Contacts of the helix formed by residues 737 - 742 (chain A) 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 GLY 737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A VAL 2.6 20.3 + - - -
276A LYS 4.3 7.2 - - - -
277A GLY* 4.6 3.8 - - - -
711A LEU* 4.8 0.2 - - - +
736A LYS* 1.3 78.3 - - - +
738A ILE* 1.3 60.9 + - - -
739A GLU* 3.1 13.0 - - - -
740A ASN* 3.0 20.8 + - - +
741A PHE* 3.8 9.4 + - - -
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Residues in contact with ILE 738 (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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276A LYS* 3.7 44.2 + - + +
737A GLY* 1.3 67.0 - - - -
739A GLU* 1.3 78.5 + - + +
740A ASN 3.0 2.0 - - - -
741A PHE* 3.0 37.4 + - + +
742A GLU* 4.0 6.1 + - - +
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Residues in contact with GLU 739 (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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736A LYS 4.9 0.5 - - - +
737A GLY* 3.5 9.5 - - - -
738A ILE* 1.3 97.9 + - + +
740A ASN* 1.3 67.9 + - - +
742A GLU* 3.4 32.5 + - - +
745A ALA* 4.5 3.5 - - - +
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Residues in contact with ASN 740 (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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707A ARG* 2.8 35.3 + - - +
708A VAL* 4.8 0.9 - - - +
711A LEU* 3.4 13.3 - - + +
733A VAL* 3.3 17.0 + - - +
734A HIS* 2.7 48.5 + - - +
736A LYS 2.7 23.7 + - - +
737A GLY* 3.0 8.8 + - - +
739A GLU* 1.3 85.8 + - - +
741A PHE* 1.3 58.9 + - - +
742A GLU 3.1 1.1 - - - -
745A ALA* 3.4 13.2 - - - +
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Residues in contact with PHE 741 (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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272A TYR* 3.8 23.3 - + - -
275A VAL* 4.6 11.4 - - + -
276A LYS* 4.1 25.6 - - + -
645A ILE 5.3 0.7 - - - +
646A LYS* 5.6 1.7 - - - +
649A PRO* 3.4 47.7 - - + +
653A ASP* 5.1 3.1 - - + -
707A ARG* 4.8 0.4 - - - -
708A VAL* 4.4 10.5 - - - +
711A LEU* 3.7 28.7 - - + -
712A LEU* 4.1 19.5 - - + -
737A GLY 3.8 13.5 - - - -
738A ILE* 3.0 28.8 + - + +
740A ASN* 1.3 78.3 - - - +
742A GLU* 1.3 62.4 + - + +
743A PHE 3.7 1.4 + - - -
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Residues in contact with GLU 742 (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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707A ARG* 3.0 21.8 + - - -
708A VAL* 5.1 0.2 - - - -
738A ILE 4.3 7.2 - - - +
739A GLU* 3.4 20.9 - - - +
740A ASN 3.1 1.0 - - - -
741A PHE* 1.3 79.2 - - + +
743A PHE* 1.3 67.8 + - - +
744A GLY 3.4 0.9 + - - -
745A ALA* 3.5 8.5 + - + +
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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