Contacts of the strand formed by residues 288 - 293 (chain A) in PDB entry 4J2X
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 LEU 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A THR* 3.4 7.0 - - - +
274A VAL* 2.9 37.0 + - + +
276A LEU* 3.7 34.5 - - + +
285A LEU* 4.1 18.2 - - + -
286A PRO* 3.3 14.8 + - + +
287A ARG* 1.3 82.1 - - - +
289A ILE* 1.3 63.4 + - - +
290A ILE 4.0 0.2 - - - -
314A PHE* 3.7 38.6 - - + +
315A TYR 3.3 3.1 - - - +
316A LEU* 3.8 32.5 - - + -
324A LEU* 4.4 4.7 - - + -
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Residues in contact with ILE 289 (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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253A ASP* 5.7 0.4 - - - +
271A GLY* 3.7 24.5 - - - +
272A GLN 3.5 4.5 - - - +
273A THR* 3.9 17.3 - - - +
288A LEU* 1.3 75.7 - - - +
290A ILE* 1.3 71.4 + - - +
291A ARG* 3.5 28.9 + - - +
313A ALA 3.2 3.8 - - - +
314A PHE* 3.8 1.0 - - - -
315A TYR* 2.9 61.0 + - + +
317A LYS* 3.7 23.3 - - + -
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Residues in contact with ILE 290 (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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248A ILE* 4.5 6.5 - - + -
268A ILE* 3.7 17.9 - - + -
269A HIS 3.7 20.2 - - - +
270A TYR* 3.5 6.8 - - + -
271A GLY 2.6 33.3 + - - -
272A GLN 3.4 6.0 + - - +
274A VAL* 3.9 13.6 - - + +
288A LEU 4.0 0.8 - - - -
289A ILE* 1.3 72.3 - - - +
291A ARG* 1.4 59.2 + - - +
306A VAL* 3.8 20.9 - - + -
312A CYS* 3.6 32.3 - - + -
313A ALA 3.6 2.9 - - - -
314A PHE* 3.7 31.6 - - + -
356A ILE* 3.9 9.9 - - + -
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Residues in contact with ARG 291 (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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270A TYR* 3.4 8.3 - - - -
271A GLY* 4.9 3.8 - - - +
289A ILE* 3.6 22.0 - - + +
290A ILE* 1.4 78.7 - - - +
292A LYS* 1.4 63.1 + - - +
298A ALA* 4.7 3.1 - - + -
299A LEU 4.0 13.5 - - - +
300A LEU* 3.4 40.4 + - - +
312A CYS* 3.4 6.1 - - - -
313A ALA* 2.8 48.7 + - + +
315A TYR* 3.3 51.1 - - - -
323A TYR* 3.3 20.8 + - - -
346A GLU* 4.2 5.1 + - - -
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Residues in contact with LYS 292 (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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195A LYS 5.6 5.4 - - - -
270A TYR* 3.2 39.7 - - + +
291A ARG* 1.4 72.8 - - - +
293A VAL* 1.3 76.2 + - - +
294A ASP* 4.2 0.7 - - - +
298A ALA* 3.3 6.2 - - - -
299A LEU* 2.9 48.5 + - + -
302A ALA* 4.3 13.5 - - + -
304A ASP* 4.8 4.3 - - - +
310A HIS* 3.4 36.7 - - + +
311A LYS* 3.3 23.6 + - - +
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Residues in contact with VAL 293 (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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292A LYS* 1.3 95.7 + - - +
294A ASP* 1.4 60.0 + - - +
295A LYS 3.4 25.8 - - - +
297A THR 3.3 15.7 - - - +
299A LEU* 4.3 2.0 - - - -
311A LYS* 3.6 27.4 + - + +
312A CYS 3.5 33.4 - - - +
313A ALA* 3.8 11.9 - - + -
348A ILE* 4.4 9.9 - - + -
353A SER* 3.8 19.5 - - - +
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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