Contacts of the helix formed by residues 705 - 711 (chain B) in PDB entry 5MJA
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 LEU 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703B GLY 3.6 0.4 + - - -
704B ALA* 1.3 70.0 - - - +
706B ASP* 1.4 66.0 + - - +
708B PHE* 3.3 3.8 + - + +
709B LEU* 3.0 56.8 + - + +
724B MET* 4.1 9.4 - - + -
728B ILE* 3.7 24.0 - - + -
747B ALA* 3.4 19.4 + - + +
750B ILE* 2.8 24.8 + - + +
752B VAL* 3.7 25.6 - - + -
758B CYS* 4.1 10.8 - - - -
813B VAL* 4.8 0.2 - - + -
817B VAL* 3.6 24.7 - - + -
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Residues in contact with ASP 706 (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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704B ALA* 3.5 11.3 - - - +
705B LEU* 1.4 77.5 - - - +
707B SER* 1.4 61.3 + - - +
709B LEU* 3.6 2.0 + - - -
710B ARG* 2.8 62.8 + - - +
747B ALA* 3.6 23.6 + - + +
748B ARG* 3.3 31.4 - - - +
816B GLU* 4.5 7.4 - - - +
821B GLY* 3.8 12.7 - - - -
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Residues in contact with SER 707 (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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702B ASN 5.6 0.2 + - - -
704B ALA* 3.5 19.4 + - - +
706B ASP* 1.4 78.7 + - - +
708B PHE* 1.3 66.8 + - - +
710B ARG* 3.4 23.4 + - - +
711B GLN* 3.0 40.1 + - - +
901B 7O3 5.8 2.4 - - - +
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Residues in contact with PHE 708 (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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702B ASN* 3.4 45.8 - - + +
704B ALA 3.1 19.7 + - - +
705B LEU* 3.3 12.5 + - + +
707B SER* 1.3 77.9 + - - +
709B LEU* 1.3 62.9 + - + +
711B GLN* 3.4 5.3 + - + +
712B ASN* 2.7 52.2 + - - +
716B PHE* 3.5 37.2 - + - -
724B MET* 4.9 5.2 - - + -
752B VAL* 4.0 21.3 - - + -
756B LEU* 3.5 22.9 - - + -
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Residues in contact with LEU 709 (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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705B LEU* 3.0 46.4 + - + +
706B ASP* 3.9 3.1 - - - +
708B PHE* 1.3 75.5 - - + +
710B ARG* 1.4 62.7 + - - +
712B ASN* 3.1 14.5 + - - +
713B ASP* 3.1 15.1 + - - -
716B PHE* 4.1 18.2 - - + -
721B LEU* 3.9 24.7 - - + -
724B MET* 4.2 6.3 - - - -
747B ALA* 5.8 0.4 - - + -
816B GLU 4.2 6.5 - - - +
817B VAL* 3.6 36.3 - - + +
820B PHE* 3.7 24.0 - - + +
821B GLY* 4.2 2.2 - - - +
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Residues in contact with ARG 710 (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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706B ASP* 2.8 53.3 + - - +
707B SER* 3.4 20.8 + - - +
709B LEU* 1.4 74.8 - - - +
711B GLN* 1.3 59.3 + - + +
712B ASN 3.2 0.7 + - - -
713B ASP* 3.8 15.9 + - - +
820B PHE 3.4 12.3 - - - +
821B GLY 2.9 34.0 + - - +
822B GLU 5.3 1.0 - - - -
823B ARG* 5.4 1.6 - - - +
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Residues in contact with GLN 711 (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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707B SER* 3.0 33.2 + - - +
708B PHE* 3.7 6.7 - - - +
709B LEU 3.3 0.2 - - - -
710B ARG* 1.3 75.9 - - + +
712B ASN* 1.3 69.7 + - - +
713B ASP 3.7 1.3 - - - -
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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