Contacts of the strand formed by residues 357 - 372 (chain D) in PDB entry 2C11
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 GLU 357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353D ARG* 3.3 2.6 - - - -
354D PHE 2.8 32.1 + - - +
355D GLN 3.3 2.9 + - - +
356D GLY* 1.3 75.3 - - - +
358D ARG* 1.3 72.4 + - - +
359D LEU* 3.4 7.6 + - + +
533D ALA* 3.7 14.7 - - - -
601D ARG* 2.8 36.8 + - - -
710D PHE* 3.4 23.8 - - + -
711D PHE* 5.8 0.6 - - + -
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Residues in contact with ARG 358 (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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110D LEU* 3.9 27.0 - - - +
113D LEU* 4.5 5.3 - - - +
114D ASP* 2.9 35.8 + - - -
351D ASP* 3.2 28.9 - - - +
352D VAL 3.3 8.3 - - - +
353D ARG* 2.7 53.8 - - + +
356D GLY 3.6 4.6 + - - -
357D GLU* 1.3 81.7 - - - +
359D LEU* 1.3 61.6 + - - +
360D VAL 3.5 17.9 - - - +
361D TYR* 4.5 6.5 - - - +
531D ASP* 3.6 21.9 + - + +
533D ALA* 4.4 4.2 + - - -
534D GLY 5.0 1.0 + - - -
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Residues in contact with LEU 359 (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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335D TRP* 3.7 31.4 - - + -
352D VAL 3.0 7.4 + - - +
354D PHE* 4.0 10.5 - - + -
357D GLU* 3.7 14.1 - - + +
358D ARG* 1.3 75.0 - - - +
360D VAL* 1.3 66.1 + - + +
483D GLY 4.2 0.4 - - - +
485D ILE* 4.4 8.3 - - + -
530D LEU* 3.3 13.3 - - + +
531D ASP 2.7 38.7 + - - -
532D VAL* 3.6 2.4 + - - +
603D TYR* 3.7 31.4 - - + +
710D PHE* 3.3 40.6 - - + -
711D PHE* 5.2 0.2 - - + -
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Residues in contact with VAL 360 (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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351D ASP* 3.4 2.6 - - - -
352D VAL* 3.0 36.9 + - + -
358D ARG* 3.5 7.1 - - - +
359D LEU* 1.3 85.1 - - + +
361D TYR* 1.3 61.5 + - - +
362D GLU* 3.2 20.0 - - - +
363D ILE* 3.1 43.7 - - + -
485D ILE* 4.4 12.8 - - + -
529D ASP 3.6 13.9 - - - +
530D LEU* 3.2 25.8 - - + +
531D ASP* 4.9 0.4 - - - -
705D LEU* 4.4 1.6 - - + -
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Residues in contact with TYR 361 (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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60D PHE* 3.5 27.3 - + - -
104D PRO 3.6 9.0 + - - -
106D LYS* 3.4 34.2 - - + -
109D ALA* 3.2 26.1 - - + +
110D LEU* 3.3 30.1 - - + -
113D LEU* 5.8 0.9 - - + -
350D PHE* 3.1 14.8 - + - +
351D ASP* 2.9 24.9 + - + +
358D ARG* 4.5 7.6 - - - +
360D VAL* 1.3 74.3 - - - +
362D GLU* 1.3 77.4 + - + +
529D ASP* 3.1 27.9 + - - +
531D ASP* 3.3 21.7 + - - +
637D ARG* 4.6 5.6 - - - -
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Residues in contact with GLU 362 (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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103D LEU* 4.8 8.7 - - - +
349D ILE 3.3 7.2 - - - +
350D PHE* 3.5 30.5 - - + +
360D VAL* 3.2 9.4 - - - +
361D TYR* 1.3 99.8 - - + +
363D ILE* 1.3 59.4 + - - +
364D SER* 2.6 31.8 + - - +
366D GLN* 4.1 1.6 + - - -
527D LYS* 3.3 35.8 + - + +
529D ASP* 2.8 37.1 + - + +
637D ARG* 4.4 5.0 + - - -
642D PRO 4.7 1.0 - - - +
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Residues in contact with ILE 363 (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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347D PRO 4.7 0.2 - - - +
348D ARG* 3.7 1.7 - - - -
349D ILE* 2.8 37.7 + - + +
352D VAL* 5.4 4.5 - - + -
360D VAL* 3.1 31.6 - - + -
362D GLU* 1.3 71.4 - - - +
364D SER* 1.3 60.8 + - - +
477D THR* 6.1 1.1 - - + -
479D PHE* 6.5 0.4 - - + -
485D ILE* 4.5 14.6 - - + -
487D ILE* 4.0 26.2 - - + -
526D PHE* 5.5 3.6 - - + -
527D LYS 3.2 9.0 - - - +
528D VAL* 3.8 12.6 - - + -
703D PHE* 4.8 4.7 - - + -
705D LEU* 3.3 33.9 - - + -
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Residues in contact with SER 364 (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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345D SER* 5.9 1.1 - - - -
347D PRO 3.8 4.3 - - - -
348D ARG* 3.5 23.8 - - - +
350D PHE* 5.2 0.2 - - - -
362D GLU* 2.6 31.6 + - - -
363D ILE* 1.3 76.0 - - - +
365D LEU* 1.3 67.1 + - - +
366D GLN* 3.0 17.5 + - - -
526D PHE* 3.4 7.3 - - - +
527D LYS* 2.7 37.8 + - - +
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Residues in contact with LEU 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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345D SER* 3.2 38.7 - - - +
346D GLY 4.3 1.1 - - - +
347D PRO* 2.9 28.8 + - + +
364D SER* 1.3 77.6 - - - +
366D GLN* 1.3 63.2 + - - +
367D GLU 3.6 15.9 - - - +
391D MET* 3.9 17.3 - - + -
475D TRP* 3.8 37.5 - - + -
524D ALA* 4.0 2.5 - - + -
525D HIS 3.6 16.4 - - - +
526D PHE* 3.6 34.0 - - + -
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Residues in contact with GLN 366 (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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345D SER* 4.1 21.5 - - - -
362D GLU* 4.1 1.2 + - - -
364D SER* 3.0 27.1 + - - -
365D LEU* 1.3 80.5 + - - +
367D GLU* 1.3 67.7 + - - +
387D GLY* 5.7 0.2 - - - -
391D MET* 4.6 0.3 - - - +
525D HIS 2.8 16.3 + - - +
526D PHE 4.3 0.7 - - - -
527D LYS* 3.4 37.4 - - + +
642D PRO 3.7 7.2 + - - -
643D SER* 3.0 35.9 + - - -
644D SER* 3.0 24.4 + - - +
645D SER* 4.4 7.1 - - - +
677D TRP* 3.7 5.8 - - + -
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Residues in contact with GLU 367 (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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365D LEU* 3.6 9.3 - - - +
366D GLN* 1.3 82.7 - - + +
368D ALA* 1.3 81.1 + - - +
385D VAL* 3.5 21.7 - - + +
387D GLY* 2.6 39.3 + - - -
391D MET* 4.0 8.0 - - - +
524D ALA* 3.5 3.0 - - - -
525D HIS* 3.2 27.5 + - + -
627D TRP* 3.6 26.5 - - + +
645D SER* 3.1 38.1 + - - +
646D SER 4.2 8.1 - - - +
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367D GLU* 1.3 86.7 + - - +
369D LEU* 1.3 61.3 + - - +
385D VAL* 3.4 3.8 - - - -
386D ASP* 2.9 51.9 + - + +
391D MET* 4.3 10.1 - - + -
473D TYR* 4.6 11.9 - - + +
475D TRP* 4.8 12.3 - - + -
523D SER 3.7 8.1 - - - +
524D ALA* 4.4 3.1 - - + +
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Residues in contact with LEU 369 (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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368D ALA* 1.3 75.0 - - - +
370D ALA* 1.3 65.3 - - - +
371D ILE* 3.1 40.2 - - + +
383D ARG 4.2 3.8 - - - +
384D TYR 3.2 25.4 - - - +
385D VAL* 4.4 3.4 - - + +
386D ASP* 4.7 1.1 - - - -
473D TYR* 4.7 4.7 + - - -
521D THR* 4.3 1.1 - - - +
522D HIS* 3.6 3.1 - - - +
523D SER* 3.2 32.7 + - - +
625D PHE* 3.4 49.4 - - + -
627D TRP* 3.8 15.2 - - + -
628D GLU* 3.6 25.1 - - + +
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Residues in contact with ALA 370 (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 LEU* 1.3 77.8 - - - +
371D ILE* 1.3 61.9 + - - +
372D TYR* 3.4 23.4 - - + +
383D ARG* 3.5 0.3 - - - -
384D TYR* 3.0 34.1 + - + -
386D ASP* 5.0 0.2 - - - +
471D PAQ 3.4 27.8 - - + +
473D TYR* 4.8 1.8 - - - +
520D HIS* 5.5 0.2 - - + -
521D THR 3.0 12.6 - - - +
522D HIS* 4.6 8.3 - - + +
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Residues in contact with ILE 371 (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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546C PHE* 4.2 14.6 - - + -
562C LEU* 4.0 5.1 - - + +
369D LEU* 3.1 41.3 - - + -
370D ALA* 1.3 71.9 - - - +
372D TYR* 1.3 62.4 + - - +
382D THR 3.8 2.2 - - - -
383D ARG* 3.3 34.3 - - + +
520D HIS* 2.9 23.6 - - - -
521D THR* 2.9 21.0 + - - +
615D LEU* 3.8 22.7 - - + +
625D PHE* 3.7 12.8 - - + -
628D GLU* 3.5 20.9 - - - +
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Residues in contact with TYR 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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562C LEU* 3.8 5.4 - - - +
370D ALA* 3.4 31.6 - - + -
371D ILE* 1.3 75.1 - - - +
373D GLY* 1.3 62.1 + - - +
379D ALA* 3.4 24.8 - - - +
380D MET 3.9 2.4 - - - +
382D THR* 2.8 26.1 + - + +
383D ARG* 2.6 30.4 + - - +
384D TYR* 3.8 14.8 - + - -
470D ASN* 4.2 0.7 + - - -
471D PAQ 3.4 27.9 + - - -
496D SER* 3.6 28.3 + - - -
518D THR* 3.5 23.8 - - - -
519D VAL 3.6 2.5 - - - -
520D HIS* 3.5 35.0 + + + -
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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