Contacts of the helix formed by residues 356 - 373 (chain A) in PDB entry 2V3E
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.3 2.2 - - - +
12A SER* 4.0 1.3 - - - -
353A ARG* 3.0 21.4 + - - -
354A LEU 3.4 0.2 - - - -
355A GLY* 1.3 74.2 - - - +
357A TRP* 1.3 62.6 + - - +
358A ASP* 3.7 0.2 - - - +
359A ARG* 3.1 40.7 + - - +
360A GLY 3.5 7.8 + - - -
414A GLN* 4.2 1.0 + - - -
415A PRO* 3.3 17.3 - - - +
416A MET 4.9 0.5 + - - -
1503A PO4 2.5 32.4 + - - -
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Residues in contact with TRP 357 (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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12A SER* 2.8 22.3 + - - +
13A SER* 3.9 9.0 - - - -
42A SER* 3.6 17.5 - - - -
43A THR 3.3 31.4 - - - -
44A ARG* 3.5 38.8 - - + -
48A ARG* 3.6 15.7 - - - -
355A GLY 3.2 3.0 + - - -
356A SER* 1.3 70.1 - - - +
358A ASP* 1.3 64.4 + - - +
360A GLY* 2.9 4.7 + - - -
361A MET* 2.9 59.6 + - + +
415A PRO* 3.8 14.1 - - + -
418A TYR* 6.1 0.9 - - + -
419A HIS* 3.2 34.3 - + - -
487A TYR* 3.4 32.9 + + + -
488A SER* 4.1 4.0 - - - -
1503A PO4 4.3 0.2 - - - +
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A SER* 3.7 3.8 - - - +
357A TRP* 1.3 77.1 - - - +
359A ARG* 1.3 59.5 + - - +
361A MET* 3.2 24.1 + - + +
362A GLN* 2.9 53.1 + - - +
1503A PO4 3.1 26.5 + - - +
242B SER* 4.4 11.7 + - - -
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Residues in contact with ARG 359 (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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343A VAL* 3.5 27.9 - - + +
344A GLY* 3.9 15.2 - - - +
349A GLU* 4.1 14.8 - - - +
350A GLN 2.7 23.6 + - - +
351A SER 3.0 19.6 + - - -
353A ARG* 3.6 29.7 - - - +
356A SER* 3.1 27.3 + - - +
358A ASP* 1.3 77.7 + - - +
360A GLY* 1.3 63.3 + - - +
362A GLN* 3.4 19.2 + - - +
363A TYR* 3.3 16.8 + - - -
399A ASP* 2.8 35.8 + - - +
416A MET* 3.5 18.8 - - + +
1503A PO4 5.1 0.2 + - - -
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A SER 3.5 6.1 + - - -
357A TRP 2.9 7.8 + - - -
359A ARG* 1.3 77.1 - - - +
361A MET* 1.3 61.3 + - - +
363A TYR* 3.0 14.2 + - - +
364A SER 3.1 10.0 + - - -
415A PRO* 4.0 2.0 - - - -
416A MET* 3.8 20.2 - - - +
419A HIS* 3.2 29.4 + - - -
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Residues in contact with MET 361 (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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357A TRP* 2.9 48.3 + - + +
358A ASP* 3.6 32.1 - - + +
360A GLY* 1.3 71.9 - - - +
362A GLN* 1.3 56.1 + - - +
364A SER* 3.4 8.6 + - - -
365A HIS* 2.8 34.9 + - - +
419A HIS* 3.6 8.4 - - + -
461A LEU* 3.9 3.4 - - + +
462A ASN 4.4 2.5 - - - +
463A ARG* 3.7 47.3 - - + +
487A TYR* 4.0 16.4 - - + -
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Residues in contact with GLN 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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312A TRP* 3.4 22.7 - - + -
343A VAL* 3.8 14.7 - - + +
349A GLU* 5.7 3.9 + - - +
358A ASP* 2.9 40.6 + - - +
359A ARG* 3.5 27.3 - - - +
361A MET* 1.3 77.0 - - - +
363A TYR* 1.3 63.1 + - - +
365A HIS* 4.1 4.2 + - - +
366A SER* 3.1 24.9 + - - -
242B SER* 4.9 12.9 + - - -
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Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A TRP* 3.7 22.2 - + - -
342A CYS* 3.6 16.4 - - - +
343A VAL* 3.9 15.0 - - + -
359A ARG 3.3 8.2 + - - +
360A GLY 3.0 9.9 + - - +
362A GLN* 1.3 79.1 - - - +
364A SER* 1.3 58.4 + - - +
366A SER* 3.3 2.8 + - - -
367A ILE* 2.9 38.0 + - + +
378A TRP* 3.6 24.9 - + + -
380A ASP* 2.4 37.5 + - - -
399A ASP 5.0 1.2 + - - -
401A PRO* 3.9 6.2 - - + +
416A MET* 3.4 45.6 - - + -
419A HIS* 4.6 7.2 - - + -
420A LEU* 3.8 16.8 - - + +
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY 3.1 2.0 + - - -
361A MET 3.4 3.3 + - - -
363A TYR* 1.3 79.2 - - - +
365A HIS* 1.3 57.0 + - - +
367A ILE* 3.8 0.6 - - - -
368A ILE* 2.9 34.9 + - - +
419A HIS* 2.8 33.6 + - - -
423A PHE* 3.6 17.1 - - - -
461A LEU* 3.2 23.2 - - - +
489A ILE* 3.5 20.9 - - - -
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Residues in contact with HIS 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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361A MET 2.8 20.5 + - - +
362A GLN* 4.1 4.3 + - - +
364A SER* 1.3 78.2 + - - +
366A SER* 1.3 62.3 + - - +
368A ILE* 4.0 3.5 - - - +
369A THR* 2.8 47.3 + - + -
445A ASP* 3.5 32.9 + - - -
461A LEU* 3.5 6.0 - - - +
463A ARG* 3.6 37.1 + - - +
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A TRP* 3.5 26.8 - - - +
315A ASP* 4.5 7.1 + - - -
362A GLN 3.1 19.1 + - - -
363A TYR 3.7 2.9 - - - -
365A HIS* 1.3 78.9 + - - +
367A ILE* 1.3 56.9 + - - +
369A THR* 3.3 3.8 + - - -
370A ASN* 2.6 46.5 + - - +
378A TRP* 2.8 26.8 + - - -
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Residues in contact with ILE 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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81A PHE* 3.8 13.5 - - + -
363A TYR 2.9 26.0 + - - +
364A SER 3.3 3.8 + - - +
366A SER* 1.3 74.1 - - - +
368A ILE* 1.3 66.0 + - - +
370A ASN* 3.6 1.2 - - - +
371A LEU* 2.9 32.8 + - + +
378A TRP* 3.5 34.8 - - + -
420A LEU* 3.7 35.0 - - + -
423A PHE* 3.5 46.0 - - + -
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Residues in contact with ILE 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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364A SER 2.9 24.5 + - - +
365A HIS 4.0 3.1 - - - +
367A ILE* 1.3 72.5 - - - +
369A THR* 1.3 59.4 + - - +
371A LEU* 3.3 2.6 + - - +
372A LEU* 2.9 49.2 + - + +
423A PHE* 3.7 23.3 - - + -
445A ASP* 3.6 34.5 - - + +
446A ALA 3.9 21.1 - - - +
447A VAL* 4.0 14.1 - - + -
459A VAL* 4.6 8.1 - - + +
461A LEU* 3.7 22.9 - - + +
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Residues in contact with THR 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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285A ARG* 4.8 11.4 - - - +
320A ALA* 3.9 24.9 - - + -
365A HIS* 2.8 43.9 + - + -
366A SER* 3.8 4.9 - - - -
368A ILE* 1.3 77.5 - - - +
370A ASN* 1.3 65.1 - - - +
372A LEU* 3.3 8.9 + - - +
373A TYR* 3.2 30.1 + - + +
445A ASP* 5.4 0.7 + - - -
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Residues in contact with ASN 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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285A ARG* 4.1 19.0 - - - +
310A VAL* 4.5 6.6 - - - +
312A TRP* 6.3 0.2 - - - +
315A ASP* 4.9 1.6 + - - -
324A LEU* 4.3 6.4 - - - +
338A ALA* 3.4 24.3 - - - +
366A SER* 2.6 44.2 + - - +
367A ILE 3.6 3.8 - - - +
369A THR* 1.3 72.2 - - - +
371A LEU* 1.3 57.3 + - + +
373A TYR 2.9 19.6 + - - -
375A VAL* 3.2 44.2 + - + +
378A TRP* 3.8 12.9 + - + -
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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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76A GLN* 2.7 28.4 + - - +
78A VAL* 4.5 20.0 - - + -
81A PHE* 4.6 15.7 - - + -
367A ILE* 2.9 42.2 + - + +
368A ILE 3.7 3.6 - - - +
370A ASN* 1.3 74.3 - - + +
372A LEU* 1.3 59.0 + - - +
373A TYR 3.3 0.3 + - - -
375A VAL* 3.5 18.2 - - + +
376A VAL 5.3 3.1 - - - -
377A GLY 5.4 1.3 - - - +
423A PHE* 4.1 13.0 - - + -
427A ILE* 4.6 7.6 - - + -
433A ARG* 2.8 18.4 + - - -
447A VAL* 4.1 28.9 - - + -
449A LEU* 4.6 4.9 - - + -
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Residues in contact with LEU 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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368A ILE* 2.9 40.1 + - + +
369A THR* 3.7 7.9 - - - +
370A ASN 3.2 0.4 - - - -
371A LEU* 1.3 76.3 - - - +
373A TYR* 1.3 75.6 - - + +
374A HIS* 3.6 3.4 + - - -
433A ARG* 3.4 29.2 + - - +
434A VAL 6.2 0.2 - - - +
436A LEU* 6.1 3.6 - - + +
445A ASP* 6.1 0.4 - - - -
446A ALA 3.8 19.5 - - - +
447A VAL* 4.0 17.3 - - + -
448A ALA 5.5 0.2 - - - +
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Residues in contact with TYR 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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320A ALA* 3.5 27.4 - - + -
321A LYS* 3.5 37.9 - - + +
324A LEU* 3.7 30.9 - - + +
325A GLY* 4.0 13.7 - - - -
336A LEU* 3.8 3.1 - - - +
369A THR* 3.2 29.5 + - + +
370A ASN 2.9 9.3 + - - +
372A LEU* 1.3 90.6 - - + +
374A HIS* 1.3 75.0 + + - +
375A VAL* 3.3 7.3 + - - +
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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