Contacts of the strand formed by residues 672 - 684 (chain B) in PDB entry 2Y74
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535B LEU 3.6 3.4 - - - -
536B GLU* 3.9 3.6 - - - +
537B ASN 2.8 22.4 + - - -
636B GLN* 3.6 31.8 + - + +
668B THR* 3.9 32.7 - - + +
669B ILE 4.6 0.2 + - - -
670B ALA 3.8 13.0 - - - +
671B GLY* 1.3 88.1 - - - +
673B ASP* 1.3 60.7 + - - +
674B LEU* 3.0 22.2 + - + +
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Residues in contact with ASP 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 3.0 34.3 + - - +
529B ASP* 3.7 0.2 - - - +
535B LEU* 3.2 36.2 + - + +
536B GLU* 4.5 0.6 - - - +
636B GLN* 3.7 4.9 - - - +
637B ARG* 2.9 44.1 + - + +
672B LYS* 1.3 70.6 - - - +
674B LEU* 1.3 60.3 + - - +
802B CA 2.6 26.6 - - - -
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASP* 3.2 4.9 - - - +
530B LEU 3.7 4.7 + - - +
535B LEU 4.1 1.2 + - - -
537B ASN* 3.3 34.2 + - + +
538B TRP 3.7 0.9 - - - +
539B VAL* 3.5 25.8 - - + -
589B LEU* 4.2 13.0 - - + +
634B VAL* 4.0 8.7 - - + -
635B THR 3.5 7.4 - - - +
636B GLN* 4.5 1.3 - - - -
669B ILE* 3.3 47.3 - - + +
672B LYS* 3.0 24.2 + - + +
673B ASP* 1.3 77.2 + - - +
675B VAL* 1.3 60.5 + - - +
802B CA 2.5 27.7 - - - -
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Residues in contact with VAL 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B LYS* 3.8 30.7 - - + -
528B VAL 3.8 11.4 - - - +
529B ASP* 3.8 14.8 - - + +
589B LEU* 5.3 0.7 - - - -
634B VAL* 3.5 4.4 - - - -
635B THR* 2.9 52.9 + - - +
636B GLN 4.2 0.2 - - - +
637B ARG* 3.7 29.2 - - + -
674B LEU* 1.3 76.0 - - - +
676B ALA* 1.3 66.2 + - - +
677B TRP* 3.5 17.8 + - + +
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Residues in contact with ALA 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B LYS* 3.7 0.9 - - - -
528B VAL* 2.7 50.6 + - + +
589B LEU* 4.6 9.2 - - + +
605B ILE* 3.5 32.5 - - + -
632B LEU* 4.6 3.1 - - + -
633B ALA 3.4 8.7 - - - +
634B VAL* 4.2 11.2 - - + +
675B VAL* 1.3 74.0 - - - +
677B TRP* 1.3 61.5 + - - +
678B VAL* 4.2 0.7 - - + -
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Residues in contact with TRP 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLN* 3.8 7.6 - - + -
525B HIS* 3.6 32.0 + + + +
526B PHE 3.3 5.2 - - - -
527B LYS* 3.5 48.9 - - + -
630B TYR* 6.0 0.2 - - - +
631B GLN 4.0 0.2 - - - +
632B LEU* 3.2 6.4 - - - +
633B ALA* 2.8 41.8 + - - +
635B THR* 2.9 29.1 + - + +
641B GLU* 4.2 11.9 - - + -
642B PRO 4.4 1.3 - - - -
644B SER* 3.8 18.6 - - - -
660B PHE* 3.5 25.9 - + + -
663B PHE* 3.9 24.0 - + - -
675B VAL* 3.5 32.8 + - + +
676B ALA* 1.3 74.3 - - - +
678B VAL* 1.3 62.7 + - - +
679B THR* 5.2 0.3 + - - -
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B HIS* 3.6 1.6 + - - -
526B PHE* 2.8 45.1 + - + +
528B VAL* 4.3 16.6 - - + -
605B ILE* 3.9 17.3 - - + -
607B MET* 3.9 24.5 - - + -
631B GLN 3.6 2.7 - - - +
632B LEU* 3.9 20.2 - - + -
676B ALA 4.9 0.2 - - - -
677B TRP* 1.3 79.7 - - - +
679B THR* 1.3 69.3 + - - +
680B ALA* 4.8 1.6 - - + +
702B GLY 4.8 2.7 - - - +
703B PHE* 3.5 32.8 - - + -
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Residues in contact with THR 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B SER* 4.3 11.2 - - - -
524B ALA 3.5 11.9 - - - +
525B HIS* 2.9 21.7 + - - -
579B VAL* 5.9 1.8 - - + -
607B MET* 4.9 2.9 - - - +
609B SER* 3.8 10.4 + - - -
611B ALA* 5.4 5.6 - - + +
627B TRP* 3.0 26.9 + - + +
628B GLU* 4.5 7.2 - - - +
630B TYR* 2.7 28.0 + - - +
631B GLN* 2.8 20.9 + - - +
677B TRP 5.2 0.2 + - - -
678B VAL* 1.3 75.1 - - - +
680B ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B PHE* 4.6 1.4 - - - -
523B SER* 3.2 4.2 - - - -
524B ALA* 2.8 32.0 + - - +
526B PHE* 4.5 10.0 - - + -
608B LEU 4.1 5.2 - - - +
609B SER* 3.4 6.7 - - - +
611B ALA* 5.5 0.7 - - - -
678B VAL* 4.0 3.2 + - + -
679B THR* 1.3 76.2 - - - +
681B GLY* 1.3 58.2 + - - +
701B VAL* 3.7 12.1 - - + -
702B GLY* 3.5 39.0 - - - +
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Residues in contact with GLY 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B PHE* 5.2 0.4 - - - -
522B HIS* 3.1 15.9 - - - -
523B SER* 3.9 3.4 - - - -
609B SER* 3.1 5.9 + - - -
610B PHE 3.0 22.3 + - - -
611B ALA* 3.1 11.3 + - - +
680B ALA* 1.3 76.2 - - - +
682B PHE* 1.3 76.0 + - - +
701B VAL* 3.8 8.5 - - - +
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Residues in contact with PHE 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A ARG* 6.1 0.7 - - - -
489B PHE* 5.2 5.8 - + - -
491B ALA* 4.8 11.0 - - + -
521B THR* 3.5 1.8 - - - -
522B HIS* 2.9 64.6 + + + +
610B PHE* 3.3 30.3 - + + +
611B ALA* 3.9 1.6 - - - +
612B GLY 4.0 8.0 - - - +
681B GLY* 1.3 80.4 - - - +
683B LEU* 1.3 70.8 + - - +
684B HIS* 4.1 13.9 - + + -
699B ASN* 3.8 44.0 - - + -
701B VAL* 3.8 20.6 - - + -
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Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A ASP 4.1 12.3 - - - -
544A MET* 3.9 38.6 - - + -
585A ARG* 3.9 31.2 - - + +
586A TYR* 3.5 39.6 + - + -
604A ARG* 5.0 3.5 + - - -
519B VAL* 3.8 23.6 - - + -
520B HIS 3.6 11.7 - - - +
521B THR* 4.0 6.7 - - + -
610B PHE 4.0 4.6 + - - -
612B GLY* 4.3 1.6 - - - +
682B PHE* 1.3 84.0 - - - +
684B HIS* 1.3 66.4 + - - +
685B ILE* 4.2 7.4 - - + -
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Residues in contact with HIS 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A TYR* 3.6 9.2 - - - -
495B ILE* 4.3 11.7 - - + -
519B VAL* 3.6 1.0 - - - +
520B HIS* 2.8 57.7 + + + +
522B HIS* 4.3 0.7 - - + -
682B PHE* 3.9 15.0 + + + -
683B LEU* 1.3 74.9 - - - +
685B ILE* 1.3 65.9 + - - +
686B PRO* 3.2 18.9 - - + +
687B HIS* 4.5 4.0 - + - -
690B ASP* 2.8 36.7 + - - -
694B THR* 4.4 9.0 - - + -
801B CU 2.2 30.3 - - - -
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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