Contacts of the helix formed by residues 594 - 605 (chain B) in PDB entry 4MVY
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 SER 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551B ASP* 3.6 21.1 - - - -
580B PHE* 4.5 3.5 - - - -
592B ASP* 4.0 6.8 + - - -
593B TYR* 1.3 88.3 - - - +
595B ASP* 1.3 58.9 + - - +
596B LYS* 3.9 8.1 + - - +
597B ASN* 3.2 29.5 + - - +
598B MET* 2.9 28.9 + - - +
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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
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550B LYS* 4.8 6.1 + - - +
551B ASP* 4.8 1.4 + - - -
568B LYS* 2.8 28.4 + - - -
571B GLU* 4.9 1.7 - - - +
572B PHE* 3.6 17.1 - - + -
593B TYR* 2.7 32.7 + - - -
594B SER* 1.3 70.4 - - - +
596B LYS* 1.3 60.5 + - - +
598B MET* 3.4 1.2 - - - +
599B ILE* 2.8 43.3 + - + +
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Residues in contact with LYS 596 (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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594B SER* 4.0 8.0 - - - +
595B ASP* 1.3 78.9 - - - +
597B ASN* 1.3 67.6 + - - +
599B ILE* 3.5 7.6 + - - +
600B ALA* 3.0 27.2 + - + +
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Residues in contact with ASN 597 (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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580B PHE* 3.6 14.1 - - + -
584B GLU* 3.8 25.8 + - - -
592B ASP 5.4 1.8 - - - +
594B SER* 3.2 21.3 + - - +
596B LYS* 1.3 84.9 - - - +
598B MET* 1.3 66.1 + - - +
600B ALA* 3.3 8.9 + - - +
601B ARG* 3.0 34.1 + - - +
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Residues in contact with MET 598 (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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572B PHE* 3.7 37.7 - - + -
576B ALA* 3.5 37.2 - - + +
577B LEU* 3.6 11.9 - - + +
580B PHE* 3.5 33.3 - - - -
593B TYR* 3.7 28.7 - - + +
594B SER 2.9 18.2 + - - +
595B ASP* 3.4 4.5 - - - +
597B ASN* 1.3 76.7 - - - +
599B ILE* 1.3 57.7 + - - +
601B ARG* 3.4 2.1 + - - +
602B LEU* 2.9 35.9 + - + +
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Residues in contact with ILE 599 (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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572B PHE* 3.7 31.9 - - + -
595B ASP* 2.8 30.7 + - + +
596B LYS* 3.8 6.7 - - - +
598B MET* 1.3 70.2 - - - +
600B ALA* 1.3 62.0 + - - +
602B LEU* 4.2 5.8 - - - -
603B ASN* 2.8 51.1 + - - +
765B ARG* 3.9 18.8 - - + +
766B SER 3.7 20.0 - - - +
767B THR* 5.0 6.1 - - - -
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Residues in contact with ALA 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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596B LYS* 3.0 19.2 + - + +
597B ASN* 3.3 12.3 + - - +
599B ILE* 1.3 78.0 - - - +
601B ARG* 1.3 58.8 + - + +
603B ASN* 4.2 3.2 - - - +
604B GLY* 2.9 26.9 + - - -
605B GLU* 4.5 2.6 - - - +
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Residues in contact with ARG 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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579B TYR* 4.2 14.1 - - + -
580B PHE* 3.8 18.6 - - + -
583B ARG* 3.6 33.8 - - - +
584B GLU* 2.7 39.7 + - - +
597B ASN* 3.0 21.6 + - - +
598B MET 4.0 2.9 - - - +
600B ALA* 1.3 74.5 - - + +
602B LEU* 1.3 65.5 + - - +
605B GLU* 3.0 60.3 + - - +
606B LEU* 3.3 9.2 + - - +
802B GOL 3.2 41.6 + - - -
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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
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572B PHE* 4.1 24.0 - - + +
576B ALA* 4.5 4.7 - - + -
598B MET* 2.9 25.8 + - + +
599B ILE* 3.8 5.4 - - - +
601B ARG* 1.3 79.0 - - - +
603B ASN* 1.3 65.8 + - - +
606B LEU* 3.4 17.0 + - + +
607B ALA* 2.9 27.9 + - + +
762B PHE* 4.1 28.9 - - + -
763B SER 4.2 11.7 - - - +
765B ARG* 3.4 40.2 - - + +
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Residues in contact with ASN 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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599B ILE* 2.8 33.6 + - - +
600B ALA* 4.2 3.6 - - - +
602B LEU* 1.3 78.7 - - - +
604B GLY* 1.3 57.4 + - - +
607B ALA* 3.6 6.1 - - - +
608B ASP* 3.0 36.8 + - - +
764B LYS* 3.4 24.5 - - - +
765B ARG 3.1 41.8 + - - +
767B THR* 5.4 3.0 - - - +
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Residues in contact with GLY 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 ALA 2.9 20.5 + - - -
603B ASN* 1.3 74.8 - - - +
605B GLU* 1.3 64.9 + - - +
608B ASP* 3.3 20.3 - - - +
609B THR* 3.3 16.6 + - - -
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Residues in contact with GLU 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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579B TYR* 2.6 34.8 + - + +
583B ARG* 4.0 4.9 - - - +
600B ALA 4.5 2.1 - - - +
601B ARG* 3.0 60.2 + - - +
604B GLY* 1.3 80.2 - - - +
606B LEU* 1.3 60.6 + - - +
607B ALA 3.6 0.2 - - - -
609B THR* 3.3 9.7 + - - +
610B LEU 3.1 24.3 + - - -
669B PHE* 3.4 21.5 - - + -
673B ARG* 4.8 10.3 - - - +
802B GOL 4.9 2.4 + - - -
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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