Contacts of the helix formed by residues 606 - 613 (chain A) in PDB entry 1VOM
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 ASN 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A SER* 5.5 2.2 - - - +
604A SER 3.6 6.9 + - - -
605A ASP* 1.3 75.6 + - - +
607A VAL* 1.3 68.1 + - + +
609A THR* 3.8 7.7 - - - +
610A LYS* 3.5 21.0 + - - +
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Residues in contact with VAL 607 (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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340A GLU* 4.5 14.4 - - + +
343A SER* 3.5 24.2 - - - +
344A ILE* 5.3 1.3 - - + -
347A ILE* 3.8 19.1 - - + -
429A LEU* 4.8 1.8 - - + -
432A TRP* 4.1 49.8 - - + -
605A ASP* 2.6 16.6 + - - +
606A ASN* 1.3 74.3 - - + +
608A VAL* 1.3 64.7 + - - +
609A THR 3.1 1.8 - - - -
610A LYS* 2.9 16.4 + - - +
611A LEU* 3.1 15.6 + - + +
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Residues in contact with VAL 608 (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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346A LYS* 6.5 0.2 - - + -
347A ILE* 3.7 28.0 - - + -
382A PHE* 4.1 17.3 - - + +
425A LEU* 5.0 2.2 - - + -
600A PHE* 3.8 26.7 - - + +
603A SER* 3.4 32.8 - - - +
605A ASP* 2.9 24.2 + - + +
607A VAL* 1.3 74.2 - - - +
609A THR* 1.3 62.0 - - - +
611A LEU* 3.1 17.3 + - - +
612A PHE* 3.2 21.2 - - + -
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Residues in contact with THR 609 (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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600A PHE 4.7 5.6 - - - -
601A LYS 4.3 5.0 + - - +
603A SER* 3.1 20.8 + - - -
605A ASP 2.8 19.4 + - - -
606A ASN* 3.8 8.9 - - - +
607A VAL 3.1 0.2 - - - -
608A VAL* 1.3 76.5 - - - +
610A LYS* 1.3 55.1 + - + +
612A PHE* 3.1 2.3 + - - -
613A ASN* 2.6 64.6 + - + +
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Residues in contact with LYS 610 (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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432A TRP* 4.6 22.2 - - + +
606A ASN 3.5 10.4 + - - +
607A VAL* 2.9 10.3 + - - +
609A THR* 1.3 80.8 - - + +
611A LEU* 1.3 66.3 + - - +
613A ASN* 4.9 1.1 - - + +
614A ASP* 2.9 63.8 + - + +
617A ILE* 4.3 4.2 - - + +
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Residues in contact with LEU 611 (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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347A ILE* 3.9 24.2 - - + -
425A LEU* 4.0 22.0 - - + +
428A ARG* 3.2 39.9 + - + +
429A LEU* 3.9 19.5 - - - +
432A TRP* 3.6 36.8 - - + -
607A VAL* 3.1 19.2 + - + +
608A VAL* 3.1 10.3 + - - +
610A LYS* 1.3 79.0 - - - +
612A PHE* 1.3 66.6 + - + +
617A ILE* 3.6 9.9 - - + +
618A ALA* 3.4 8.1 - - - +
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Residues in contact with PHE 612 (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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421A LEU* 4.4 7.4 - - + -
424A ALA* 5.4 0.9 - - + -
425A LEU* 3.5 36.3 - - + -
428A ARG* 3.5 26.4 + - - -
592A LEU* 4.6 6.7 - - + -
596A LEU 4.6 0.9 - - - -
597A GLU* 4.0 30.6 - - + +
600A PHE* 3.4 38.1 - + + -
601A LYS* 3.7 39.5 + - + +
608A VAL* 3.2 18.2 - - + +
609A THR 3.1 3.6 + - - +
610A LYS 3.1 0.4 - - - -
611A LEU* 1.3 87.6 - - + +
613A ASN* 1.3 58.6 + - - +
618A ALA* 3.2 17.9 - - - +
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Residues in contact with ASN 613 (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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601A LYS* 3.0 52.5 + - - +
609A THR* 2.6 49.2 + - + +
610A LYS* 4.9 0.9 - - + -
612A PHE* 1.3 73.3 - - - +
614A ASP* 1.3 62.1 + - - +
615A PRO* 3.2 9.9 - - - +
618A ALA* 4.5 0.9 - - - -
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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