Contacts of the helix formed by residues 592 - 612 (chain B) in PDB entry 2W8D
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 592 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B TYR* 4.3 16.4 - - + +
587B GLU 4.7 11.2 + - - +
588B SER* 5.8 2.4 + - - +
590B VAL* 3.4 21.4 + - + +
591B ASP* 1.3 72.6 + - - +
593B SER* 1.3 62.8 + - - +
594B GLU 3.3 2.5 - - - -
595B ASP* 3.3 13.4 + - + +
596B SER* 3.1 24.5 + - - +
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Residues in contact with SER 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B ASP* 2.7 31.6 + - - -
592B LYS* 1.3 75.4 - - - +
594B GLU* 1.3 65.8 + - - +
596B SER* 3.1 10.7 + - - -
597B LEU* 3.0 31.7 + - - +
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Residues in contact with GLU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B VAL* 3.8 27.8 - - + +
564B PHE* 3.8 12.3 - - + -
566B SER* 2.5 33.3 + - - -
567B PRO* 5.9 1.2 - - - +
568B LYS* 4.0 14.0 - - - +
569B TYR* 3.4 27.7 - - + -
591B ASP* 4.1 5.4 + - - +
592B LYS 3.3 0.6 - - - -
593B SER* 1.3 82.2 - - - +
595B ASP* 1.3 57.7 + - - +
597B LEU* 3.0 13.0 + - + +
598B VAL* 3.0 31.0 + - - +
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Residues in contact with ASP 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B GLY 4.8 4.3 - - - +
564B PHE* 3.7 21.3 - - + -
571B LYS* 3.2 28.6 + - - +
576B TYR* 3.5 18.2 + - + +
591B ASP 5.1 0.6 + - - -
592B LYS* 3.3 16.5 + - + +
593B SER 3.2 0.2 - - - -
594B GLU* 1.3 80.0 - - - +
596B SER* 1.3 61.8 + - - +
598B VAL* 3.2 3.6 + - - +
599B LYS* 3.1 40.0 + - - +
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Residues in contact with SER 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 5.3 0.2 + - - -
592B LYS* 3.1 15.1 + - - +
593B SER* 3.1 11.9 + - - -
595B ASP* 1.3 75.1 + - - +
597B LEU* 1.3 65.4 + - - +
599B LYS* 3.5 7.7 + - - +
600B LYS* 3.3 28.2 + - - +
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Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.2 17.6 + - - +
230B ASN* 5.7 4.7 - - - +
556B VAL* 5.0 16.8 - - + -
593B SER* 3.0 22.8 + - - +
594B GLU* 3.0 15.5 + - + +
596B SER* 1.3 77.7 - - - +
598B VAL* 1.3 63.6 + - - +
600B LYS* 3.6 3.3 + - - +
601B GLU* 3.1 25.4 + - - +
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Residues in contact with VAL 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B VAL* 3.7 22.2 - - + +
558B PRO* 3.9 32.9 - - + +
562B GLY* 4.2 15.3 - - - +
563B ASP 4.5 0.2 - - - +
564B PHE* 3.5 40.6 - - + -
594B GLU 3.0 8.4 + - - +
595B ASP* 3.2 8.9 + - - +
596B SER 3.2 0.2 - - - -
597B LEU* 1.3 74.8 - - - +
599B LYS* 1.3 68.3 + - + +
601B GLU* 3.4 2.7 + - - +
602B LEU* 3.1 31.9 + - + +
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Residues in contact with LYS 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B ASP* 3.1 36.5 + - - +
596B SER* 3.5 7.2 + - - +
598B VAL* 1.3 80.6 - - + +
600B LYS* 1.3 54.7 + - + +
602B LEU* 3.3 6.1 + - - +
603B GLU* 2.7 38.0 + - - +
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Residues in contact with LYS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 3.6 45.7 - - + +
596B SER 3.3 15.6 + - - +
597B LEU 4.1 0.9 - - - +
599B LYS* 1.3 78.2 - - + +
601B GLU* 1.3 58.6 + - - +
603B GLU* 3.8 22.7 - - - +
604B MSE 2.8 42.4 + - + +
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Residues in contact with GLU 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.9 5.7 - - + -
309B TYR* 2.5 38.8 + - + +
524B VAL* 4.1 0.7 - - - +
544B SER* 3.9 22.1 + - - +
554B ARG* 2.9 41.7 + - - +
556B VAL 4.5 1.0 - - - +
558B PRO* 3.7 11.5 - - + +
597B LEU 3.1 19.4 + - - +
598B VAL* 3.8 3.8 - - - +
599B LYS 3.4 0.2 - - - -
600B LYS* 1.3 74.4 - - - +
602B LEU* 1.3 62.8 + - - +
604B MSE 4.1 3.7 - - - +
605B SER* 3.2 23.2 + - - -
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Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 3.8 38.8 - - + -
558B PRO* 4.0 10.1 - - + -
559B PHE 3.8 21.5 - - - +
560B ARG* 4.0 26.0 - - - +
562B GLY* 4.1 19.5 - - - +
598B VAL* 3.1 27.5 + - + +
599B LYS* 3.7 5.2 - - - +
601B GLU* 1.3 74.0 - - - +
603B GLU* 1.3 63.7 + - - +
605B SER* 3.5 2.9 + - - -
606B ASP* 3.0 33.1 + - - +
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Residues in contact with GLU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B LYS 2.7 21.1 + - - +
600B LYS* 3.2 28.9 + - - +
602B LEU* 1.3 74.8 - - - +
604B MSE 1.3 77.1 + - + +
606B ASP* 4.0 5.1 - - - +
607B LYS* 3.1 44.8 + - + +
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Residues in contact with MSE 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLU* 3.5 19.5 - - - +
223B VAL* 4.2 30.4 - - + +
226B TYR* 3.7 36.1 - - + -
227B MSE 5.0 10.5 - - - -
600B LYS* 2.8 27.4 + - + +
601B GLU* 4.1 3.1 - - - +
603B GLU* 1.3 99.0 - - + +
605B SER* 1.3 67.3 + - - +
607B LYS* 3.4 36.3 + - + +
608B ILE* 3.5 27.2 + - - +
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Residues in contact with SER 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.7 14.8 - - - +
309B TYR* 2.9 50.3 + - - +
544B SER* 3.5 21.1 + - - -
601B GLU 3.2 9.9 + - - -
602B LEU 3.9 2.9 - - - -
604B MSE 1.3 76.5 - - - +
606B ASP* 1.3 62.6 + - - +
608B ILE* 3.1 15.0 + - - +
609B ILE* 3.1 15.1 + - - +
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Residues in contact with ASP 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR 5.1 1.2 - - - +
310B PRO 4.2 0.3 - - - +
311B LEU* 5.5 1.2 - - - +
312B ALA* 5.7 0.9 - - - +
560B ARG* 2.4 44.0 + - - -
602B LEU* 3.0 25.5 + - - +
603B GLU* 4.0 5.6 - - - +
605B SER* 1.3 76.2 + - - +
607B LYS* 1.3 54.1 + - - +
609B ILE* 4.6 4.6 - - - +
610B ASN* 2.8 57.2 + - - +
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Residues in contact with LYS 607 (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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219B ASP* 5.2 5.6 - - + +
222B GLU* 3.9 22.5 + - - +
223B VAL* 3.9 21.3 - - + -
603B GLU* 3.1 36.4 + - + +
604B MSE 3.4 36.1 - - + +
605B SER 3.3 0.4 + - - -
606B ASP* 1.3 73.9 - - - +
608B ILE* 1.3 58.2 + - - +
610B ASN* 4.8 2.2 - - - -
611B GLY* 2.9 27.5 + - - -
613B LEU* 3.5 11.3 - - + +
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Residues in contact with ILE 608 (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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223B VAL* 3.5 24.7 - - + -
227B MSE 3.5 32.5 - - + -
308B LEU* 4.0 22.9 - - + -
323B ASN* 4.4 0.3 + - - -
542B LEU* 4.2 10.8 - - + -
604B MSE 3.5 10.7 + - - +
605B SER 3.1 7.4 + - - +
607B LYS* 1.3 76.7 - - - +
609B ILE* 1.3 56.6 + - + +
612B ASP* 2.7 30.8 + - - -
613B LEU* 3.1 24.0 + - + +
614B LEU* 3.8 35.4 - - + -
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Residues in contact with ILE 609 (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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302B PHE* 3.4 40.6 - - + -
308B LEU* 3.6 24.2 - - + -
309B TYR 3.4 17.5 - - - +
310B PRO 6.0 0.2 - - - -
311B LEU* 3.8 28.3 - - + -
316B VAL* 4.7 3.1 - - + -
320B LYS* 4.0 21.5 + - + -
323B ASN* 2.9 32.3 + - - +
325B LEU* 5.4 2.9 - - + -
605B SER* 3.1 11.9 + - - +
606B ASP* 4.4 3.6 - - - +
608B ILE* 1.3 80.1 - - + +
610B ASN* 1.3 65.0 + - - +
612B ASP* 3.5 2.6 + - - +
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Residues in contact with ASN 610 (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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215B ALA 5.3 0.2 + - - -
311B LEU* 4.2 12.3 - - - +
320B LYS* 4.6 13.6 + - - +
606B ASP* 2.8 43.4 + - - +
607B LYS* 4.4 2.2 - - - +
609B ILE* 1.3 83.7 - - - +
611B GLY* 1.3 58.4 + - - +
612B ASP* 3.4 0.6 - - - +
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Residues in contact with GLY 611 (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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215B ALA* 3.5 22.8 + - - -
607B LYS 2.9 16.5 + - - -
610B ASN* 1.3 76.2 - - - +
612B ASP* 1.3 61.2 + - - +
613B LEU* 3.4 12.8 - - - +
615B ARG* 2.7 28.6 + - - -
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Residues in contact with ASP 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLN 4.4 3.8 - - - +
323B ASN* 3.3 33.0 + - - +
324B THR* 3.0 33.4 + - - +
608B ILE 2.7 13.0 + - - -
609B ILE 3.5 1.3 + - - +
610B ASN 3.4 2.7 - - - +
611B GLY* 1.3 79.2 - - - +
613B LEU* 1.3 60.9 + - - +
614B LEU* 3.4 2.2 + - - -
615B ARG* 2.9 51.8 + - - +
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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