Contacts of the strand formed by residues 268 - 273 (chain D) in PDB entry 5X22
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 ALA 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261D LEU* 3.8 20.0 - - + -
262D LYS 3.4 14.4 - - - +
263D GLU* 3.9 11.4 - - + +
264D LEU* 4.5 1.1 - - - +
267D GLY* 1.3 75.1 - - - +
269D PHE* 1.3 76.1 + - - +
283D PHE* 3.7 2.5 - - - -
284D LEU* 2.9 44.7 + - + +
290D PRO* 5.5 5.2 - - + -
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Residues in contact with PHE 269 (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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219D GLU* 5.1 5.6 - - + -
221D ALA* 4.1 10.3 - - + -
260D GLU 3.4 2.4 - - - +
261D LEU* 3.5 4.8 - - - +
262D LYS* 2.9 50.2 + - + +
264D LEU* 4.1 24.0 - - + -
268D ALA* 1.3 81.4 - - - +
270D LEU* 1.3 62.8 + - - +
271D VAL* 4.0 9.0 - - + -
281D THR* 4.4 13.9 - - + -
282D TYR 3.5 12.1 - - - -
283D PHE* 3.7 16.6 - + - -
284D LEU* 5.0 0.2 - - - -
317D VAL* 5.4 2.5 - - + -
337D LEU* 3.6 31.9 - - + -
339D TRP* 4.2 35.0 - + - -
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Residues in contact with LEU 270 (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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259D VAL* 3.6 25.1 - - + -
260D GLU 3.7 0.4 - - - -
261D LEU* 3.6 28.3 - - + -
269D PHE* 1.3 71.4 - - - +
271D VAL* 1.3 61.7 + - - +
272D LEU* 3.7 11.3 + - + -
281D THR* 3.7 1.1 - - - -
282D TYR* 2.9 49.8 + - + +
284D LEU* 3.8 26.6 - - + +
290D PRO* 5.7 0.7 - - + -
292D VAL* 3.9 18.6 - - + -
304D LEU* 3.6 42.4 - - + +
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Residues in contact with VAL 271 (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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258D VAL 3.5 1.9 - - - +
260D GLU* 2.9 56.4 + - - +
262D LYS* 5.9 3.6 - - + -
269D PHE* 5.0 9.2 - - + -
270D LEU* 1.3 76.6 - - - +
272D LEU* 1.3 62.2 + - - +
273D ARG* 3.9 28.8 + - - +
278D PRO* 3.9 15.7 - - + -
280D ALA 3.5 10.5 - - - +
281D THR* 4.2 18.6 - - + +
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Residues in contact with LEU 272 (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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253D ALA* 4.4 2.0 - - + -
255D GLU 3.3 28.0 - - - +
257D GLY* 4.7 4.0 - - - +
258D VAL 3.3 5.8 - - - +
259D VAL* 3.7 20.9 - - + -
270D LEU* 3.7 21.5 + - + +
271D VAL* 1.3 75.9 - - - +
273D ARG* 1.3 61.9 + - - +
278D PRO* 3.6 2.0 - - - +
279D VAL* 2.8 27.8 + - + -
280D ALA* 2.9 28.4 + - + +
282D TYR* 3.6 24.0 - - + -
298D VAL* 3.7 21.1 - - + -
304D LEU* 4.4 10.5 - - + -
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Residues in contact with ARG 273 (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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257D GLY* 4.2 2.0 - - - -
258D VAL* 2.9 56.7 + - + +
260D GLU* 2.4 43.1 + - + +
271D VAL* 3.9 17.4 - - - +
272D LEU* 1.3 78.2 - - - +
274D ARG* 1.3 62.5 + - - +
275D GLU 4.3 6.1 - - - -
276D ASP* 2.7 35.1 + - - +
277D GLU 3.5 6.5 - - - +
278D PRO* 3.6 15.1 - - + +
279D VAL* 3.7 6.7 - - - +
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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