Contacts of the strand formed by residues 325 - 331 (chain A) in PDB entry 2EIT
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ASP 3.5 8.1 - - - +
295A ILE* 3.6 22.2 - - + -
310A VAL* 4.6 2.7 - - + +
313A SER* 3.0 32.4 + - - -
314A ALA* 3.2 29.0 - - + +
323A SER 3.6 2.4 + - - -
324A ALA* 1.3 68.7 - - - +
326A SER* 1.3 60.7 + - - +
327A ARG 4.5 5.4 - - - +
422A VAL 5.0 0.9 - - - +
423A LEU* 3.5 7.5 - - + +
475A ILE* 3.8 8.6 - - + +
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Residues in contact with SER 326 (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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291A GLY 5.0 1.0 + - - -
292A LYS* 3.4 37.7 + - - +
293A ASP 2.9 16.8 + - - -
324A ALA* 3.1 7.6 + - - -
325A ALA* 1.3 74.3 - - - +
327A ARG* 1.3 62.2 + - - +
418A ILE* 6.1 2.5 - - - -
419A PHE 6.4 0.2 - - - -
422A VAL 4.0 13.0 - - - +
423A LEU* 3.7 6.8 - - - -
424A SER* 3.0 26.9 + - - -
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Residues in contact with ARG 327 (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* 3.0 41.3 + - + +
293A ASP* 3.0 4.0 + - - +
294A ALA* 3.2 32.7 - - + +
295A ILE* 3.0 25.1 + - - +
325A ALA* 4.5 2.8 - - - +
326A SER* 1.3 84.9 + - - +
328A LEU* 1.3 60.5 + - - +
329A ILE* 4.1 5.7 - - + +
409A PRO 5.7 1.2 + - - -
414A ALA* 3.4 26.1 + - - +
415A GLN* 5.4 1.0 - - - +
423A LEU* 4.0 4.7 - - - +
424A SER* 3.3 7.9 - - - +
426A ILE* 4.2 19.4 - - + +
437A VAL* 3.0 31.5 + - - +
438A ALA* 2.8 24.4 + - - +
440A ASP 4.9 0.4 + - - -
441A THR* 3.4 17.5 + - - +
464A PHE* 5.5 1.8 - - - -
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Residues in contact with LEU 328 (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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295A ILE* 3.4 16.2 - - + +
297A VAL* 3.9 7.9 - - + -
310A VAL* 3.7 31.0 - - + -
327A ARG* 1.3 73.0 - - - +
329A ILE* 1.3 60.0 + - - +
330A LEU* 3.6 39.3 - - + -
338A VAL* 4.3 1.3 - - + -
339A LEU* 5.3 2.2 - - + -
342A VAL* 4.0 27.1 - - + -
423A LEU* 4.1 16.1 - - + +
424A SER 2.9 9.6 + - - +
425A VAL* 3.3 18.9 - - + +
426A ILE 2.8 27.2 + - - +
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Residues in contact with ILE 329 (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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294A ALA* 3.6 28.9 - - + -
295A ILE 2.8 12.2 + - - +
296A ILE* 3.2 8.8 - - + +
297A VAL 2.9 27.2 + - - +
327A ARG* 4.1 5.4 - - + +
328A LEU* 1.3 73.0 - - - +
330A LEU* 1.3 62.2 + - - +
426A ILE* 3.4 15.5 - - + +
428A VAL* 3.7 32.8 - - + -
434A ALA* 3.7 19.3 - - + +
437A VAL* 3.7 15.7 - - + -
438A ALA* 3.6 32.3 - - + +
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Residues in contact with LEU 330 (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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297A VAL* 3.7 23.3 - - + +
328A LEU* 3.6 38.4 - - + -
329A ILE* 1.3 74.1 - - - +
331A THR* 1.3 63.3 + - - +
334A ALA 4.4 0.7 - - - +
335A TYR* 3.6 47.3 - - + +
338A VAL* 3.8 14.4 - - + -
339A LEU* 4.1 10.3 - - + +
425A VAL* 3.7 25.4 - - + -
426A ILE 2.9 7.8 + - - +
427A ARG* 3.5 5.0 - - - +
428A VAL* 2.9 25.4 + - - -
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Residues in contact with THR 331 (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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297A VAL 3.2 13.2 + - - +
298A ASP* 3.3 29.8 - - + -
299A GLU* 3.5 9.9 + - - +
329A ILE 4.1 0.2 + - - -
330A LEU* 1.3 75.2 - - - +
332A GLN* 1.3 66.9 + - - +
333A GLY 4.0 2.4 + - - -
334A ALA* 3.0 6.8 + - - +
335A TYR* 3.0 19.2 + - - +
428A VAL* 3.3 11.2 - - + -
429A LYS 4.1 6.7 - - - -
430A ASP* 3.6 28.3 - - - +
431A PHE* 3.8 7.6 - - + +
434A ALA* 4.5 6.1 - - + -
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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