Contacts of the helix formed by residues 669 - 677 (chain B) in PDB entry 5MBV
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 669 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B MET 3.1 12.2 + - - -
666B SER* 2.9 19.2 - - - +
667B ALA 3.2 9.6 + - - -
668B ARG* 1.3 77.5 - - - +
670B ILE* 1.3 62.7 + - - +
671B ALA 3.3 2.5 - - - +
672B GLU* 3.6 19.1 + - + +
673B ASN* 2.8 29.5 + - - +
808C PRO* 5.6 6.1 - - - +
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Residues in contact with ILE 670 (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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620B MET* 3.3 51.8 - - + +
621B MET* 3.7 21.1 - - - +
664B LEU* 4.6 10.5 - - + +
665B MET* 3.5 36.9 + - + +
668B ARG* 3.7 20.2 - - + +
669B ASN* 1.3 77.2 - - - +
671B ALA* 1.3 62.2 + - - +
673B ASN* 3.7 8.7 - - - +
674B LEU* 2.8 41.0 + - + +
684B LEU* 6.3 0.4 - - + -
687B ILE* 5.9 0.2 - - + -
817C HIS* 5.1 3.1 - - + +
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Residues in contact with ALA 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B MET* 3.7 34.4 + - + +
669B ASN* 3.3 0.8 - - - -
670B ILE* 1.3 83.7 - - - +
672B GLU* 1.3 60.3 + - - +
674B LEU* 4.2 0.3 - - - +
675B LEU* 3.3 28.4 + - - +
684B LEU* 3.9 15.1 - - + +
805C GLU 5.8 3.1 - - - +
806C TRP* 4.0 21.5 - - + -
809C ALA* 4.5 4.3 - - + -
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Residues in contact with GLU 672 (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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669B ASN* 3.6 21.4 + - + +
670B ILE 3.2 0.2 - - - -
671B ALA* 1.3 76.8 - - - +
673B ASN* 1.3 67.8 + - - +
675B LEU* 3.4 4.1 + - - +
676B ALA* 3.2 20.8 + - - +
808C PRO* 3.0 51.5 - - + +
809C ALA* 4.1 14.7 - - + +
811C SER* 4.3 0.2 + - - -
812C GLN* 5.2 3.2 - - - -
813C ALA* 3.5 7.3 + - - +
814C GLY* 2.8 38.0 + - - +
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Residues in contact with ASN 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B MET 5.9 0.2 + - - -
668B ARG 4.0 7.5 + - - -
669B ASN* 2.8 29.1 + - - +
670B ILE* 3.2 6.5 + - - +
672B GLU* 1.3 81.2 - - - +
674B LEU* 1.3 60.4 + - - +
676B ALA* 3.3 3.9 + - - +
677B THR* 2.9 27.2 + - - -
814C GLY* 4.5 3.1 - - - -
815C LYS* 3.3 41.4 + - - +
817C HIS* 3.3 29.6 - - + +
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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
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619B SER 4.9 4.9 - - - +
620B MET* 5.1 7.4 - - + +
670B ILE* 2.8 27.8 + - + +
671B ALA 4.2 4.0 - - - +
673B ASN* 1.3 75.7 - - - +
675B LEU* 1.3 64.8 + - - +
677B THR* 3.1 23.2 + - - +
680B GLY* 3.2 24.3 - - - +
683B ARG* 3.7 42.0 - - + +
684B LEU* 4.1 17.9 - - + -
687B ILE* 3.8 29.2 - - + -
817C HIS* 3.7 19.1 - - + +
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Residues in contact with LEU 675 (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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671B ALA 3.3 12.5 + - - +
672B GLU* 3.4 6.2 + - - +
673B ASN 3.4 0.2 - - - -
674B LEU* 1.3 76.7 - - - +
676B ALA* 1.3 60.6 + - - +
677B THR 3.9 3.8 - - - +
681B GLU* 3.7 34.8 + - + +
684B LEU* 3.7 20.2 - - + -
789C PHE* 4.1 28.3 - - + +
809C ALA* 3.4 44.4 - - + +
812C GLN* 3.7 25.5 + - + -
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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
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672B GLU 3.2 12.8 + - - +
673B ASN 3.6 7.9 - - - +
674B LEU 3.1 0.6 - - - -
675B LEU* 1.3 76.1 - - - +
677B THR* 1.3 62.9 + - - +
678B ALA* 3.6 2.1 + - - -
812C GLN* 4.9 13.0 + - + +
814C GLY 3.3 26.9 - - - +
815C LYS 3.9 2.0 - - - -
816C ALA* 3.9 23.2 - - + +
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Residues in contact with THR 677 (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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673B ASN 2.9 15.1 + - - -
674B LEU* 3.1 16.6 + - - +
675B LEU 3.9 4.2 - - - +
676B ALA* 1.3 77.8 - - - +
678B ALA* 1.3 76.3 + - - +
679B GLY 3.3 0.7 + - - -
680B GLY* 3.0 18.1 + - - +
681B GLU 4.6 0.3 + - - -
683B ARG* 5.3 12.8 - - - +
816C ALA* 4.2 7.2 - - + -
817C HIS* 3.1 36.5 + - + +
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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