Contacts of the helix formed by residues 365 - 383 (chain B) 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 SER 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B ASP* 3.7 21.1 + - - -
363B VAL* 3.3 2.8 + - - +
364B VAL* 1.3 82.3 - - - +
366B ALA* 1.3 59.3 + - - +
367B GLU* 3.3 10.2 + - - +
368B GLN* 3.0 26.9 + - - +
369B GLU* 2.9 28.1 + - - +
397B TYR* 3.7 16.2 - - - -
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B SER* 1.3 75.1 - - - +
367B GLU* 1.3 56.8 + - - +
369B GLU* 3.4 7.1 + - - +
370B ARG* 2.9 29.5 + - - +
397B TYR* 3.4 32.8 + - + +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B SER* 3.2 9.6 + - - +
366B ALA* 1.3 76.0 - - - +
368B GLN* 1.3 67.1 + - - +
370B ARG* 2.7 49.7 + - - +
371B LYS* 2.9 28.7 + - + +
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TRP* 3.8 23.9 - - + +
211B ASP* 5.9 0.2 - - - +
320B GLN* 4.5 0.7 - - - +
363B VAL* 4.2 8.1 - - + -
364B VAL* 3.7 26.0 - - + +
365B SER* 3.0 27.7 + - - +
367B GLU* 1.3 81.0 - - - +
369B GLU* 1.3 66.7 + - - +
371B LYS* 3.2 27.3 + - - +
372B VAL* 2.9 31.2 + - + +
418B ILE 4.6 0.7 - - - +
419B PHE* 4.0 22.1 - - - +
2518B NAD 5.0 4.6 + - - -
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B VAL* 3.7 12.9 - - + +
365B SER 2.9 14.2 + - - +
366B ALA* 3.5 11.9 - - - +
368B GLN* 1.3 75.2 - - - +
370B ARG* 1.3 58.0 + - - +
372B VAL* 3.9 0.5 - - - +
373B LEU* 2.9 51.1 + - + +
391B ARG* 2.4 46.4 + - - +
397B TYR* 3.5 24.5 - - + -
399B ILE* 4.0 14.8 - - + -
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA 2.9 16.8 + - - +
367B GLU* 2.7 41.5 + - - +
369B GLU* 1.3 77.3 + - - +
371B LYS* 1.3 70.8 + - - +
373B LEU* 4.0 5.5 - - - +
374B SER* 2.8 49.4 + - - +
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Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLU* 2.9 17.6 + - + +
368B GLN* 3.6 24.5 + - - +
370B ARG* 1.3 88.8 - - - +
372B VAL* 1.3 64.4 + - + +
374B SER* 3.2 7.0 + - - -
375B TYR* 3.0 42.5 + - + -
417B GLU* 3.2 25.2 + - - +
418B ILE 3.2 23.4 + - - +
419B PHE* 4.2 10.4 - - - +
2518B NAD 6.0 1.6 + - - -
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B VAL* 4.7 6.1 - - + -
368B GLN* 2.9 25.7 + - - +
371B LYS* 1.3 75.7 - - + +
373B LEU* 1.3 64.7 + - - +
375B TYR* 3.1 4.2 + - - +
376B ILE* 3.0 29.2 + - + +
399B ILE* 3.8 24.2 - - + -
418B ILE* 4.0 19.3 - - + +
419B PHE 4.2 4.5 - - - +
420B GLY* 3.9 20.2 - - - -
421B PRO* 4.2 9.0 - - + -
422B VAL* 3.9 26.0 - - + -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B GLU* 2.9 42.1 + - + +
370B ARG* 4.1 4.7 - - - +
372B VAL* 1.3 76.1 - - - +
374B SER* 1.3 63.0 + - - +
376B ILE* 3.2 23.5 + - + +
377B GLU* 3.0 27.8 + - + +
389B GLY 5.1 1.8 - - - +
390B LYS* 4.6 2.2 - - - -
391B ARG* 4.1 36.6 - - + +
399B ILE* 4.4 11.7 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 2.8 39.9 + - - +
371B LYS* 3.5 7.0 - - - -
372B VAL 3.2 0.2 - - - -
373B LEU* 1.3 77.4 - - - +
375B TYR* 1.3 58.3 + - - +
377B GLU* 3.2 10.8 + - - +
378B ILE* 3.0 35.9 + - - +
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Residues in contact with TYR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B LYS* 3.0 49.4 + - + -
372B VAL 3.1 7.1 + - - +
374B SER* 1.3 73.2 - - - +
376B ILE* 1.3 55.6 + - - +
378B ILE* 3.3 14.2 + - + +
379B GLY* 2.8 31.5 + - - -
404B PHE* 4.9 1.2 - - - -
412B ARG* 4.1 16.4 + - + -
413B ILE* 3.6 18.1 - - + +
416B GLU* 2.7 47.9 + - + +
417B GLU 4.2 3.9 + - - -
418B ILE* 3.7 44.2 - - + -
422B VAL* 5.9 0.7 - - + -
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Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL* 3.0 32.0 + - + +
373B LEU* 3.4 25.1 - - + +
375B TYR* 1.3 77.1 - - - +
377B GLU* 1.3 66.5 + - - +
379B GLY 3.2 0.7 + - - -
380B LYS* 3.1 37.7 + - - +
385B LEU* 5.5 0.2 - - + -
389B GLY* 3.4 42.0 - - - +
399B ILE* 4.2 7.2 - - + -
402B THR* 4.1 17.0 - - + +
404B PHE* 3.5 14.5 - - + -
422B VAL* 4.2 14.6 - - + -
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 3.0 18.2 + - + +
374B SER* 3.2 11.6 + - - +
376B ILE* 1.3 79.6 - - - +
378B ILE* 1.3 63.5 + - + +
380B LYS* 2.8 50.9 + - - +
381B ASN* 3.4 16.6 + - - -
389B GLY 5.4 0.2 - - - +
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B SER* 3.0 23.4 + - - +
375B TYR* 3.6 22.4 - - + +
377B GLU* 1.3 73.8 - - + +
379B GLY* 1.3 62.3 + - - +
381B ASN* 3.0 20.0 + - - +
382B GLU* 3.3 38.6 + - + +
412B ARG* 3.5 47.1 - - + +
413B ILE* 4.3 4.0 - - + -
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TYR 2.8 19.9 + - - -
376B ILE 3.2 3.1 + - - -
378B ILE* 1.3 74.5 - - - +
380B LYS* 1.3 55.2 + - - +
381B ASN 3.0 0.2 - - - -
382B GLU* 3.0 2.2 + - - -
383B GLY 2.8 31.7 + - - +
404B PHE* 3.4 18.8 - - - -
413B ILE* 3.7 22.7 - - - -
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ILE* 3.1 28.3 + - - +
377B GLU* 2.8 43.3 + - - +
378B ILE 3.2 0.4 - - - -
379B GLY* 1.3 76.2 - - - +
381B ASN* 1.3 63.4 + - - +
383B GLY 3.7 10.3 - - - +
385B LEU* 4.1 24.5 - - + +
389B GLY 4.6 5.9 + - - -
404B PHE* 3.9 12.8 - - + -
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Residues in contact with ASN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLU 3.4 19.0 + - - -
378B ILE* 3.0 10.0 + - - +
379B GLY 3.0 0.4 - - - -
380B LYS* 1.3 83.3 - - - +
382B GLU* 1.3 63.1 + - + +
383B GLY 4.7 0.4 - - - -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ILE* 3.5 23.7 - - + +
379B GLY 3.0 3.2 + - - +
381B ASN* 1.3 84.2 - - + +
383B GLY* 1.3 59.4 + - - +
406B GLU 4.0 2.3 - - - +
407B VAL* 5.2 0.2 - - - -
408B PRO* 3.3 23.8 - - + +
411B ALA* 3.6 16.8 - - + -
412B ARG* 2.9 32.8 + - - +
413B ILE* 3.0 42.4 + - + +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B GLY 2.8 17.3 + - - +
380B LYS* 3.7 13.7 - - - +
381B ASN 4.7 0.3 - - - -
382B GLU* 1.3 80.0 - - - +
384B GLN* 1.3 61.1 + - - -
385B LEU 4.0 1.2 + - - -
404B PHE* 4.3 3.1 - - - -
405B THR 3.5 10.3 - - - -
406B GLU* 4.0 6.7 - - - -
407B VAL* 4.4 11.4 - - - -
413B ILE* 4.8 1.2 - - - +
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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