Contacts of the strand formed by residues 257 - 262 (chain D) in PDB entry 2W8B
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 LYS 257 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D PHE* 3.4 5.0 - - - -
252D SER* 2.9 31.9 + - - +
254D ASP* 4.8 3.9 + - - +
255D GLY 3.4 0.4 - - - -
256D SER* 1.3 108.8 + - - +
258D LEU* 1.3 61.1 + - - +
259D ALA 4.1 0.2 - - - -
272D VAL* 3.6 20.2 - - + -
273D MET 3.2 6.7 - - - +
274D ASP* 4.8 12.4 + - + -
275D LEU* 3.8 8.7 - - - +
295D TRP* 3.9 16.2 - - + -
299D SER 3.9 19.7 - - - +
300D GLN* 4.5 4.9 - - - -
319D ILE* 4.0 20.2 - - + -
160G GLU* 5.0 5.9 + - - +
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Residues in contact with LEU 258 (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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215D ALA* 4.1 7.6 - - + -
226D LEU* 4.2 4.9 - - + -
228D ILE* 4.5 4.0 - - + -
239D VAL* 4.1 25.1 - - + -
249D PRO* 4.1 13.7 - - + -
250D ALA 3.6 15.0 - - - +
251D PHE* 3.7 45.1 - - + -
257D LYS* 1.3 74.6 - - - +
259D ALA* 1.3 62.4 + - - +
260D PHE* 3.4 24.5 - - + -
272D VAL* 3.3 4.0 - - - +
273D MET* 2.8 36.3 + - + +
275D LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 259 (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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249D PRO* 3.2 1.7 - - - +
250D ALA* 2.9 31.1 + - + +
258D LEU* 1.3 74.7 - - - +
260D PHE* 1.3 67.3 - - - +
270D LEU* 6.4 0.2 - - + -
271D TYR 3.4 8.7 - - - +
272D VAL* 4.3 2.9 - - + -
293D PRO* 4.1 11.7 - - + -
295D TRP* 3.8 28.8 - - + +
302D LEU* 3.9 25.6 - - + -
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Residues in contact with PHE 260 (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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226D LEU* 3.6 18.6 - - + -
239D VAL* 4.0 14.6 - - + -
240D ALA* 4.3 7.0 - - + -
247D GLY 3.4 11.7 - - - +
248D ALA 3.5 11.9 - - - +
249D PRO* 4.1 2.2 - - + -
258D LEU* 3.4 26.5 - - + -
259D ALA* 1.3 82.8 - - - +
261D ALA* 1.3 62.5 + - - +
262D LEU* 3.7 34.3 - - + -
270D LEU* 3.5 6.4 - - - +
271D TYR* 2.9 49.0 + - + -
272D VAL 4.2 1.1 - - - -
273D MET* 3.7 19.7 - - + -
280D ILE* 4.1 21.1 - - + -
293D PRO* 4.1 6.2 - - - +
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Residues in contact with ALA 261 (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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245D HIS* 3.8 3.3 - - + +
246D ASN* 3.6 1.0 - - - -
247D GLY 2.9 36.6 + - - +
248D ALA* 4.2 2.7 + - + -
260D PHE* 1.3 74.6 - - - +
262D LEU* 1.3 65.8 + - - +
268D LEU* 4.2 10.3 - - + -
269D ASN 3.2 10.8 - - - +
270D LEU* 4.6 1.3 - - + -
290D ASN 3.9 4.9 - - - +
291D THR* 3.3 38.1 - - - +
293D PRO* 5.0 0.2 - - + -
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Residues in contact with LEU 262 (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 ALA* 3.9 6.3 - - + -
242D PHE* 3.6 27.4 - - + -
245D HIS 3.2 8.1 - - - +
246D ASN* 3.3 31.2 - - - +
260D PHE* 3.7 24.2 - - + -
261D ALA* 1.3 81.1 - - - +
263D SER* 1.3 58.0 + - - +
264D LYS* 4.2 14.8 - - + +
265D THR* 5.0 0.2 + - - -
267D SER 3.5 2.1 - - - +
268D LEU* 4.2 2.0 - - - -
269D ASN* 2.8 31.1 + - - +
271D TYR* 3.5 48.3 + - + -
280D ILE* 5.0 2.7 - - + -
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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