Contacts of the strand formed by residues 739 - 744 (chain A) 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 LEU 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A ASN* 3.9 20.4 - - + +
703A TYR 3.5 15.3 - - - +
704A TYR* 3.7 25.4 - - + -
714A ALA* 4.7 8.1 - - + -
715A PRO* 4.7 17.9 - - + +
717A CYS* 3.7 29.8 - - - -
722A THR* 5.9 0.2 - - - +
737A GLY 3.8 2.8 + - - +
738A GLN* 1.3 79.8 + - - +
740A LEU* 1.3 63.8 + - - +
741A GLN* 3.9 19.3 - - + +
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Residues in contact with LEU 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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701A LYS 3.8 0.5 - - - +
703A TYR* 2.8 44.3 + - + +
730A PHE* 3.7 30.1 - - + -
734A LEU* 4.6 17.0 - - + -
738A GLN* 5.1 9.2 - - - +
739A LEU* 1.3 76.7 - - - +
741A GLN* 1.3 70.4 + - - +
751A PRO* 4.1 6.1 - - + -
753A TYR* 3.6 39.0 - - + +
1070A PHE* 3.7 28.9 - - + -
1074A ASN* 3.8 5.8 - - - +
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Residues in contact with GLN 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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700A ILE* 4.6 2.7 - - + -
701A LYS 4.0 5.2 - - - -
702A ASN* 3.3 18.4 + - - +
717A CYS* 3.1 34.8 - - - +
718A LYS 5.5 0.2 - - - +
719A TYR* 4.6 5.1 + - - +
739A LEU* 3.9 11.7 - - + +
740A LEU* 1.3 75.3 - - - +
742A ALA* 1.3 65.2 + - - +
751A PRO* 3.3 8.3 - - - +
752A ILE* 2.8 42.3 + - + +
753A TYR* 5.5 0.8 - - - -
754A LEU* 4.2 16.9 + - - +
780A PHE* 3.3 27.8 - - - -
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Residues in contact with ALA 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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700A ILE* 3.3 7.8 - - - +
701A LYS 3.2 26.7 + - - -
703A TYR* 4.0 11.9 - - + -
730A PHE* 3.6 26.5 - - + -
741A GLN* 1.3 78.3 - - - +
743A PHE* 1.3 61.0 + - - +
744A GLU* 3.7 15.2 - - - +
750A ALA 3.3 13.0 - - - +
751A PRO* 4.0 0.2 - - + -
752A ILE* 3.5 10.5 - - - +
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Residues in contact with PHE 743 (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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679A ILE* 4.1 16.2 - - + -
681A ALA* 3.9 21.8 - - + -
683A TYR* 4.3 13.9 - + - -
692A MET* 5.4 0.9 - - + -
698A THR* 4.1 16.2 - - + +
699A LYS 3.4 4.0 - - - -
700A ILE* 3.8 20.6 - - + -
742A ALA* 1.3 71.5 - - - +
744A GLU* 1.3 71.6 + - - +
745A ASN 4.4 0.2 - - - -
748A PHE* 4.4 20.0 - + + -
749A ARG* 3.6 4.0 - - - -
750A ALA* 2.8 26.9 + - + +
752A ILE* 3.6 35.1 - - + +
780A PHE* 5.0 2.2 - - + -
782A VAL* 3.7 28.9 - - + -
77J LEU* 4.7 9.9 - - + -
85J PHE* 4.6 5.6 - + - -
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Residues in contact with GLU 744 (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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589A ILE* 4.0 2.6 - - - +
698A THR* 2.9 3.2 + - - -
699A LYS* 2.7 48.3 + - + +
701A LYS* 3.7 28.0 - - + +
703A TYR* 3.1 33.7 + - - +
742A ALA* 3.7 7.7 - - - +
743A PHE* 1.3 80.5 - - - +
745A ASN* 1.3 61.5 + - - +
748A PHE 4.2 1.6 - - - +
749A ARG* 2.9 51.0 + - - +
788A LEU* 5.0 1.9 - - - +
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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