Contacts of the strand formed by residues 778 - 782 (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 ASP 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A LEU 5.2 2.7 - - - +
679A ILE* 3.7 9.2 - - + +
680A LEU 3.3 20.8 + - - +
718A LYS* 2.9 22.6 + - - +
719A TYR* 2.8 39.6 + - + +
754A LEU* 3.9 22.8 - - + +
755A HIS 4.0 4.0 - - - +
756A LYS* 5.7 1.0 - - - +
776A LEU* 3.3 9.3 - - - +
777A VAL* 1.3 90.0 - - - +
779A ILE* 1.3 59.2 - - - +
780A PHE* 5.1 0.9 - - + -
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Residues in contact with ILE 779 (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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680A LEU* 3.3 24.2 - - + +
681A ALA 4.6 0.4 - - - +
682A GLU* 4.1 20.4 - - + +
754A LEU* 3.9 0.7 - - - +
755A HIS* 2.8 33.1 + - - +
756A LYS 3.8 9.4 - - - +
757A MET* 3.7 50.5 - - + +
758A PRO* 5.2 1.1 - - + -
778A ASP* 1.3 74.5 - - - +
780A PHE* 1.3 72.1 + - - +
74J MET* 4.1 17.3 - - + -
136J ILE* 4.8 2.5 - - + -
137J THR* 4.0 19.3 - - + -
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Residues in contact with PHE 780 (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* 3.7 42.6 - - + -
680A LEU 2.9 10.5 + - - +
681A ALA* 3.7 6.0 - - + -
682A GLU* 2.9 30.7 + - - +
700A ILE* 4.5 4.7 - - + -
719A TYR* 3.8 22.7 - + + -
741A GLN* 3.3 24.2 - - - -
743A PHE* 5.0 1.1 - + + -
752A ILE* 3.7 33.7 - - + -
753A TYR 3.3 7.4 - - - -
754A LEU* 3.6 41.5 - - + -
778A ASP* 5.1 0.9 - - + -
779A ILE* 1.3 74.9 - - - +
781A VAL* 1.3 60.8 - - - +
782A VAL* 3.9 4.4 + - + +
85J PHE* 4.7 4.0 - + - -
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Residues in contact with VAL 781 (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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682A GLU* 3.7 3.6 - - - +
684A SER* 4.8 2.0 - - - -
751A PRO 3.7 1.2 - - - +
752A ILE* 3.4 2.9 - - - -
753A TYR* 3.0 33.7 + - + +
755A HIS* 3.5 28.3 - - + +
779A ILE 4.2 0.2 + - - -
780A PHE* 1.3 71.7 - - - +
782A VAL* 1.3 65.5 + - - +
783A GLY 4.0 0.3 + - - -
1077A LEU* 3.8 42.2 - - + +
137J THR* 3.3 35.0 - - + +
139J PRO* 4.8 2.2 - - + -
140J LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 782 (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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681A ALA* 4.3 4.5 - - + -
682A GLU 3.1 9.3 + - - +
683A TYR* 3.6 36.7 - - + -
684A SER* 2.8 31.0 + - - -
743A PHE* 3.7 26.7 - - + -
748A PHE* 5.1 2.5 - - + -
750A ALA* 3.7 25.1 - - + -
751A PRO 3.4 6.1 - - - +
752A ILE* 3.7 12.6 - - + -
780A PHE* 4.2 7.9 - - + +
781A VAL* 1.3 76.8 - - - +
783A GLY* 1.3 67.4 + - - +
785A GLN* 5.6 1.8 - - + -
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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