Contacts of the strand formed by residues 672 - 684 (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 LYS 672 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535D LEU 4.1 0.9 - - - -
536D GLU* 4.2 3.4 - - - -
537D ASN 3.0 22.1 + - - -
636D GLN* 3.6 30.7 - - + +
668D THR* 3.8 29.8 - - + +
669D ILE* 4.7 0.4 - - - -
670D ALA 5.4 1.1 - - - -
671D GLY* 1.3 88.9 + - - +
673D ASP* 1.3 68.4 + - - +
674D LEU* 3.1 25.6 + - + +
5O FUC 5.4 5.1 + - - -
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Residues in contact with ASP 673 (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 32.1 + - - +
529D ASP* 3.4 0.2 - - - +
531D ASP* 3.2 2.4 - - - +
535D LEU* 3.4 34.1 + - + +
536D GLU* 4.6 3.8 + - - +
636D GLN* 3.5 6.9 - - - +
637D ARG* 2.9 42.5 + - + +
672D LYS* 1.3 73.2 - - - +
674D LEU* 1.3 60.2 + - - +
1776D CA 2.2 33.4 - - - -
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Residues in contact with LEU 674 (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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529D ASP* 2.9 5.0 - - - +
530D LEU 3.3 5.4 + - - +
535D LEU 4.5 1.0 + - - -
537D ASN* 3.5 31.8 - - + +
538D TRP 4.1 1.6 - - - +
539D VAL* 3.6 30.1 - - + -
589D LEU* 4.1 13.6 - - + +
634D VAL* 3.9 9.9 - - + -
635D THR 3.3 13.9 - - - +
636D GLN 4.5 0.2 - - - +
637D ARG 4.5 0.4 - - - -
669D ILE* 3.6 35.4 - - + +
672D LYS* 3.1 21.9 + - + +
673D ASP* 1.3 78.6 + - - +
675D VAL* 1.3 61.3 + - - +
1776D CA 2.4 29.9 - - - -
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Residues in contact with VAL 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D LYS* 3.7 29.4 - - + -
528D VAL 3.6 12.1 - - - +
529D ASP* 4.0 12.8 - - + +
589D LEU* 5.2 0.2 - - - -
634D VAL* 3.4 5.4 - - - -
635D THR* 2.9 44.4 + - - +
636D GLN 4.0 0.9 - - - +
637D ARG* 3.7 26.9 - - + -
674D LEU* 1.3 75.6 - - - +
676D ALA* 1.3 73.9 + - - +
677D TRP* 3.7 17.7 - - + +
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Residues in contact with ALA 676 (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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526D PHE 3.7 0.2 - - - +
527D LYS 3.8 0.2 - - - -
528D VAL* 2.8 48.2 + - + +
589D LEU* 4.8 7.0 - - + +
605D ILE* 3.6 31.4 - - + -
632D LEU* 4.3 5.6 - - + -
633D ALA 3.4 6.7 - - - +
634D VAL* 4.3 11.0 - - + +
675D VAL* 1.3 78.4 - - - +
677D TRP* 1.3 61.1 + - - +
678D VAL* 4.2 1.8 - - + -
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Residues in contact with TRP 677 (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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366D GLN* 4.2 1.6 - - + -
525D HIS* 3.5 34.8 + + + +
526D PHE 3.2 4.7 - - - -
527D LYS* 3.8 39.7 - - + -
630D TYR* 5.8 0.7 - - - +
631D GLN 4.4 0.2 - - - -
632D LEU* 3.2 7.1 - - - +
633D ALA* 2.7 44.1 + - + +
635D THR* 3.0 27.0 + - + +
636D GLN 5.8 0.2 - - - -
641D GLU* 4.1 15.0 - - + -
643D SER 4.3 0.9 - - - -
644D SER* 3.6 25.6 - - - -
660D PHE* 3.5 23.8 - + + -
663D PHE* 3.8 26.2 - + - -
675D VAL* 3.7 26.1 + - + +
676D ALA* 1.3 76.9 - - - +
678D VAL* 1.3 63.1 + - - +
679D THR* 4.2 0.7 + - - -
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Residues in contact with VAL 678 (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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525D HIS* 3.6 2.6 - - - -
526D PHE* 2.8 40.8 + - - +
528D VAL* 4.1 21.5 - - + -
605D ILE* 4.3 12.6 - - + -
607D MET* 3.9 21.5 - - + -
631D GLN 3.6 9.6 - - - +
632D LEU* 3.9 16.4 - - + +
676D ALA* 4.8 2.0 - - + -
677D TRP* 1.3 77.9 - - - +
679D THR* 1.3 72.0 + - - +
680D ALA* 5.4 1.3 - - + -
702D GLY 5.2 1.6 - - - +
703D PHE* 3.7 31.4 - - + -
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Residues in contact with THR 679 (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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523D SER* 4.4 11.9 - - - +
524D ALA 3.4 3.8 - - - +
525D HIS* 3.3 9.8 + - - -
579D VAL* 5.7 2.5 - - + -
607D MET* 5.0 2.4 - - - +
609D SER* 4.0 8.3 + - - -
627D TRP* 2.9 43.7 + - + +
628D GLU* 4.5 7.6 - - - +
630D TYR* 2.6 29.6 + - - +
631D GLN* 3.0 17.7 + - - +
677D TRP 5.1 0.5 + - - -
678D VAL* 1.3 78.2 - - - +
680D ALA* 1.3 66.9 + - - +
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Residues in contact with ALA 680 (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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489D PHE* 3.5 11.7 - - + -
523D SER* 3.4 2.3 - - - -
524D ALA 3.0 31.0 + - - +
526D PHE* 5.1 6.7 - - + -
609D SER* 3.3 12.1 - - - +
611D ALA* 5.5 0.7 - - - -
678D VAL* 4.2 2.4 + - + -
679D THR* 1.3 78.9 - - - +
681D GLY* 1.3 57.5 + - - +
701D VAL* 3.9 17.9 - - + -
702D GLY* 3.9 25.6 - - - +
703D PHE* 5.7 0.2 - - + -
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Residues in contact with GLY 681 (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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489D PHE* 4.7 1.1 - - - -
522D HIS 3.0 15.3 - - - -
523D SER* 4.2 2.7 - - - -
609D SER* 3.0 6.9 + - - -
610D PHE 3.2 22.7 + - - -
611D ALA* 3.3 12.2 + - - +
612D GLY 5.3 0.2 - - - -
680D ALA* 1.3 75.3 - - - +
682D PHE* 1.3 75.2 + - - +
701D VAL* 3.9 8.3 - - - +
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Residues in contact with PHE 682 (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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489D PHE* 4.8 6.3 - + - -
491D ALA* 4.3 15.5 - - + -
521D THR* 3.6 2.2 - - - -
522D HIS* 3.0 65.6 + + + -
610D PHE* 3.5 27.6 - + + +
612D GLY 4.0 8.8 - - - +
681D GLY* 1.3 81.7 - - - +
683D LEU* 1.3 73.2 + - - +
684D HIS* 3.8 13.0 + + + -
694D THR* 6.5 0.4 - - + -
699D ASN* 3.8 44.4 - - + -
701D VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 683 (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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543C ASP* 4.0 7.4 - - - +
544C MET* 3.8 47.1 - - + +
562C LEU* 5.4 1.3 - - + -
585C ARG* 3.9 35.0 - - + +
586C TYR* 3.3 27.9 + - + -
604C ARG* 5.5 0.9 + - - -
519D VAL* 3.9 24.0 - - + -
520D HIS 3.6 14.4 - - - +
521D THR* 4.3 5.2 - - + -
610D PHE 4.2 4.2 + - - -
612D GLY* 4.2 2.4 - - - +
682D PHE* 1.3 83.9 - - - +
684D HIS* 1.3 65.5 + - - +
685D ILE* 4.1 12.1 - - + -
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Residues in contact with HIS 684 (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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586C TYR* 3.3 6.3 - - - -
495D ILE* 4.2 8.7 - - + -
520D HIS* 2.8 45.5 + + + +
522D HIS* 3.8 8.8 + - + -
682D PHE* 3.8 9.9 + + + -
683D LEU* 1.3 74.1 - - - +
685D ILE* 1.3 67.2 + - - +
686D PRO* 3.2 23.5 - - + +
687D HIS* 4.7 3.7 + + - -
690D ASP* 2.9 24.5 + - - -
694D THR* 3.4 36.2 - - + +
1777D CU 2.1 29.4 - - - -
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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
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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