Contacts of the strand formed by residues 332 - 340 (chain A) in PDB entry 1EX0
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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A TYR* 2.9 12.6 + - - +
322A ASN* 3.4 16.6 - - - +
325A LEU* 3.7 26.2 - - + -
326A ARG* 2.6 40.5 + - + -
330A ILE 3.7 8.1 - - - +
331A PRO* 1.4 76.7 - - - +
333A ARG* 1.3 56.1 + - - +
377A GLU 3.2 11.9 - - - +
392A TRP* 3.9 4.9 - - - -
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.2 36.5 + - + -
322A ASN* 3.4 9.9 - - - +
326A ARG* 4.0 5.6 - - - +
332A ALA* 1.3 74.7 - - - +
334A ILE* 1.3 59.7 + - - +
335A VAL* 4.6 1.5 - - + +
376A ASN* 3.5 3.6 - - - -
377A GLU* 2.7 65.1 + - + +
392A TRP* 3.3 47.3 - - + +
466A THR* 3.8 36.2 - - - +
475A MET* 4.3 7.3 - - - +
477A ILE* 3.9 22.6 - - - +
480A THR* 4.9 8.7 + - - +
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A VAL 5.3 7.1 - - - +
212A ILE* 4.3 25.8 - - + -
213A PHE* 5.7 1.7 - - - -
227A TYR* 3.3 29.5 + - + +
315A TRP 5.9 0.2 - - - +
318A ALA* 3.6 32.8 - - + +
319A GLY* 3.8 11.4 - - - +
322A ASN* 3.9 4.2 - - - -
333A ARG* 1.3 74.4 - - - +
335A VAL* 1.3 67.9 + - - +
336A THR* 5.0 2.0 - - - +
374A CYS* 4.3 10.1 - - + -
375A TRP 3.6 11.0 - - - +
376A ASN* 3.8 18.6 - - - +
465A VAL 4.0 0.2 - - - +
466A THR* 2.5 30.9 + - - -
467A LYS 4.4 1.6 + - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 4.1 1.5 + - - +
334A ILE* 1.3 78.5 - - - +
336A THR* 1.3 65.3 + - - +
374A CYS* 3.2 7.8 - - - +
375A TRP* 3.0 72.7 + - + +
377A GLU* 3.6 27.4 - - + +
464A ILE* 4.1 13.0 - - + -
465A VAL 3.4 3.1 - - - -
466A THR* 4.3 3.8 - - - +
477A ILE* 3.4 29.6 - - + -
481A TYR* 4.3 1.6 - - - +
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Residues in contact with THR 336 (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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212A ILE* 4.9 0.3 - - - +
213A PHE* 2.9 49.5 + - - +
334A ILE* 5.0 1.9 - - - +
335A VAL* 1.3 73.2 + - - +
337A ASN* 1.3 60.6 + - - +
338A TYR* 3.9 15.6 - - + -
372A TYR* 3.7 29.4 - - + -
373A HIS 3.7 4.0 - - - +
374A CYS* 3.5 12.5 - - - -
463A LEU 3.8 1.0 - - - +
464A ILE* 3.3 6.2 - - - -
465A VAL* 2.9 39.6 + - - +
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Residues in contact with ASN 337 (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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335A VAL* 4.2 1.0 - - - +
336A THR* 1.3 73.2 - - - +
338A TYR* 1.3 67.7 + - - +
339A PHE 3.8 2.7 + - - -
340A SER* 2.8 36.6 + - - +
372A TYR* 3.2 4.2 - - - -
373A HIS 2.9 31.9 + - - +
375A TRP* 3.5 34.9 - - + -
434A GLU 3.6 13.1 + - - -
435A VAL* 3.8 4.2 - - - +
461A GLY* 3.3 17.7 - - - -
463A LEU 3.7 1.8 - - - -
464A ILE* 3.2 23.7 - - + +
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Residues in contact with TYR 338 (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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213A PHE* 3.5 10.6 - - - +
214A TYR 2.9 28.8 + - - -
216A GLU* 3.7 16.6 - - - -
217A VAL* 3.5 34.1 - - + -
220A ILE* 3.2 26.0 - - + +
336A THR* 3.9 11.9 - - + -
337A ASN* 1.3 73.1 + - - +
339A PHE* 1.3 75.2 + - - +
371A ASN 3.6 12.3 - - - +
372A TYR* 3.9 12.1 - - + -
461A GLY* 3.5 0.9 + - - -
462A LYS* 3.1 21.0 + - + +
463A LEU* 2.8 49.7 + - + +
465A VAL* 3.9 22.4 - - + -
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Residues in contact with PHE 339 (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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216A GLU* 5.4 1.1 - - + -
217A VAL* 3.7 30.7 - - + -
337A ASN* 3.8 2.0 + - - -
338A TYR* 1.3 71.3 - - + +
340A SER* 1.3 60.7 + - - +
369A VAL* 3.5 18.8 - - + -
370A TRP 3.2 8.1 - - - -
371A ASN* 3.1 27.6 + - - -
459A HIS* 3.3 60.1 - + + +
460A ILE* 3.5 7.7 - - - +
461A GLY 2.8 27.7 + - - -
462A LYS* 4.0 17.5 - - + -
605A HIS* 6.1 0.7 - + - -
623A LYS* 5.3 2.2 - - + -
624A SER* 3.8 34.5 - - - -
1330A PO4 5.1 0.7 - - - -
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Residues in contact with SER 340 (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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337A ASN* 2.8 30.7 + - - +
339A PHE* 1.3 73.4 - - - +
341A ALA* 1.3 58.7 + - - +
342A HIS 3.3 5.5 + - - -
369A VAL* 3.5 4.8 - - - +
370A TRP* 2.8 42.7 + - - +
373A HIS* 3.6 26.3 - - - +
375A TRP* 3.8 2.3 - - - -
434A GLU* 2.5 27.7 + - - +
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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