Contacts of the helix formed by residues 334 - 347 (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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A VAL* 3.5 27.1 - - + +
298A ASP 3.6 18.8 - - - +
299A GLU* 4.1 0.2 - - - +
303A PHE* 4.2 8.1 - - + -
330A LEU* 4.4 2.7 - - + -
331A THR* 3.0 12.4 + - - +
333A GLY* 1.3 77.5 - - - +
335A TYR* 1.3 66.2 + - - +
336A GLU 3.6 0.9 - - - -
337A PRO* 3.3 2.9 - - - +
338A VAL* 3.0 36.8 + - + +
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Residues in contact with TYR 335 (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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330A LEU* 3.6 23.4 - - + +
331A THR 3.0 13.9 + - - +
332A GLN* 3.3 13.8 + - - +
333A GLY 3.5 0.2 - - - -
334A ALA* 1.3 76.3 - - - +
336A GLU* 1.3 89.6 + - + +
339A LEU* 2.9 52.0 + - + +
405A THR* 2.5 37.6 + - - +
406A GLU* 3.6 22.2 + - - +
425A VAL* 4.0 12.1 - - + -
427A ARG* 3.6 43.5 - - + -
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 4.7 5.3 + - - +
335A TYR* 1.3 99.4 - - + +
337A PRO* 1.4 73.7 - - + +
339A LEU* 4.2 3.5 - - - +
340A GLU* 3.0 28.7 + - - +
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Residues in contact with PRO 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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303A PHE* 3.5 33.0 - - + -
333A GLY 3.7 17.9 - - - +
334A ALA 3.3 12.8 - - - +
336A GLU* 1.4 93.8 - - + +
338A VAL* 1.3 59.7 + - - +
340A GLU* 3.6 3.1 - - + +
341A ARG* 2.9 45.0 + - - +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.8 25.4 - - + -
303A PHE* 3.4 36.6 - - + +
306A ALA* 4.9 7.4 - - + -
307A ALA* 5.0 3.4 - - - +
310A VAL* 5.3 0.7 - - + -
328A LEU* 4.3 4.3 - - + -
330A LEU* 3.8 22.0 - - + -
334A ALA* 3.0 19.6 + - + +
337A PRO* 1.3 73.3 - - - +
339A LEU* 1.3 62.7 + - - +
341A ARG* 3.1 7.3 + - - +
342A VAL* 2.8 43.3 + - + +
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Residues in contact with LEU 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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328A LEU* 5.3 1.1 - - + -
330A LEU* 4.1 9.3 - - + +
335A TYR* 2.9 52.1 + - + +
336A GLU* 4.2 4.7 - - - +
338A VAL* 1.3 77.7 - - - +
340A GLU* 1.3 57.1 + - - +
342A VAL* 3.2 9.2 + - + -
343A LEU* 2.8 64.3 + - + +
386A VAL* 5.0 1.8 - - + -
403A VAL* 4.3 6.1 - - + -
405A THR* 3.5 16.8 - - + +
425A VAL* 4.0 25.4 - - + -
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Residues in contact with GLU 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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336A GLU* 3.0 20.0 + - - +
337A PRO* 3.6 1.4 - - + +
339A LEU* 1.3 75.0 - - - +
341A ARG* 1.3 91.0 + - - +
343A LEU* 3.4 8.4 + - - +
344A LYS* 3.0 63.6 + - + +
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Residues in contact with ARG 341 (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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303A PHE* 3.7 32.5 - - - +
304A ASP* 2.9 33.9 + - - +
307A ALA* 3.5 17.3 - - + -
337A PRO* 2.9 42.2 + - - +
338A VAL 3.1 3.4 + - - +
340A GLU* 1.3 101.5 + - - +
342A VAL* 1.3 63.9 + - - +
344A LYS* 3.4 4.8 + - - +
345A ARG* 3.0 30.7 + - + +
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Residues in contact with VAL 342 (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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307A ALA* 4.0 20.4 - - - +
310A VAL* 4.1 10.3 - - + -
311A VAL* 4.0 15.2 - - + +
315A TYR* 5.5 1.6 - - + -
328A LEU* 4.0 14.8 - - + -
338A VAL* 2.8 38.1 + - + +
339A LEU* 3.7 12.8 - - + +
341A ARG* 1.3 72.3 - - - +
343A LEU* 1.3 58.8 + - - +
345A ARG* 3.4 1.6 + - - +
346A ALA* 2.8 34.0 + - + +
403A VAL* 5.0 6.7 - - + -
423A LEU* 4.2 23.3 - - + -
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Residues in contact with LEU 343 (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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339A LEU* 2.8 40.7 + - + +
340A GLU* 3.8 6.3 - - - +
342A VAL* 1.3 76.8 - - - +
344A LYS* 1.3 57.3 + - + +
346A ALA* 4.1 2.2 - - - +
347A GLU* 3.0 36.9 + - - +
386A VAL* 3.9 35.9 - - + +
387A LEU* 3.9 25.7 - - + +
403A VAL* 4.0 16.8 - - + -
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Residues in contact with LYS 344 (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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340A GLU* 3.0 42.1 + - + +
341A ARG* 3.7 6.3 - - + +
343A LEU* 1.3 75.8 - - + +
345A ARG* 1.3 62.7 + - + +
347A GLU* 3.4 21.7 - - - +
348A ARG* 3.2 40.0 + - - +
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Residues in contact with ARG 345 (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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304A ASP* 3.5 32.5 + - - +
307A ALA* 4.0 10.4 - - + +
308A GLU* 3.5 45.1 - - - +
311A VAL* 3.9 14.6 - - + -
341A ARG* 3.0 17.4 + - + +
342A VAL 3.9 3.1 - - - +
344A LYS* 1.3 76.6 - - + +
346A ALA* 1.3 64.1 + - - +
348A ARG* 3.1 46.1 + - - +
349A LEU* 3.7 10.5 + - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 4.3 4.7 - - + +
315A TYR* 4.0 26.7 - - + +
342A VAL* 2.8 24.9 + - + +
343A LEU* 4.6 0.2 - - - -
345A ARG* 1.3 74.2 - - - +
347A GLU* 1.3 62.8 + - - +
348A ARG 3.1 1.1 + - - -
349A LEU* 3.2 29.3 + - + +
387A LEU* 3.6 22.6 - - + +
401A PRO* 4.2 9.2 - - + +
403A VAL* 5.0 0.7 - - + -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.0 18.6 + - - +
344A LYS* 3.4 29.6 - - - +
346A ALA* 1.3 77.3 - - - +
348A ARG* 1.3 63.5 + - + +
349A LEU 3.4 3.6 + - - +
387A LEU* 3.8 24.7 - - + +
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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