Contacts of the strand formed by residues 734 - 739 (chain F) in PDB entry 6MZL
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 THR 734 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709F GLY 5.9 2.0 - - - +
710F HIS* 4.4 10.2 + - - -
729F GLY* 3.4 22.0 - - - -
730F SER* 2.4 35.4 + - - -
732F ASP* 2.9 29.2 + - - +
733F ASN* 1.3 77.2 - - - +
735F VAL* 1.3 65.9 + - - +
736F ARG* 4.1 9.2 - - - +
758F HIS* 5.4 5.2 - - + -
759F ILE 3.8 3.8 - - - -
760F ASN* 3.5 20.2 - - - +
761F LEU* 4.8 0.2 - - - +
766F GLN* 4.0 2.5 - - - +
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Residues in contact with VAL 735 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461F ILE* 5.6 0.2 - - + -
727F ALA* 6.0 1.8 - - + -
728F SER 3.4 13.2 - - - +
734F THR* 1.3 73.3 - - - +
736F ARG* 1.3 66.3 + - - +
737F LEU* 4.2 8.3 + - + +
757F GLY 4.5 0.2 - - - +
758F HIS* 3.3 1.4 - - - -
759F ILE* 2.7 57.1 + - + +
761F LEU* 4.5 12.6 - - + -
766F GLN* 3.3 30.3 - - - +
769F LEU* 6.3 1.3 - - + -
778F THR* 6.2 0.9 - - + -
780F VAL* 5.2 4.5 - - + -
782F HIS* 5.3 0.4 - - + -
792F LEU* 4.1 35.2 - - + -
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Residues in contact with ARG 736 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708F LYS 2.6 29.7 + - - -
709F GLY* 3.1 31.9 + - - -
710F HIS* 3.6 27.2 + - + +
728F SER* 3.1 34.6 + - - -
734F THR* 4.1 7.5 + - - +
735F VAL* 1.3 73.7 - - - +
737F LEU* 1.3 66.4 + - - +
738F TRP* 3.6 32.4 - - + +
756F THR 5.5 2.5 - - - +
757F GLY 4.4 4.3 - - - +
758F HIS* 3.7 34.0 + - + +
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Residues in contact with LEU 737 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F PRO* 6.2 1.6 - - + -
725F ILE* 5.0 7.9 - - + -
726F LEU 3.3 15.7 - - - +
727F ALA* 4.0 17.5 - - + -
728F SER 5.3 0.2 - - - +
735F VAL* 4.1 7.9 + - + -
736F ARG* 1.3 76.8 - - - +
738F TRP* 1.3 76.6 - - - +
739F ASP* 5.3 5.8 - - - +
756F THR* 3.3 31.5 - - + +
757F GLY 4.0 7.3 + - - +
759F ILE* 5.7 9.4 - - + -
778F THR* 5.4 3.1 - - - +
792F LEU* 5.0 14.6 - - + -
793F ALA 4.3 8.5 - - - +
794F ALA* 4.0 28.0 - - + -
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Residues in contact with TRP 738 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693F VAL* 5.8 1.2 - - - +
707F LEU* 3.6 45.9 - - + +
708F LYS 4.2 7.2 - - - -
710F HIS* 3.7 23.1 + - - -
724F GLU 3.6 6.1 - - - +
725F ILE* 3.6 1.6 - - - -
726F LEU* 3.2 61.3 + - + +
728F SER* 4.1 5.2 - - - -
736F ARG* 3.6 52.3 + - + +
737F LEU* 1.3 87.4 - - - +
739F ASP* 1.3 62.4 + - - +
740F ALA* 3.4 11.0 + - + +
753F THR* 6.1 0.4 - - - -
754F THR 5.2 4.5 - - - -
755F ALA* 3.7 25.8 - - + -
756F THR* 3.5 18.4 - - - -
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Residues in contact with ASP 739 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724F GLU 4.4 3.4 - - - -
725F ILE* 3.6 32.3 - - - +
737F LEU* 5.3 4.5 - - - +
738F TRP* 1.3 69.0 + - - +
740F ALA* 1.3 59.5 + - - +
741F ILE* 4.2 2.5 - - - -
755F ALA* 3.9 15.0 - - - +
756F THR* 2.5 28.1 + - - +
796F ALA* 3.5 37.9 + - - +
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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