Contacts of the helix formed by residues 775 - 787 (chain A) in PDB entry 4Z4H
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 SER 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PRO* 4.3 1.8 - - - -
30A ASP* 3.3 22.0 - - - -
746A PHE* 4.2 2.0 - - - -
773A ARG 3.6 2.0 + - - -
774A PHE* 1.3 78.1 - - - +
776A SER* 1.3 64.1 + - - +
777A ASP* 3.6 8.1 + - - +
778A GLU* 3.4 22.4 + - - +
779A LEU* 3.2 22.2 + - - +
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Residues in contact with SER 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 4.5 1.6 + - - +
29A PRO* 4.1 2.2 - - - +
30A ASP* 2.7 40.7 + - - -
31A PHE* 4.0 0.5 - - - -
32A GLY 3.7 20.2 - - - -
737A ASP* 4.2 1.6 + - - -
746A PHE* 3.7 25.0 - - - -
775A SER* 1.3 73.0 - - - +
777A ASP* 1.3 62.4 + - - +
779A LEU* 4.1 0.3 - - - +
780A GLN* 3.0 41.6 + - - +
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Residues in contact with ASP 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 4.4 0.8 + - - -
31A PHE 4.7 1.1 - - - +
32A GLY* 3.7 4.6 - - - -
33A THR* 2.9 39.1 + - - +
34A SER* 3.1 33.0 + - - -
411A ARG* 4.2 2.6 + - - -
413A LEU* 5.3 0.5 - - - +
775A SER* 3.2 8.3 + - - +
776A SER* 1.3 81.4 - - - +
778A GLU* 1.3 63.0 + - - +
780A GLN* 4.0 3.9 - - - +
781A ILE* 3.1 35.7 + - + +
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Residues in contact with GLU 778 (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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584A PRO* 3.8 15.2 - - + +
585A PRO* 3.6 23.9 - - + +
586A VAL* 3.1 38.8 + - - +
774A PHE* 3.5 24.4 - - + -
775A SER* 3.4 17.7 + - - +
776A SER 3.4 0.6 - - - -
777A ASP* 1.3 78.6 - - - +
779A LEU* 1.3 57.9 + - - +
781A ILE* 3.9 5.1 - - - +
782A LEU* 2.9 28.1 + - + +
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Residues in contact with LEU 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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665A ILE* 5.4 0.2 - - + -
667A TYR* 4.4 0.2 - - - +
703A THR* 4.7 5.8 - - + -
705A ILE* 3.9 26.2 - - + -
746A PHE* 4.0 16.8 - - + -
748A PHE* 4.5 11.0 - - + -
767A VAL* 3.6 31.4 - - + -
770A ASP* 5.3 0.2 - - - +
774A PHE* 4.0 23.9 - - + -
775A SER 3.2 17.1 + - - +
776A SER 4.1 1.8 - - - +
778A GLU* 1.3 78.5 - - - +
780A GLN* 1.3 60.6 + - - +
782A LEU* 4.0 20.6 - - + -
783A THR* 2.9 36.4 + - - +
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Residues in contact with GLN 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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28A ARG* 5.8 0.2 - - - +
32A GLY* 4.1 3.8 - - - -
411A ARG* 3.2 26.7 + - - -
413A LEU* 3.9 16.5 - - + +
735A THR* 3.8 11.9 - - + +
737A ASP* 3.2 32.9 + - - +
746A PHE* 5.1 1.2 - - - -
748A PHE* 3.7 40.8 - - + +
750A LEU* 4.1 2.8 - - - +
776A SER* 3.0 31.5 + - - +
777A ASP* 4.0 4.5 - - - +
779A LEU* 1.3 77.5 - - - +
781A ILE* 1.3 61.5 + - + +
783A THR* 3.6 2.3 + - - -
784A TYR* 3.1 22.7 + - - +
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Residues in contact with ILE 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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34A SER* 3.9 26.9 - - - +
413A LEU* 4.6 14.1 - - + -
414A GLN 5.9 3.1 - - - +
584A PRO* 4.8 9.9 - - + -
777A ASP* 3.1 25.5 + - + +
778A GLU* 3.9 4.5 - - - +
780A GLN* 1.3 74.1 - - + +
782A LEU* 1.3 60.7 - - - +
784A TYR* 3.3 8.2 + - + +
785A GLN* 2.9 54.1 + - + +
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Residues in contact with LEU 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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584A PRO* 3.9 16.8 - - + +
586A VAL* 4.1 5.8 - - + -
587A PHE* 3.8 29.2 - - + -
593A PHE* 3.9 28.5 - - + -
665A ILE* 4.5 6.7 - - + -
667A TYR* 4.2 4.5 - - - +
774A PHE* 4.0 27.6 - - + -
778A GLU* 2.9 19.1 + - + +
779A LEU* 3.7 15.9 - - + +
781A ILE* 1.3 76.2 - - - +
783A THR* 1.3 63.2 + - - +
785A GLN* 3.1 6.7 + - + +
786A LEU* 3.0 36.6 + - + +
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Residues in contact with THR 783 (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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667A TYR* 2.8 25.7 + - - +
705A ILE* 5.0 0.7 - - - +
748A PHE* 4.0 10.2 - - - -
750A LEU* 4.0 7.9 - - + -
765A TYR* 3.4 47.7 - - + +
779A LEU* 2.9 19.9 + - - +
780A GLN 3.9 3.8 - - - -
782A LEU* 1.3 77.9 - - - +
784A TYR* 1.3 63.6 + - - +
786A LEU* 3.3 5.8 + - - +
787A CYS* 3.3 21.3 + - - -
800A PRO* 3.9 8.6 - - + +
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Residues in contact with TYR 784 (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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413A LEU* 3.5 45.6 + - + -
414A GLN 3.6 18.6 - - - -
415A PRO* 3.9 12.0 - - + +
416A PRO* 5.0 1.6 - - + -
433A GLY* 5.3 2.3 + - - -
732A ALA* 3.5 11.8 + - - +
733A GLY* 3.4 26.2 + - - -
750A LEU* 3.8 14.5 - - + +
752A SER* 3.7 32.0 + - - -
780A GLN 3.1 16.2 + - - +
781A ILE* 3.6 6.7 - - + +
783A THR* 1.3 79.2 - - - +
785A GLN* 1.3 62.2 + - + +
787A CYS* 3.2 9.0 + - - +
788A HIS* 2.8 44.2 + + - -
796A SER* 3.9 0.6 - - - -
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Residues in contact with GLN 785 (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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414A GLN 5.9 1.1 - - - +
416A PRO* 3.7 32.2 - - + +
578A LEU* 3.5 29.0 - - + +
582A GLY 3.1 22.9 + - - +
583A ARG* 3.8 15.1 + - - +
584A PRO* 3.8 13.0 - - + +
587A PHE* 6.5 0.2 - - + -
781A ILE* 2.9 38.2 + - + +
782A LEU* 3.1 6.0 + - + +
784A TYR* 1.3 78.1 - - + +
786A LEU* 1.3 58.1 + - + +
788A HIS* 2.9 29.9 + - - +
789A THR* 3.5 9.4 - - - +
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Residues in contact with LEU 786 (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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578A LEU* 5.3 2.2 - - + -
587A PHE* 5.1 1.6 - - + -
593A PHE* 3.7 30.5 - - + -
622A PRO* 3.9 30.1 - - + -
625A TYR* 4.7 5.8 - - - +
667A TYR* 3.5 40.6 - - + +
782A LEU* 3.0 24.5 + - + +
783A THR 3.7 5.2 - - - +
784A TYR 3.3 0.2 - - - -
785A GLN* 1.3 76.9 - - - +
787A CYS* 1.3 59.0 + - - +
788A HIS 3.1 0.9 - - - -
789A THR* 2.9 27.8 + - + +
800A PRO* 4.0 11.9 - - + -
801A ALA* 3.1 17.2 + - - +
802A PRO* 4.6 5.2 - - + -
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Residues in contact with CYS 787 (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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750A LEU* 5.1 0.4 - - - -
752A SER* 3.5 25.4 - - - +
765A TYR* 4.2 5.4 - - - -
783A THR* 3.3 17.5 + - - -
784A TYR* 3.2 11.8 + - - +
785A GLN 3.1 0.6 - - - -
786A LEU* 1.3 76.0 - - - +
788A HIS* 1.3 58.1 + - - +
789A THR 3.5 0.4 - - - -
790A TYR* 4.5 2.1 - - - +
795A ARG 3.9 2.3 - - - +
796A SER* 3.4 11.3 - - - +
797A VAL* 3.1 40.5 + - - +
799A ILE* 3.6 32.5 - - - -
800A PRO* 3.6 5.6 - - - -
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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