Contacts of the helix formed by residues 361 - 376 (chain A) in PDB entry 5E97
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.9 12.8 - - + -
346A SER* 5.4 4.0 - - - +
355A LEU 3.5 10.4 + - - +
356A SER* 3.5 27.8 - - - +
357A ASP 5.0 0.2 - - - -
358A THR 3.1 15.0 + - - +
360A ALA* 1.3 79.1 - - - +
362A GLY* 1.3 61.1 + - - +
363A PHE 3.4 0.5 + - - -
364A MET* 3.4 7.5 + - - +
365A TRP* 3.2 19.9 + - - +
382A ARG* 5.4 0.2 - - - +
403A ASP* 3.6 14.7 - - - +
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Residues in contact with GLY 362 (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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359A PHE 3.0 7.1 + - - -
361A ALA* 1.3 77.0 - - - +
363A PHE* 1.3 60.2 + - - +
365A TRP 4.3 0.4 - - - -
366A LEU* 2.8 34.3 + - - +
403A ASP* 3.2 17.3 + - - -
406A LEU* 3.7 8.2 - - - +
529A TYR* 3.5 23.1 - - - -
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Residues in contact with PHE 363 (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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310A PHE 3.8 11.0 - - - +
311A LEU* 3.4 28.0 - - + -
316A LEU* 4.5 7.9 - - + -
359A PHE* 4.1 4.7 - + - -
360A ALA* 3.3 32.5 - - - +
361A ALA 3.3 1.2 - - - -
362A GLY* 1.3 75.2 - - - +
364A MET* 1.3 57.5 + - - +
367A ASP* 2.9 35.7 + - - +
455A ILE* 3.6 21.4 - - + +
456A ASN 4.2 0.9 - - - -
457A LEU* 3.5 26.2 - - + -
488A LEU* 4.5 4.3 - - + -
527A PHE* 3.5 41.1 - - + -
528A SER 3.8 6.3 - - - -
529A TYR* 3.6 27.4 - + - -
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Residues in contact with MET 364 (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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299A TYR* 3.5 30.7 + - + -
300A LEU* 3.7 21.1 - - + -
309A ASP 3.9 9.6 - - - +
310A PHE* 4.1 23.1 - - + +
315A VAL* 3.6 31.4 - - + -
316A LEU* 3.6 22.2 - - + -
346A SER* 3.7 31.0 - - - +
360A ALA 4.6 1.0 + - - -
361A ALA 3.4 9.0 + - - +
362A GLY 3.4 0.4 - - - -
363A PHE* 1.3 79.4 - - - +
365A TRP* 1.3 62.2 + - - +
368A LYS* 3.0 26.9 + - - +
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Residues in contact with TRP 365 (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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344A THR* 4.2 9.2 - - + -
345A SER* 5.9 2.5 - - - -
361A ALA 3.2 8.6 + - - +
362A GLY 4.0 2.7 - - - +
363A PHE 3.3 0.2 - - - -
364A MET* 1.3 79.5 - - - +
366A LEU* 1.3 63.5 + - - +
368A LYS* 4.5 11.0 - - + -
369A LEU* 3.0 54.3 + - + +
380A VAL* 3.8 25.8 - - + -
382A ARG* 3.2 65.3 - - + +
403A ASP* 3.8 16.8 - - - +
406A LEU* 3.9 21.5 - - + -
407A SER* 2.8 25.6 + - - +
57B LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 366 (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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362A GLY 2.8 20.4 + - - +
365A TRP* 1.3 74.8 - - - +
367A ASP* 1.3 57.6 + - - +
369A LEU* 3.3 5.7 + - + +
370A GLY* 3.0 25.6 + - - -
406A LEU* 4.2 19.7 - - + +
410A PHE* 3.6 26.2 - - + -
434A TYR* 4.7 0.5 - - - -
453A TYR* 3.6 37.0 - - + -
454A ALA 4.5 4.3 - - - +
455A ILE* 3.9 15.9 - - + -
529A TYR* 3.7 30.7 - - + -
530A SER 5.0 1.8 - - - +
531A PHE* 4.1 11.7 - - + -
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Residues in contact with ASP 367 (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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299A TYR* 4.9 1.7 + - - +
316A LEU* 3.6 20.6 - - + +
363A PHE 2.9 20.1 + - - +
364A MET 4.1 2.2 - - - +
366A LEU* 1.3 76.7 - - - +
368A LYS* 1.3 58.2 + - - +
370A GLY* 3.2 1.0 + - - -
371A LEU* 2.8 42.7 + - - +
432A ARG* 2.8 42.4 + - - -
434A TYR* 2.6 29.9 + - - -
455A ILE* 3.6 9.9 - - + +
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Residues in contact with LYS 368 (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 HIS* 3.1 25.7 + - - -
299A TYR* 3.4 25.9 + - + +
319A PHE* 3.9 21.7 - - + -
341A LEU* 4.0 4.0 - - + -
344A THR* 2.7 40.5 + - + +
345A SER 3.2 22.6 + - - +
364A MET 3.0 19.0 + - - +
365A TRP* 3.7 15.9 - - + +
367A ASP* 1.3 76.2 - - - +
369A LEU* 1.3 58.1 + - - +
371A LEU* 5.1 0.2 - - - -
372A SER* 2.8 45.3 + - - +
380A VAL* 4.8 2.0 - - + -
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Residues in contact with LEU 369 (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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365A TRP* 3.0 64.7 + - + +
366A LEU* 3.6 9.4 - - + +
368A LYS* 1.3 76.6 - - - +
370A GLY* 1.3 56.9 + - - +
372A SER* 4.5 0.7 - - - -
373A ALA* 2.9 28.1 + - - +
380A VAL* 4.1 15.0 - - + -
406A LEU* 6.0 0.9 - - + -
407A SER* 5.9 0.2 - - - -
410A PHE* 3.8 33.9 - - + -
453A TYR* 4.1 2.2 - - - -
56B PHE* 3.3 28.9 - - + -
57B LEU* 3.9 21.3 - - + -
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Residues in contact with GLY 370 (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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366A LEU 3.0 12.0 + - - -
367A ASP 3.6 2.7 - - - -
369A LEU* 1.3 78.7 - - - +
371A LEU* 1.3 56.5 + - - +
373A ALA* 3.9 1.4 - - - +
374A ARG* 2.9 30.8 + - - +
434A TYR* 3.4 25.8 - - - -
436A HIS* 5.3 0.7 + - - -
453A TYR* 3.3 21.2 + - - -
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Residues in contact with LEU 371 (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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299A TYR* 5.6 0.2 - - - +
316A LEU 4.3 6.1 - - - +
319A PHE* 3.9 25.4 - - + -
320A ILE* 3.8 35.2 - - + -
367A ASP* 2.8 38.3 + - - +
368A LYS* 5.1 0.2 - - - -
370A GLY* 1.3 71.0 - - - +
372A SER* 1.3 66.6 + - - +
374A ARG* 3.3 5.5 + - + -
375A MET* 2.8 41.7 + - + +
432A ARG* 4.1 7.2 - - - +
434A TYR* 3.3 25.6 - - + +
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Residues in contact with SER 372 (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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319A PHE* 3.3 23.5 - - - -
323A VAL* 5.5 0.2 - - - -
341A LEU* 3.8 4.5 - - - +
368A LYS 2.8 23.7 + - - -
369A LEU 3.8 2.5 - - - -
371A LEU* 1.3 76.1 - - - +
373A ALA* 1.3 63.6 + - - +
375A MET* 3.9 1.6 - - - -
376A GLY 3.2 5.4 + - - -
377A ILE* 2.9 43.5 + - - +
380A VAL* 3.6 30.8 - - - +
56B PHE* 4.1 1.3 - - - -
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Residues in contact with ALA 373 (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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369A LEU 2.9 17.7 + - - +
370A GLY 3.9 1.8 - - - +
372A SER* 1.3 79.4 - - - +
374A ARG* 1.3 61.1 + - - +
375A MET 3.3 0.9 + - - -
376A GLY* 3.5 6.4 + - - -
418A VAL* 3.6 20.4 - - + +
436A HIS* 3.5 36.3 - - + +
50B HIS* 3.6 9.0 - - - +
52B VAL* 4.0 10.9 - - + +
56B PHE* 3.6 14.1 - - + -
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Residues in contact with ARG 374 (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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370A GLY 2.9 19.3 + - - +
371A LEU* 3.7 9.6 - - + +
373A ALA* 1.3 78.0 - - - +
375A MET* 1.3 61.4 - - + +
418A VAL* 4.0 8.6 - - + +
419A LEU 3.7 18.4 - - - -
420A MET* 3.5 39.4 - - - +
434A TYR* 4.8 11.2 - - + -
49B LEU* 3.6 32.5 - - - +
50B HIS* 3.1 16.0 + - - -
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Residues in contact with MET 375 (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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320A ILE* 3.6 36.8 - - + +
323A VAL* 3.6 31.9 - - + -
324A GLN* 3.5 34.8 - - + +
327A PHE* 3.4 18.1 - - + -
371A LEU* 2.8 32.9 + - + +
372A SER 4.3 2.0 - - - +
374A ARG* 1.3 80.8 - - + +
376A GLY* 1.3 58.2 + - - +
377A ILE 3.6 0.9 - - - -
50B HIS* 3.7 7.8 + - - -
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Residues in contact with GLY 376 (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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327A PHE* 3.6 17.9 - - - -
338A LYS* 6.0 1.4 - - - +
339A VAL 4.3 4.7 + - - +
372A SER 3.2 2.8 + - - -
373A ALA 3.5 3.3 + - - -
374A ARG 3.5 2.8 - - - -
375A MET* 1.3 78.8 - - - +
377A ILE* 1.3 64.8 + - - +
378A GLU* 3.5 5.4 + - - +
50B HIS* 3.6 29.7 - - - -
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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
------------------------------------------------------------
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