Contacts of the helix formed by residues 689 - 696 (chain C) in PDB entry 4MG5
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 ILE 689 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ASP* 3.6 39.0 - - + -
539A LEU* 3.8 21.8 - - + +
542A GLU* 3.0 29.2 + - - +
688C LYS* 1.3 71.1 - - - +
690C LEU* 1.3 58.0 + - - +
692C ARG* 3.0 25.4 + - - +
693C LEU* 2.9 46.3 + - + +
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ILE* 3.5 31.2 - - + -
376A VAL* 3.7 32.5 - - + +
379A LEU* 3.7 20.9 - - + -
380A GLU* 3.7 20.2 - - + +
539A LEU* 4.1 8.1 - - + +
542A GLU* 4.3 2.3 + - + +
543A MET* 3.8 27.1 - - + -
688C LYS* 3.4 5.5 - - + +
689C ILE* 1.3 78.5 - - - +
691C HIS* 1.3 62.8 + - - +
693C LEU* 3.3 5.2 + - - +
694C LEU* 3.0 31.6 + - + +
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Residues in contact with HIS 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.0 40.7 - - + +
373A HIS* 6.1 0.7 - - - -
376A VAL* 4.0 19.0 - - + +
688C LYS* 3.0 35.5 + - + +
690C LEU* 1.3 80.1 - - - +
692C ARG* 1.3 60.3 + - - +
694C LEU* 3.5 3.8 + - - +
695C GLN* 3.3 40.7 + - - +
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Residues in contact with ARG 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688C LYS 3.0 11.7 + - - +
689C ILE* 3.3 23.7 + - - +
691C HIS* 1.3 76.5 + - - +
693C LEU* 1.3 86.2 + - - +
695C GLN* 3.2 18.5 + - - +
696C GLU* 3.0 60.2 + - - +
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Residues in contact with LEU 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A VAL* 4.8 18.8 - - + -
358A ILE* 3.5 39.1 - - + +
359A ASN* 4.6 5.9 + - - +
362A LYS* 3.0 20.1 + - - -
539A LEU* 4.1 12.1 - - + -
689C ILE* 2.9 34.7 + - + +
690C LEU 3.3 1.3 + - - +
692C ARG* 1.3 106.9 - - - +
694C LEU* 1.3 57.6 + - - +
696C GLU* 3.2 14.3 - - + +
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Residues in contact with LEU 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ILE* 3.9 22.0 - - + +
362A LYS* 3.0 30.8 - - + +
367A PHE* 4.0 15.5 - - + -
372A LEU* 3.7 15.4 - - + +
375A GLN* 3.5 28.0 - - + +
376A VAL* 3.8 41.3 - - + +
379A LEU* 4.1 5.6 - - + -
690C LEU* 3.0 28.5 + - + +
691C HIS 3.7 1.1 - - - +
692C ARG 3.2 0.2 - - - -
693C LEU* 1.3 76.0 - - - +
695C GLN* 1.3 65.4 + - - +
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Residues in contact with GLN 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LYS* 4.8 0.2 + - - -
372A LEU* 3.5 32.3 - - + +
691C HIS* 3.3 23.6 + - - +
692C ARG* 3.2 14.0 + - - +
694C LEU* 1.3 82.5 - - - +
696C GLU* 1.3 66.6 + - - +
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Residues in contact with GLU 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ASN* 4.6 2.6 - - - +
362A LYS* 3.1 23.5 + - - -
692C ARG* 3.0 62.6 + - - +
693C LEU* 3.2 12.1 + - + +
695C GLN* 1.3 87.0 - - - +
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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