Contacts of the strand formed by residues 771 - 774 (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 TYR 771 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A LEU* 3.6 19.3 - - + +
634A HIS* 3.7 37.8 - + + -
635A SER 3.5 16.2 + - - +
636A VAL* 3.4 20.4 - - + -
637A GLN* 2.9 24.9 + - - +
764A ILE* 4.1 17.9 - - + -
765A ILE 3.6 1.6 - - - -
766A ARG* 3.5 45.7 + - + -
770A GLY* 1.3 73.4 - - - -
772A TYR* 1.3 66.2 + - - +
16J PHE* 4.5 12.8 - + - -
45J ILE* 4.3 24.3 + - + +
47J LEU* 3.8 19.7 + - + +
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Residues in contact with TYR 772 (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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636A VAL* 4.3 1.8 - - - -
637A GLN* 3.2 43.4 + - + -
638A PRO 5.3 1.1 - - - -
639A LEU* 3.6 21.3 - - + -
674A LYS* 3.6 48.1 + - + -
764A ILE* 3.3 8.0 - - - +
765A ILE* 2.7 57.1 + - + +
767A THR* 5.0 7.6 - - - -
769A GLN* 5.9 4.0 - - + +
770A GLY* 5.1 9.9 - - - -
771A TYR* 1.3 85.2 - - - +
773A ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 773 (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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636A VAL* 3.7 16.2 - - + -
637A GLN 3.4 15.0 + - - +
638A PRO* 4.5 1.1 - - + +
639A LEU* 3.5 15.4 + - - +
762A PHE* 3.8 32.3 - - + -
763A LEU 3.4 12.1 - - - +
764A ILE* 3.8 16.2 - - + -
765A ILE* 5.8 0.7 - - - -
772A TYR* 1.3 75.5 - - - +
774A ARG* 1.3 73.7 + - - +
18J LEU* 5.0 0.7 - - + -
28J VAL* 4.4 0.4 - - + -
32J VAL* 4.2 19.1 - - + +
39J LEU* 3.9 23.6 - - + -
43J LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 774 (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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639A LEU* 3.7 18.4 - - + -
643A ILE* 3.4 27.9 - - + +
673A GLY 2.5 37.2 + - - -
674A LYS 3.9 9.9 - - - -
675A ASP 3.1 25.9 + - - +
676A GLY 2.4 24.4 + - - -
677A ASP* 4.4 4.0 + - - +
678A LEU* 3.4 18.0 - - - +
762A PHE* 4.5 2.2 - - - +
763A LEU* 3.2 42.0 + - + +
765A ILE* 4.4 8.9 - - + +
773A ILE* 1.3 85.2 - - - +
775A GLU* 1.3 70.9 + - - +
776A LEU* 3.8 1.2 + - + -
32J VAL* 4.6 4.5 - - - -
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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
------------------------------------------------------------
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