + - - -
317A LEU* 3.7 3.4 - - - +
318A ALA* 3.0 28.2 + - - +
356A LEU* 4.2 3.4 - - - -
374A ILE 3.6 5.6 - - - -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLY* 1.3 70.1 - - - -
268A GLY* 1.3 62.0 + - - +
269A ILE* 3.5 36.1 - - + +
291A MET* 3.5 13.4 - - - +
293A GLY 3.6 2.3 + - - -
294A ALA 2.9 15.7 + - - +
318A ALA* 4.2 2.9 - - - -
351A GLU* 4.5 8.8 + - - -
352A GLY* 3.6 28.7 - - - +
355A VAL* 4.8 2.5 - - + -
356A LEU* 3.9 15.4 - - + +
374A ILE 3.0 8.3 + - - -
375A ALA* 3.7 33.9 - - + -
376A THR* 3.0 36.3 + - - +
377A LEU* 4.2 10.7 + - + +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 4.9 1.2 - - - +
266A GLY 3.4 1.0 + - - -
267A LYS* 1.3 75.1 - - - +
269A ILE* 1.3 62.3 + - - +
291A MET* 3.3 25.6 - - - +
294A ALA* 3.7 7.6 - - - -
318A ALA 2.9 20.9 + - - -
319A CYS* 3.0 26.3 - - - +
320A ALA 3.1 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