Contacts of the helix formed by residues 737 - 742 (chain B) in PDB entry 4MW0
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LYS* 5.8 0.7 - - - -
275B VAL* 2.6 20.6 + - - +
276B LYS 4.0 5.6 - - - -
277B GLY* 4.4 4.7 - - - -
736B LYS* 1.3 75.1 - - - +
738B ILE* 1.3 56.2 + - - +
739B GLU* 3.1 15.9 - - - -
740B ASN* 2.8 31.2 + - - +
741B PHE* 3.7 7.2 + - - -
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Residues in contact with ILE 738 (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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-2B GLY* 5.9 4.0 - - - +
-1B SER 4.2 9.6 - - - +
0B MET* 5.4 1.8 - - - -
237B LYS* 3.9 29.8 - - + +
276B LYS* 3.1 41.5 + - + +
737B GLY* 1.3 70.0 - - - -
739B GLU* 1.3 71.7 + - + +
741B PHE* 2.9 43.3 + - + +
742B GLU* 4.2 4.0 + - - +
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Residues in contact with GLU 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS* 5.0 4.7 + - - -
733B VAL* 5.1 1.0 - - - +
736B LYS 4.0 1.4 - - - +
737B GLY* 3.4 14.3 - - - -
738B ILE* 1.3 89.9 + - + +
740B ASN* 1.3 79.5 + - - +
741B PHE 3.5 0.5 + - - -
742B GLU* 3.6 32.6 + - - +
745B ALA* 4.6 3.5 - - - +
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Residues in contact with ASN 740 (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 ARG* 2.8 31.4 + - - +
708B VAL* 5.0 0.2 - - - +
711B LEU* 3.4 10.1 - - + +
733B VAL* 3.2 17.2 + - - +
734B HIS* 2.8 46.4 + - - +
736B LYS 2.8 24.4 + - - +
737B GLY 2.8 16.5 + - - +
739B GLU* 1.3 87.1 + - - +
741B PHE* 1.3 61.2 + - - -
742B GLU 3.2 2.0 - - - -
745B ALA* 3.6 12.7 - - - +
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Residues in contact with PHE 741 (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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272B TYR* 3.8 31.9 - + - -
275B VAL* 4.1 15.3 - - + -
276B LYS* 3.9 26.2 - - + -
645B ILE 5.2 0.7 - - - +
646B LYS* 6.1 0.2 - - - -
649B PRO* 3.4 46.2 - - + +
653B ASP* 5.4 1.3 - - + -
707B ARG* 4.7 0.2 - - - -
708B VAL* 4.0 14.8 - - - +
711B LEU* 3.8 26.2 - - + -
712B LEU* 4.2 16.4 - - + -
737B GLY 3.8 13.7 - - - -
738B ILE* 2.9 33.0 + - + +
740B ASN* 1.3 79.1 - - - +
742B GLU* 1.3 62.1 + - + +
743B PHE 3.6 1.4 + - - -
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Residues in contact with GLU 742 (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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649B PRO* 5.5 0.4 - - - -
707B ARG* 3.0 19.5 + - - -
708B VAL* 4.8 0.2 - - - -
738B ILE 4.6 2.9 - - - +
739B GLU* 3.7 27.6 - - - +
740B ASN 3.2 1.0 - - - -
741B PHE* 1.3 78.1 - - + +
743B PHE* 1.3 71.2 + - - +
744B GLY 3.3 0.7 + - - -
745B ALA* 3.5 8.6 + - + +
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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