Contacts of the helix formed by residues 599 - 609 (chain B) in PDB entry 3NMW
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 CYS 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A HIS* 3.7 19.1 - - + -
564B ARG* 3.9 14.8 - - - -
595B LEU 4.4 0.2 + - - -
596B SER 4.2 0.2 - - - +
597B ALA 3.4 1.6 - - - -
598B HIS* 1.3 83.2 - - + +
600B THR* 1.3 64.3 + - - +
601B GLU* 3.6 15.9 - - + +
602B ASN* 3.4 40.8 + - - +
603B LYS* 3.4 29.0 + - - +
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Residues in contact with THR 600 (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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464A HIS* 5.1 1.9 - - + +
467A ASN* 6.0 1.3 - - - +
511A GLY 5.3 4.9 + - - -
512A ASP* 4.1 26.7 - - - +
513A VAL 6.3 0.9 - - - -
599B CYS* 1.3 73.3 - - - +
601B GLU* 1.3 71.0 + - - +
603B LYS* 3.2 21.2 + - + +
604B ALA* 2.9 23.4 + - - +
644B SER* 6.0 0.7 - - - +
645B LEU* 3.9 12.6 - - + +
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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
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564B ARG* 3.6 38.1 + - - +
599B CYS* 3.3 11.9 - - + +
600B THR* 1.3 82.0 + - - +
602B ASN* 1.3 57.8 + - - +
604B ALA* 3.3 5.9 + - - +
605B ASP* 2.9 38.5 + - - +
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Residues in contact with ASN 602 (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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560B LYS 5.5 0.4 + - - -
564B ARG* 3.5 35.1 - - - +
569B VAL* 3.5 28.9 - - + +
595B LEU* 3.0 35.1 + - - +
596B SER* 4.6 1.3 - - - -
598B HIS* 3.6 21.4 + - - +
599B CYS* 3.4 14.4 - - - +
600B THR 3.3 0.4 - - - -
601B GLU* 1.3 77.5 - - - +
603B LYS* 1.3 63.3 + - - +
605B ASP* 3.4 6.7 + - - +
606B ILE* 3.1 29.5 + - - +
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Residues in contact with LYS 603 (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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468A GLU* 5.0 11.0 + - - -
596B SER 2.7 32.0 + - - +
597B ALA* 3.8 16.8 + - - +
599B CYS* 3.5 17.8 + - - +
600B THR* 3.2 21.3 + - + +
602B ASN* 1.3 77.7 - - - +
604B ALA* 1.3 62.3 + - - +
606B ILE* 3.2 6.1 + - - +
607B CYS* 3.2 24.9 + - - -
641B ASN* 2.9 31.1 - - - +
642B VAL* 3.8 19.0 - - + +
644B SER* 4.0 15.5 - - - +
645B LEU* 3.6 13.7 - - + -
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Residues in contact with ALA 604 (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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600B THR 2.9 16.2 + - - +
601B GLU* 3.7 6.3 - - - +
603B LYS* 1.3 77.1 - - - +
605B ASP* 1.3 65.5 + - - +
607B CYS* 3.3 6.5 + - - +
608B ALA* 3.0 25.3 + - - +
645B LEU* 3.4 16.5 - - + +
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Residues in contact with ASP 605 (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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564B ARG* 5.2 6.2 - - - +
569B VAL* 3.9 19.4 - - + +
570B LYS* 4.9 11.2 + - + +
601B GLU* 2.9 25.8 + - - +
602B ASN* 3.7 10.2 - - - +
603B LYS 3.3 0.2 - - - -
604B ALA* 1.3 75.3 - - - +
606B ILE* 1.3 67.4 + - - +
608B ALA* 3.4 13.2 + - - +
609B VAL* 3.5 17.8 + - - +
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Residues in contact with ILE 606 (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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569B VAL* 3.5 18.6 - - + -
573B MSE 4.2 17.3 - - + -
592B LEU* 4.3 18.4 - - + +
595B LEU* 5.9 0.2 - - + -
596B SER* 3.5 33.2 - - - +
602B ASN 3.1 15.1 + - - +
603B LYS 3.2 6.5 + - - +
605B ASP* 1.3 77.5 - - - +
607B CYS* 1.3 65.3 + - - +
608B ALA 3.2 1.2 + - - -
609B VAL* 3.3 10.8 + - - +
612B ALA* 3.3 16.7 - - + +
613B LEU* 5.0 0.9 - - + -
616B LEU* 4.0 26.5 - - + -
638B ILE* 4.0 11.0 - - + -
642B VAL* 4.1 14.6 - - + -
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Residues in contact with CYS 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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603B LYS 3.2 15.6 + - - +
604B ALA* 3.3 9.4 + - - +
606B ILE* 1.3 80.1 - - - +
608B ALA* 1.3 60.3 + - - +
609B VAL 3.5 5.8 + - - +
612B ALA* 5.3 0.2 - - - -
613B LEU* 3.9 29.1 - - + +
642B VAL* 3.9 26.2 - - - -
645B LEU* 4.8 8.7 - - + -
646B ILE* 4.1 13.0 - - - -
652B HIS* 3.7 34.8 + - + +
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Residues in contact with ALA 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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604B ALA 3.0 16.0 + - - +
605B ASP* 3.8 10.8 - - - +
606B ILE 3.1 0.8 - - - -
607B CYS* 1.3 78.2 - - - +
609B VAL* 1.3 62.1 + - - +
610B ASP* 3.3 4.0 + - - +
652B HIS* 5.5 1.8 - - - -
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Residues in contact with VAL 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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570B LYS* 4.2 24.5 - - + -
573B MSE 3.9 27.4 - - + -
574B GLU* 4.1 17.9 - - + +
577B LEU* 3.9 18.2 - - + -
605B ASP 3.5 16.4 - - - +
606B ILE 3.3 8.4 + - - +
607B CYS 4.0 5.0 - - - +
608B ALA* 1.3 78.4 - - + +
610B ASP* 1.3 73.6 + - - +
611B GLY 3.2 0.5 + - - -
612B ALA* 3.0 21.5 + - + +
613B LEU 4.7 0.5 + - - -
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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