Contacts of the strand formed by residues 451 - 468 (chain D) in PDB entry 2C10
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 TYR 451 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLY* 3.4 25.8 - - - -
236C ALA* 3.1 21.4 - - - -
237C GLY* 3.0 26.2 + - - -
238C PHE* 6.1 0.3 - - - -
239C PHE* 4.6 1.6 - - - -
302C LEU* 3.7 25.6 - - + -
760C PHE* 3.3 14.0 - - - -
443D HIS* 3.6 29.0 + + - -
445D SER* 2.9 40.2 + - - -
447D LEU 5.7 0.2 - - - -
449D SER* 3.1 34.6 + - - -
450D HIS* 1.3 73.4 - - - +
452D PHE* 1.3 62.1 + - - +
724D TYR* 4.0 16.4 - + + +
725D PHE 3.4 13.2 - - - +
726D ARG* 4.1 2.5 - - - -
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Residues in contact with PHE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C THR* 3.3 40.8 - - + +
402C VAL* 3.7 25.6 - - + -
403C ASP* 3.6 15.9 - - - -
757C HIS* 4.8 0.4 - - - +
760C PHE* 4.0 1.7 - - + -
442D ARG* 3.8 23.1 - - + -
443D HIS 3.4 17.3 - - - -
444D HIS* 4.0 20.2 - - + +
451D TYR* 1.3 75.7 - - - +
453D GLY* 1.3 61.3 + - - +
454D GLY 3.6 14.8 - - - -
723D ILE* 4.5 5.4 - - + -
724D TYR* 3.5 6.8 - - - -
725D PHE* 2.9 62.1 + + + +
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Residues in contact with GLY 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 3.8 24.1 - - - +
693C ASN* 4.6 1.7 - - - +
441D ARG* 4.5 4.4 + - - -
442D ARG* 3.5 1.7 + - - -
443D HIS* 2.9 34.5 + - - +
452D PHE* 1.3 80.9 - - - +
454D GLY* 1.3 58.6 + - - -
723D ILE 3.3 9.2 - - - -
724D TYR* 4.2 5.6 - - - -
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Residues in contact with GLY 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL* 3.8 14.8 - - - -
441D ARG* 3.5 23.7 - - - +
442D ARG* 4.2 1.6 - - - -
452D PHE* 3.6 4.9 - - - -
453D GLY* 1.3 74.0 - - - -
455D LEU* 1.3 61.5 + - - +
722D SER* 3.8 2.6 + - - -
723D ILE* 2.8 37.6 + - - +
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Residues in contact with LEU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL* 3.5 10.1 - - - +
439D PRO* 3.4 2.9 - - - +
440D LEU* 2.8 50.2 + - + +
441D ARG* 3.3 23.1 + - + +
454D GLY* 1.3 75.5 - - - +
456D ALA* 1.3 79.5 + - - +
481D PRO* 5.4 4.9 - - + -
716D SER* 4.0 10.8 - - - +
719D SER* 3.6 27.4 - - - +
721D ASP* 3.5 41.5 - - + +
722D SER* 4.4 2.0 - - - +
723D ILE* 5.8 0.2 - - - -
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Residues in contact with ALA 456 (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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401C GLY 3.7 23.1 - - - +
402C VAL* 3.8 18.3 - - - +
435D ASN* 4.5 21.8 - - - +
437D GLY 6.2 0.2 - - - -
438D LEU 3.9 7.6 - - - +
455D LEU* 1.3 94.8 - - + +
457D GLU* 1.3 61.8 + - - +
458D THR* 3.5 5.3 + - - -
481D PRO* 5.9 0.3 - - - +
721D ASP 5.4 0.4 + - - -
723D ILE* 6.0 0.4 - - - +
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Residues in contact with GLU 457 (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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696C THR* 4.5 8.0 + - - -
697C VAL* 3.4 19.3 - - - +
435D ASN* 3.7 2.9 - - - +
436D GLN* 2.8 46.9 + - + +
437D GLY 4.3 0.2 + - - -
438D LEU* 2.9 27.2 + - - +
439D PRO 4.4 0.4 - - - -
440D LEU* 3.9 19.3 - - + +
455D LEU 3.7 0.8 + - - -
456D ALA* 1.3 71.2 - - - +
458D THR* 1.3 59.5 + - - +
459D VAL* 3.5 11.6 - - + +
480D HIS* 2.4 40.4 + - - +
481D PRO* 3.9 19.1 - - + +
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Residues in contact with THR 458 (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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312C PRO* 4.0 6.3 - - - +
313C PRO* 3.7 26.0 - - + +
322D ARG* 4.1 9.4 - - - +
433D GLU* 3.5 37.2 - - + +
434D GLN 3.3 6.3 - - - +
435D ASN* 3.7 19.8 + - - -
456D ALA 3.5 6.5 + - - -
457D GLU* 1.3 74.0 - - - +
459D VAL* 1.3 63.2 + - - +
479D PHE 4.8 0.2 - - - +
481D PRO* 3.5 23.9 - - - +
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Residues in contact with VAL 459 (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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432D PHE 3.8 0.3 - - - +
433D GLU* 3.2 6.4 - - - +
434D GLN* 2.8 41.5 + - + +
436D GLN* 3.6 30.7 - - + +
457D GLU* 3.5 28.9 - - - +
458D THR* 1.3 77.6 - - - +
460D LEU* 1.3 59.7 + - - +
461D VAL* 4.0 8.7 - - + -
478D VAL* 3.6 17.9 - - + -
479D PHE 3.6 5.6 - - - +
480D HIS* 3.5 23.3 - - + +
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Residues in contact with LEU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D PHE* 4.1 20.4 - - + -
330D VAL* 4.1 20.6 - - + -
332D SER* 4.2 22.9 - - - +
335D TRP* 4.5 12.1 - - + -
337D PHE* 4.2 13.5 - - + -
431D VAL* 3.9 22.9 - - + -
432D PHE 3.4 18.6 - - - +
433D GLU* 4.3 9.4 - - + +
459D VAL* 1.3 74.8 - - - +
461D VAL* 1.3 60.8 + - - +
478D VAL* 3.4 1.6 - - - -
479D PHE* 2.7 52.0 + - + +
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Residues in contact with VAL 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D CYS 4.3 0.2 - - - -
431D VAL* 3.2 11.4 - - - +
432D PHE* 2.9 71.6 + - + +
434D GLN* 4.6 1.3 - - + -
459D VAL* 4.0 21.8 - - + -
460D LEU* 1.3 77.7 - - - +
462D VAL* 1.3 75.0 + - - +
463D ARG* 4.0 15.0 - - - +
476D ASP* 4.2 10.1 - - - +
477D THR 3.3 8.1 - - - +
478D VAL* 4.2 12.1 - - + -
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Residues in contact with VAL 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D PHE* 3.5 36.6 - - + -
339D PHE* 4.5 23.8 - - + -
349D ILE* 4.8 5.4 - - + -
429D PHE* 4.9 8.5 - - + -
430D CYS 3.5 6.1 - - - +
431D VAL* 4.0 17.5 - - + -
460D LEU* 5.7 0.2 - - + -
461D VAL* 1.3 79.9 - - - +
463D ARG* 1.3 67.3 + - - +
475D TRP 3.6 0.7 - - - +
476D ASP* 3.4 4.2 - - - -
477D THR* 2.8 42.8 + - - +
479D PHE* 4.3 6.7 - - + -
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Residues in contact with ARG 463 (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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437C GLY 2.6 31.5 + - - -
438C LEU* 3.8 18.0 - - - +
398D LEU* 3.6 3.7 - - + +
403D ASP 2.9 27.5 + - - -
404D CYS* 3.9 8.6 - - - +
429D PHE* 3.5 5.9 - - - +
430D CYS* 3.0 44.0 + - - +
432D PHE* 3.7 23.1 - - - -
461D VAL* 4.0 6.4 - - + +
462D VAL* 1.3 78.9 - - - +
464D SER* 1.3 67.3 + - - +
465D MET* 3.8 16.2 - - + -
474D VAL* 3.8 9.9 - - + +
475D TRP 3.2 6.5 - - - +
476D ASP* 2.6 42.2 + - - +
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Residues in contact with SER 464 (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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341D LEU* 4.0 9.1 - - - +
347D PRO* 4.0 25.3 - - - +
395D THR* 4.2 8.3 + - - +
398D LEU* 4.4 2.7 - - - -
428D ALA 3.2 22.2 - - - -
429D PHE* 4.3 15.0 - - - -
463D ARG* 1.3 75.1 - - - +
465D MET* 1.3 68.5 + - - +
466D SER* 5.6 0.2 + - - -
475D TRP* 3.2 32.4 + - - +
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Residues in contact with MET 465 (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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439C PRO* 3.7 18.8 - - + -
442C ARG* 3.2 46.4 - - - +
395D THR* 3.2 7.6 - - - +
396D THR* 2.7 33.8 + - - +
398D LEU* 3.7 14.7 - - + +
403D ASP* 3.4 43.1 - - + +
463D ARG* 3.8 15.3 - - + -
464D SER* 1.3 83.7 - - - +
466D SER* 1.3 56.5 + - - +
472D ASP* 5.8 0.4 - - + -
473D TYR 3.2 12.8 - - - +
474D VAL* 3.8 15.5 - - + -
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Residues in contact with SER 466 (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* 5.3 0.5 - - - +
391D MET* 2.8 29.3 + - - +
394D TYR 3.5 6.1 - - - -
395D THR* 4.1 1.3 + - - +
464D SER* 5.6 0.3 + - - -
465D MET* 1.3 73.3 - - - +
467D THR* 1.3 61.9 + - - +
468D LEU* 3.6 22.6 + - - -
471D TPQ 3.7 1.4 - - - +
472D ASP* 3.2 2.3 - - - -
473D TYR* 2.7 42.5 + - - +
475D TRP* 3.3 22.8 + - - +
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Residues in contact with THR 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ARG* 3.0 15.1 + - - -
443C HIS* 3.6 17.7 - - + -
444C HIS 3.2 21.0 + - - +
445C SER* 5.5 0.2 - - - -
394D TYR* 2.9 29.9 + - - +
396D THR* 3.2 19.5 + - - +
465D MET 4.0 1.0 + - - -
466D SER* 1.3 70.5 - - - +
468D LEU* 1.3 59.6 + - - +
469D LEU 3.6 12.1 + - - +
471D TPQ 3.3 6.3 - - - +
472D ASP* 2.6 26.1 + - - +
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ASP* 3.3 44.4 - - + +
389D PHE* 3.8 20.0 - - + -
390D GLY 4.3 6.7 - - - +
391D MET* 4.6 6.3 - - + -
394D TYR* 3.9 22.4 - - + -
466D SER* 3.6 29.1 + - - -
467D THR* 1.3 69.5 - - - +
469D LEU* 1.3 77.2 + - + +
470D ASN* 3.1 2.8 + - - +
471D TPQ 3.0 40.1 + - + +
473D TYR* 4.3 11.4 - - + -
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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
------------------------------------------------------------
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