Contacts of the strand formed by residues 672 - 684 (chain A) 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 LYS 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A LEU 2.4 22.8 - - - +
536A GLU* 3.8 4.3 - - - -
537A ASN 2.8 13.0 + - - -
636A GLN* 3.9 23.3 - - + +
668A THR* 3.5 33.8 - - + +
669A ILE 4.3 0.2 - - - -
670A ALA* 3.7 18.1 - - - +
671A GLY* 1.3 86.0 + - - +
673A ASP* 1.3 59.8 + - - +
674A LEU* 3.4 18.6 + - + +
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Residues in contact with ASP 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS* 3.0 16.7 + - - +
531A ASP* 2.9 8.2 - - - +
535A LEU* 3.0 27.6 + - + +
536A GLU* 4.9 0.4 + - - -
636A GLN* 3.4 7.1 - - - +
637A ARG* 2.7 60.6 + - + +
672A LYS* 1.3 74.0 - - - +
674A LEU* 1.3 53.1 + - - +
1736A CA 2.2 32.7 - - - -
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ASP* 2.7 11.7 - - - +
530A LEU 3.3 4.7 + - - +
535A LEU 3.9 1.6 + - - -
537A ASN* 3.0 32.6 + - + +
538A TRP 4.3 0.2 - - - +
539A VAL* 4.1 18.4 - - + -
589A LEU* 4.0 20.0 - - + +
634A VAL* 4.1 4.0 - - + -
635A THR 3.1 17.9 - - - +
636A GLN* 4.1 3.1 - - + -
637A ARG* 4.4 0.2 - - - -
669A ILE* 3.4 31.6 - - + +
672A LYS* 3.4 26.6 + - + +
673A ASP* 1.3 81.5 - - - +
675A VAL* 1.3 59.6 + - - +
1736A CA 2.3 29.6 - - - -
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Residues in contact with VAL 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A LYS* 3.7 24.0 - - + -
528A VAL 3.5 13.7 - - - +
529A ASP* 3.8 12.8 - - + +
530A LEU 4.9 0.2 - - - +
589A LEU* 5.4 1.1 - - - -
634A VAL* 3.5 3.3 - - - -
635A THR* 2.8 51.3 + - - +
637A ARG* 3.5 24.0 - - - -
641A GLU 6.1 0.4 - - - +
674A LEU* 1.3 80.0 - - - +
676A ALA* 1.3 63.3 + - - +
677A TRP* 3.4 28.7 + - + +
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Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A PHE 3.5 0.9 - - - +
527A LYS 3.8 0.2 - - - -
528A VAL* 2.8 45.6 + - + +
530A LEU* 6.2 1.1 - - + -
589A LEU* 5.1 6.5 - - + +
605A ILE* 3.8 29.8 - - + -
632A LEU* 3.9 7.2 - - + -
633A ALA 3.3 9.6 - - - +
634A VAL* 4.2 10.5 - - + +
675A VAL* 1.3 74.7 - - - +
677A TRP* 1.3 64.2 + - - +
678A VAL* 3.9 1.7 + - + -
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Residues in contact with TRP 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A GLN* 4.1 2.0 - - + -
525A HIS* 3.2 43.6 + + + +
526A PHE 3.4 4.7 - - - -
527A LYS* 3.8 39.3 - - + -
630A TYR* 5.5 1.0 - - - +
631A GLN 4.2 0.3 - - - -
632A LEU* 3.1 9.1 - - - +
633A ALA* 2.7 41.6 + - + +
635A THR* 3.0 29.4 + - + +
641A GLU* 4.2 12.3 - - + -
643A SER 4.5 2.5 - - - -
644A SER* 3.7 25.6 - - - -
660A PHE* 3.5 21.3 - + + -
663A PHE* 4.0 25.8 - + - -
675A VAL* 3.4 32.2 + - + +
676A ALA* 1.3 74.4 - - - +
678A VAL* 1.3 62.1 + - - +
679A THR* 4.7 0.5 + - - -
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Residues in contact with VAL 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A HIS* 3.3 4.7 - - - -
526A PHE* 2.9 34.4 + - + +
528A VAL* 4.2 12.8 - - + -
605A ILE* 4.2 15.0 - - + -
607A MET* 4.0 20.6 - - + -
631A GLN 3.5 8.5 - - - +
632A LEU* 3.7 17.3 - - + -
676A ALA* 4.9 2.5 - - + -
677A TRP* 1.3 74.3 - - - +
679A THR* 1.3 71.3 + - - +
680A ALA* 4.2 1.1 - - + +
702A GLY 4.3 2.7 - - - +
703A PHE* 3.2 44.4 - - + -
705A LEU* 6.5 0.2 - - + -
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Residues in contact with THR 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A SER* 4.8 6.1 - - - -
524A ALA 3.7 2.9 - - - +
525A HIS* 3.1 24.1 + - - -
579A VAL* 5.1 3.4 - - + -
607A MET* 3.3 23.4 - - - +
609A SER* 3.7 2.9 + - - -
611A ALA* 5.2 8.4 - - + +
627A TRP* 3.4 29.4 + - + +
628A GLU* 4.6 7.4 - - - +
630A TYR* 2.8 31.5 + - - +
631A GLN* 2.7 11.4 + - - +
677A TRP 4.7 0.9 + - - -
678A VAL* 1.3 75.4 - - - +
680A ALA* 1.3 68.2 + - - +
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Residues in contact with ALA 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A PHE* 3.8 6.9 - - - -
523A SER* 3.6 1.3 - - - -
524A ALA 3.1 28.9 + - - +
526A PHE* 4.8 8.5 - - + -
607A MET* 5.5 0.2 - - + -
609A SER* 3.4 17.3 - - - -
611A ALA* 5.3 0.2 - - - -
678A VAL* 4.2 1.5 - - + -
679A THR* 1.3 78.9 - - - +
681A GLY* 1.3 58.7 + - - +
701A VAL* 3.9 8.7 - - + -
702A GLY* 3.8 37.5 - - - +
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Residues in contact with GLY 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A PHE* 5.2 0.7 - - - -
522A HIS 2.9 16.6 - - - -
523A SER* 4.0 2.2 - - - -
609A SER* 3.6 5.4 - - - -
610A PHE* 3.1 10.7 + - - -
611A ALA* 2.8 32.7 + - - +
680A ALA* 1.3 76.2 - - - +
682A PHE* 1.3 70.4 - - - +
701A VAL* 4.0 4.2 - - - +
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Residues in contact with PHE 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A PHE* 5.0 5.6 - + - -
491A ALA* 4.7 12.1 - - + -
521A THR* 3.5 3.7 - - - -
522A HIS* 2.9 62.7 + + + +
610A PHE* 3.6 26.7 - + + +
611A ALA* 4.0 1.2 - - - +
612A GLY 3.9 8.0 - - - +
681A GLY* 1.3 82.0 - - - +
683A LEU* 1.3 74.5 + - - +
684A HIS* 4.6 8.1 - + + -
699A ASN* 3.7 46.2 - - + -
701A VAL* 3.9 22.4 - - + -
606B GLN* 6.2 1.1 - - - +
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A VAL* 4.2 15.7 - - + -
520A HIS 3.7 15.3 - - - +
521A THR* 3.7 16.2 - - + -
610A PHE 4.4 2.0 + - - -
612A GLY* 4.2 2.6 - - - +
682A PHE* 1.3 85.3 - - - +
684A HIS* 1.3 59.9 + - - +
685A ILE* 3.6 32.3 - - + -
543B ASP* 3.9 19.7 - - - +
544B MET* 3.7 23.6 - - + -
562B LEU* 5.2 0.4 - - + -
585B ARG* 3.8 25.5 - - + +
586B TYR* 3.5 26.9 + - + -
604B ARG* 5.0 2.3 + - - -
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Residues in contact with HIS 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A ILE* 3.7 17.9 - - + -
519A VAL* 3.7 1.0 - - - +
520A HIS* 2.7 54.4 + + + +
522A HIS* 4.0 7.0 - + + -
682A PHE* 4.0 8.4 + + + -
683A LEU* 1.3 73.8 - - - +
685A ILE* 1.3 68.2 + - - +
686A PRO* 3.2 15.1 - - - +
690A ASP* 2.9 25.3 + - - -
694A THR* 3.6 28.5 - - + +
1737A CU 2.0 29.9 - - - -
1745A CU 3.9 12.9 - - - -
586B TYR* 4.0 3.6 - - - -
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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