Contacts of the strand formed by residues 520 - 530 (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 HIS 520 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562C LEU* 4.0 3.6 - - - -
370D ALA* 5.5 0.2 - - + -
371D ILE 2.9 16.6 - - - +
372D TYR* 3.5 36.6 + + + -
471D PAQ 4.9 0.6 + - - -
495D ILE* 4.9 7.2 - - + -
496D SER 5.6 1.1 - - - -
518D THR* 2.6 27.9 + - - -
519D VAL* 1.3 79.3 - - - +
521D THR* 1.3 66.1 + - - +
522D HIS* 3.1 26.2 - + - -
683D LEU* 3.7 3.3 - - - +
684D HIS* 2.8 49.5 + + - +
686D PRO* 3.6 8.7 - - + -
1742D CU 2.2 26.1 - - - -
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Residues in contact with THR 521 (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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544C MET* 4.0 22.0 - - + -
546C PHE* 5.7 0.6 - - + -
562C LEU* 4.8 8.1 - - + -
369D LEU* 4.3 0.5 - - - +
370D ALA* 3.0 26.5 - - - +
371D ILE* 2.9 26.8 + - + +
520D HIS* 1.3 80.4 - - - +
522D HIS* 1.3 64.3 + - - +
523D SER* 4.6 2.5 + - - -
612D GLY* 4.3 13.9 - - - -
613D GLU 5.0 2.9 + - - +
628D GLU* 3.8 14.6 + - - -
682D PHE 3.6 7.9 - - - -
683D LEU* 4.0 18.6 - - + -
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Residues in contact with HIS 522 (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 3.6 4.7 + - - +
370D ALA* 4.6 4.7 - - + +
471D PAQ 3.5 34.4 - + - -
473D TYR* 4.2 12.4 + - + +
489D PHE* 4.7 9.4 - - + -
491D ALA* 4.1 14.6 - - + +
520D HIS* 3.1 17.3 + + - -
521D THR* 1.3 74.9 + - - +
523D SER* 1.3 68.4 + - - +
611D ALA* 5.3 0.7 - - - -
612D GLY 5.4 0.7 + - - -
681D GLY* 3.1 1.7 - - - -
682D PHE* 3.0 65.1 + + + +
684D HIS* 3.9 8.1 - - + -
1742D CU 2.1 32.6 - - - -
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Residues in contact with SER 523 (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* 4.6 1.1 - - - -
369D LEU* 3.2 28.8 + - - +
489D PHE* 4.8 2.5 - - - -
521D THR* 4.6 3.3 + - - -
522D HIS* 1.3 80.7 + - - +
524D ALA* 1.3 56.6 + - - +
611D ALA* 5.6 4.9 - - - -
627D TRP* 2.8 37.6 - - - -
628D GLU* 3.7 25.4 + - - +
679D THR* 4.3 7.4 - - - -
680D ALA 3.1 13.5 - - - -
681D GLY* 3.9 2.5 - - - -
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Residues in contact with ALA 524 (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* 4.0 5.4 - - + -
367D GLU 3.5 11.7 - - - +
368D ALA* 4.4 2.9 - - + +
475D TRP* 4.3 7.6 - - + -
489D PHE* 3.7 23.4 - - + -
523D SER* 1.3 75.2 - - - +
525D HIS* 1.3 60.9 + - - +
526D PHE* 3.4 29.6 - - + -
627D TRP* 3.8 0.9 - - - -
679D THR* 3.3 10.0 - - - +
680D ALA 2.9 26.0 + - - +
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Residues in contact with HIS 525 (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 2.6 - - - +
366D GLN* 2.8 27.0 + - - +
367D GLU 3.2 12.7 + - - +
524D ALA* 1.3 76.1 - - - +
526D PHE* 1.3 62.6 + - - +
627D TRP* 3.4 41.5 - + + +
630D TYR* 6.2 0.2 - - - +
644D SER* 2.6 40.9 + - - +
660D PHE* 3.6 16.9 - + - -
677D TRP* 3.5 28.2 + + - +
678D VAL 3.3 11.7 - - - -
679D THR* 3.1 26.4 + - - -
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Residues in contact with PHE 526 (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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363D ILE* 5.5 4.9 - - + -
364D SER 3.4 7.6 - - - +
365D LEU* 3.6 28.3 - - + -
366D GLN* 4.3 2.7 - - - -
475D TRP* 4.1 16.6 - + - -
487D ILE* 3.7 26.5 - - + -
488D ARG 5.6 0.4 - - - -
489D PHE* 4.3 14.8 - + + -
524D ALA* 3.4 32.3 - - + -
525D HIS* 1.3 76.4 - - - +
527D LYS* 1.3 63.1 + - - +
528D VAL* 3.9 0.8 + - + -
677D TRP* 3.4 11.4 - - - -
678D VAL* 2.8 41.1 + - + +
680D ALA* 4.5 11.2 - - + -
701D VAL 5.6 0.7 - - - -
702D GLY* 5.6 1.1 - - - -
703D PHE* 3.8 31.4 - + + -
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Residues in contact with LYS 527 (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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362D GLU* 3.3 35.1 + - - +
363D ILE* 3.2 7.6 - - - +
364D SER* 2.7 33.3 + - - +
366D GLN* 3.4 18.5 - - - +
526D PHE* 1.3 71.0 - - - +
528D VAL* 1.3 62.2 + - - +
529D ASP* 4.6 7.0 - - - +
637D ARG* 3.4 22.6 - - - +
641D GLU 3.6 5.5 + - - -
642D PRO* 2.9 43.9 + - - +
675D VAL* 3.8 17.0 - - + -
677D TRP* 3.4 27.8 - - + -
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Residues in contact with VAL 528 (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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362D GLU 3.8 1.1 - - - -
363D ILE* 3.8 30.1 - - + -
526D PHE 4.1 4.5 - - - +
527D LYS* 1.3 74.3 - - - +
529D ASP* 1.3 58.1 + - - +
530D LEU* 3.1 17.2 + - + +
589D LEU* 5.4 0.2 - - - +
605D ILE* 5.6 1.1 - - + -
675D VAL* 3.5 1.3 - - - -
676D ALA* 2.7 61.1 + - + +
678D VAL* 3.8 20.4 - - + -
703D PHE* 4.1 16.8 - - + -
705D LEU* 4.1 18.8 - - + -
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Residues in contact with ASP 529 (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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106D LYS* 2.7 24.9 + - - +
360D VAL* 3.8 4.3 - - - -
361D TYR* 3.1 39.0 + - - -
362D GLU* 2.8 31.1 + - + +
527D LYS* 3.9 3.6 - - - -
528D VAL* 1.3 69.8 - - - +
530D LEU* 1.3 59.7 + - - +
531D ASP* 3.7 0.9 - - - +
637D ARG* 4.0 13.8 + - - +
673D ASP* 3.3 2.6 - - - +
674D LEU 3.1 4.3 - - - +
675D VAL* 3.9 13.0 - - + +
1741D CA 2.5 29.6 - - - -
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Residues in contact with LEU 530 (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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359D LEU* 3.3 18.6 - - + +
360D VAL* 3.2 33.2 - - + +
528D VAL* 3.1 14.1 + - + +
529D ASP* 1.3 75.7 - - - +
531D ASP* 1.3 54.4 + - - +
532D VAL* 3.6 18.4 - - + -
537D ASN* 3.7 6.4 - - - +
589D LEU* 4.4 24.9 - - + +
603D TYR* 4.5 28.0 - - + +
605D ILE* 4.9 7.9 - - + -
674D LEU 3.4 4.7 + - - +
676D ALA* 5.7 0.2 - - + -
705D LEU* 4.4 25.6 - - + -
1741D CA 2.3 28.6 - - - -
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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