Contacts of the helix formed by residues 364 - 385 (chain D) in PDB entry 6CP3
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 GLY 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360D ALA 2.9 15.7 + - - -
361D ALA 4.9 0.2 - - - -
362D VAL 3.5 2.6 + - - -
363D VAL* 1.3 81.3 - - - +
365D GLN* 1.3 61.0 + - - -
366D GLU* 3.2 3.8 - - - -
367D HIS 3.3 0.9 + - - -
368D TYR* 3.0 27.4 + - - +
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A ASN* 5.7 5.7 + - - +
360D ALA* 3.6 20.6 + - - +
364D GLY* 1.3 69.6 - - - -
366D GLU* 1.3 60.1 + - - +
368D TYR* 4.0 13.4 - - - -
369D ASP* 2.9 72.0 + - - +
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Residues in contact with GLU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D GLY* 5.0 0.9 - - - -
365D GLN* 1.3 78.9 - - - +
367D HIS* 1.3 57.6 + - - +
369D ASP* 3.8 3.6 - - - +
370D VAL* 3.0 39.7 + - + +
438D VAL* 4.2 19.3 - - + +
439D ALA* 5.1 8.0 + - - +
442D LYS* 4.9 22.0 + - - +
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Residues in contact with HIS 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE* 5.5 2.2 - - + +
142D ASP 3.0 22.2 + - - -
143D LEU* 3.2 30.7 + - + +
146D PRO* 5.2 4.9 - - + -
358D LEU* 4.1 13.9 - - + +
363D VAL* 3.3 46.3 - - + +
364D GLY 3.3 2.2 + - - -
366D GLU* 1.3 78.9 - - - +
368D TYR* 1.3 57.0 + - - +
370D VAL* 3.4 2.4 + - - +
371D ALA* 3.0 26.5 + - - +
434D LEU* 4.1 10.4 - - + +
438D VAL* 3.4 39.3 - - + -
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Residues in contact with TYR 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 2.9 30.9 + - - -
433A ASN* 4.4 16.6 + - - -
600A ATP 3.4 20.0 + - - -
358D LEU* 3.2 39.9 - - + -
359D ASP* 4.2 1.3 - - - -
360D ALA* 3.8 38.4 - - + -
363D VAL* 4.7 2.7 - - + -
364D GLY 3.0 16.6 + - - +
365D GLN* 3.9 8.5 - - - +
367D HIS* 1.3 80.5 + - - +
369D ASP* 1.3 69.7 + - - +
371D ALA* 3.4 6.3 + - - +
372D SER* 2.9 39.0 + - - -
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Residues in contact with ASP 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D GLN* 2.9 54.1 + - - +
366D GLU* 3.9 4.3 - - - +
368D TYR* 1.3 80.4 - - - +
370D VAL* 1.3 61.4 + - + +
372D SER* 3.3 8.2 + - - -
373D LYS* 2.9 41.2 + - + +
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Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LEU* 4.0 13.7 - - + -
366D GLU* 3.0 24.8 + - + +
367D HIS* 3.8 6.3 - - - +
369D ASP* 1.3 74.5 - - + +
371D ALA* 1.3 59.4 + - - +
373D LYS* 3.3 3.9 + - - +
374D VAL* 3.0 30.5 + - + +
438D VAL* 4.3 16.8 - - + +
441D PHE* 3.7 31.0 - - + -
442D LYS* 4.0 29.6 - - + -
445D LEU* 3.7 14.2 - - + +
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LEU* 4.1 23.3 - - - +
144D LEU* 4.6 10.5 - - + +
358D LEU* 4.2 26.2 - - + -
367D HIS 3.0 17.9 + - - +
368D TYR* 3.5 5.4 - - + +
369D ASP 3.3 0.2 - - - -
370D VAL* 1.3 78.6 - - - +
372D SER* 1.3 56.3 + - - +
374D VAL* 3.8 5.4 - - - +
375D GLN* 3.0 34.1 + - - +
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Residues in contact with SER 372 (chain D).
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* 6.5 0.9 - - - -
364A ARG* 4.3 14.3 + - - +
368D TYR* 2.9 32.0 + - - -
369D ASP* 3.5 12.9 + - - -
370D VAL 3.2 0.2 - - - -
371D ALA* 1.3 77.0 - - - +
373D LYS* 1.3 58.9 + - - +
375D GLN* 3.3 9.9 + - - +
376D GLU* 2.9 43.1 + - - +
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Residues in contact with LYS 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D ASP* 2.9 29.9 + - + +
370D VAL* 3.3 3.6 + - - +
372D SER* 1.3 73.8 - - - +
374D VAL* 1.3 60.6 + - - +
376D GLU* 3.5 11.7 + - - +
377D THR* 2.8 35.3 + - - +
442D LYS* 4.2 22.4 - - - +
445D LEU* 3.7 37.1 - - + +
446D GLU* 5.2 5.7 - - - +
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Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 4.1 22.9 - - + -
144D LEU* 4.4 9.9 - - + -
370D VAL* 3.0 21.7 + - + +
371D ALA* 3.8 3.8 - - - +
373D LYS* 1.3 74.6 - - - +
375D GLN* 1.3 57.9 + - - +
377D THR* 3.3 4.0 + - - -
378D LEU* 3.0 49.6 + - + +
410D ILE* 3.9 16.2 - - + -
414D LEU* 5.8 1.8 - - + -
441D PHE* 3.9 22.0 - - + -
445D LEU* 3.8 22.2 - - + -
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Residues in contact with GLN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 4.3 6.9 - - - -
360A TYR* 3.3 47.8 - - + +
364A ARG* 3.0 29.2 + - - +
144D LEU* 5.3 9.3 - - + +
350D PRO 4.9 5.8 + - - +
351D LEU* 3.8 17.8 + - + +
354D LYS* 4.9 5.7 - - - +
358D LEU* 4.9 12.5 - - - +
371D ALA 3.0 22.3 + - - +
372D SER* 3.7 5.2 - - - +
374D VAL* 1.3 80.2 - - - +
376D GLU* 1.3 56.7 + - + +
378D LEU* 3.5 1.5 + - - -
379D GLN* 3.0 28.9 + - - +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TYR 3.5 7.4 - - - +
361A LYS* 3.1 34.1 - - - +
362A GLY* 3.6 8.5 - - - +
431A LYS* 3.2 22.1 + - - -
372D SER* 2.9 27.6 + - - +
373D LYS* 3.9 11.2 - - - +
375D GLN* 1.3 75.5 - - + +
377D THR* 1.3 60.3 + - - +
379D GLN* 3.3 1.4 + - - +
380D THR* 2.9 37.3 + - + +
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Residues in contact with THR 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D LYS* 2.8 23.4 + - - +
374D VAL* 3.7 6.1 - - - -
376D GLU* 1.3 75.4 - - - +
378D LEU* 1.3 61.2 + - + +
380D THR* 2.7 21.1 + - - -
381D TYR* 3.0 15.6 + - - +
403D THR* 4.4 13.0 - - + +
406D ARG* 4.7 5.2 - - + -
407D ALA* 3.8 29.7 - - + +
410D ILE* 4.4 14.6 - - + -
445D LEU* 4.1 9.4 - - + +
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Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D PRO* 3.8 36.3 - - + +
351D LEU* 4.1 15.2 - - + +
374D VAL* 3.0 36.3 + - + +
375D GLN* 3.9 3.8 - - - +
377D THR* 1.3 77.5 - - - +
379D GLN* 1.3 58.4 + - - +
381D TYR* 3.4 11.1 + - + +
382D LYS* 3.0 28.4 + - - +
407D ALA* 4.1 25.4 - - + +
410D ILE* 4.8 7.6 - - + -
411D GLN* 4.5 17.9 - - + +
414D LEU* 5.1 4.5 - - + -
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Residues in contact with GLN 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A GLU* 4.1 23.4 - - - +
360A TYR* 3.3 54.7 - - + +
361A LYS* 3.9 18.0 - - + +
351D LEU* 3.7 15.4 - - + +
375D GLN 3.0 10.5 + - - +
376D GLU* 3.6 3.4 - - - +
377D THR 3.3 0.4 - - - -
378D LEU* 1.3 77.5 - - - +
380D THR* 1.3 58.9 + - + +
382D LYS* 3.1 11.9 + - - +
383D SER* 2.9 44.6 + - - +
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Residues in contact with THR 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LYS* 5.6 10.1 - - + -
407A GLN* 6.2 2.9 - - - +
376D GLU* 2.9 19.4 + - + +
377D THR* 2.7 24.8 + - - -
379D GLN* 1.3 77.6 - - + +
381D TYR* 1.3 55.8 + - - +
383D SER* 3.5 6.8 + - - +
384D LEU* 2.9 39.0 + - - +
403D THR* 3.7 18.8 - - + +
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Residues in contact with TYR 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C PHE* 4.8 6.2 - - - -
377D THR 3.0 14.0 + - - +
378D LEU* 3.5 15.0 - - + +
379D GLN 3.2 0.2 - - - -
380D THR* 1.3 78.5 + - - +
382D LYS* 1.3 63.6 + - + +
384D LEU* 3.2 6.8 + - + +
385D GLN* 3.0 61.0 + - + +
403D THR* 5.4 1.3 - - - +
404D VAL* 3.7 29.2 - - + +
407D ALA* 3.6 25.4 - - + -
408D ARG* 3.4 35.7 + - + +
411D GLN* 3.9 18.9 + - - -
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Residues in contact with LYS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TYR* 6.3 0.6 - - - -
349D ASP* 5.2 8.7 + - - -
351D LEU* 3.7 28.2 - - + +
378D LEU 3.0 17.2 + - - +
379D GLN* 3.1 14.3 + - - +
381D TYR* 1.3 79.1 - - + +
383D SER* 1.3 61.7 + - - +
385D GLN* 3.5 20.4 + - + +
386D ASP* 4.6 5.5 + - - +
11G LYS* 6.0 4.5 - - - +
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Residues in contact with SER 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A GLU* 4.6 6.6 + - - -
361A LYS* 4.5 11.7 + - - -
407A GLN* 5.6 9.0 - - - -
379D GLN* 2.9 33.1 + - - +
380D THR* 3.9 7.0 - - - -
382D LYS* 1.3 75.4 - - - +
384D LEU* 1.3 65.9 + - - +
385D GLN 3.1 1.1 + - - -
386D ASP* 3.5 23.6 + - - +
387D ILE* 4.7 2.6 + - - +
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A GLN* 3.7 31.9 - - + +
380D THR* 2.9 27.4 + - - +
381D TYR* 3.2 5.6 + - + +
383D SER* 1.3 72.8 - - - +
385D GLN* 1.3 57.8 + - - +
386D ASP 3.1 10.3 + - - -
387D ILE* 3.1 31.4 + - + +
388D ILE* 3.3 26.6 - - + +
396D LEU* 4.1 22.0 - - + -
400D ASP* 4.5 15.3 - - + +
403D THR* 5.5 6.1 - - + -
404D VAL* 3.8 23.8 - - + -
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Residues in contact with GLN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C PHE* 5.3 12.8 - - - -
381D TYR* 3.0 63.0 + - + +
382D LYS* 3.6 14.4 - - + +
383D SER 3.1 1.6 - - - -
384D LEU* 1.3 76.5 - - - +
386D ASP* 1.3 61.9 + - - +
388D ILE* 4.3 21.0 - - - +
389D ALA* 3.8 22.2 + - - +
404D VAL* 5.4 0.4 - - - +
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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
------------------------------------------------------------
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