Contacts of the helix formed by residues 739 - 744 (chain B) in PDB entry 4YZC
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 ALA 739 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B TRP 3.8 2.4 + - - -
738B ILE* 1.3 80.8 - - - +
740B PRO* 1.3 73.8 - - + +
741B GLU* 3.4 26.2 - - - +
742B MET* 3.2 16.3 + - + +
743B LEU* 3.5 6.1 + - - +
755B VAL* 3.9 25.0 - - + +
758B PHE* 3.6 22.4 - - + -
759B SER* 4.8 0.2 + - - -
782B GLN* 5.0 0.2 + - - -
820B ARG* 4.0 0.9 - - - +
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Residues in contact with PRO 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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739B ALA* 1.3 83.0 - - + +
741B GLU* 1.3 71.9 + - - +
742B MET 3.1 0.9 + - - -
743B LEU* 3.1 7.2 + - + +
744B SER* 3.1 25.8 + - - -
758B PHE* 3.7 17.3 - - + -
785B ILE* 3.7 25.1 - - + +
786B LEU* 5.0 5.6 - - - -
815B MET* 3.6 41.1 - - + +
820B ARG* 3.5 14.6 - - - +
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Residues in contact with GLU 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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727B ARG* 2.7 30.1 + - - +
739B ALA* 3.4 11.5 - - - +
740B PRO* 1.3 74.3 - - - +
742B MET* 1.3 59.2 + - - +
744B SER* 3.7 11.4 - - - -
747B CYS* 4.0 20.4 - - - -
749B GLU 5.4 0.9 - - - +
750B ASN 5.6 0.4 - - - +
751B PRO* 4.3 23.0 - - + +
754B THR* 4.3 1.2 + - - -
755B VAL* 3.6 16.3 + - + +
815B MET 4.6 2.4 + - - +
817B PRO* 3.7 24.5 - - + +
820B ARG* 2.7 45.3 + - - -
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Residues in contact with MET 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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687B ARG* 5.6 0.7 - - + -
725B PHE* 3.9 17.5 - - + -
727B ARG* 3.9 29.7 - - + +
730B GLY 4.4 3.6 - - - +
731B VAL* 4.7 10.1 - - + +
732B PRO* 3.5 37.7 - - + +
738B ILE* 3.6 15.5 - - + -
739B ALA* 3.2 10.7 + - + +
740B PRO 3.0 0.8 - - - -
741B GLU* 1.3 78.2 - - - +
743B LEU* 1.3 64.1 + - - +
744B SER 3.3 0.9 + - - -
751B PRO* 3.2 36.1 - - - -
755B VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 743 (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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731B VAL* 5.4 6.7 - - - -
738B ILE* 4.5 6.5 - - + +
739B ALA 3.5 6.6 + - - +
740B PRO* 3.1 9.8 + - + +
742B MET* 1.3 78.8 - - - +
744B SER* 1.3 56.8 + - - +
782B GLN* 4.3 20.2 - - + +
786B LEU* 5.9 6.3 - - + -
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Residues in contact with SER 744 (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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727B ARG* 4.2 8.9 + - - -
740B PRO 3.1 15.2 + - - -
741B GLU* 3.7 19.9 - - - -
742B MET 3.2 2.7 - - - -
743B LEU* 1.3 79.3 - - - +
747B CYS* 4.0 31.1 + - - +
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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