Contacts of the helix formed by residues 737 - 752 (chain A) in PDB entry 4NC6
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 PRO 737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735A LYS 4.5 2.0 - - - +
736A PHE* 1.3 94.6 - - + +
738A LEU* 1.3 67.0 + - - +
739A TYR* 3.2 5.4 - - + +
740A MET* 3.2 7.3 + - + +
741A VAL* 3.0 17.8 + - - +
788A PRO* 3.7 23.8 - - + +
791A TYR* 3.6 31.4 - - + +
792A ARG* 3.8 16.2 - - + +
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Residues in contact with LEU 738 (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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614A PHE* 3.5 45.5 - - + -
617A HIS* 3.6 35.0 - - + +
657A VAL* 4.2 7.0 - - + -
660A LEU* 4.3 4.9 - - + -
736A PHE 3.5 1.4 + - - +
737A PRO* 1.3 71.5 - - - +
739A TYR* 1.3 64.7 + - - +
741A VAL* 3.1 6.2 + - + -
742A PHE* 2.8 63.0 + - + -
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Residues in contact with TYR 739 (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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572A ARG* 4.9 6.0 + - - -
737A PRO* 3.2 4.9 + - + +
738A LEU* 1.3 78.7 - - - +
740A MET* 1.3 65.5 + - - +
742A PHE* 3.5 11.0 + + - +
743A HIS* 3.5 24.8 + - + +
791A TYR 5.6 2.5 - - - +
792A ARG 6.0 1.1 - - - +
794A GLU* 3.5 59.0 + - + +
797A ALA* 4.0 17.5 - - + -
798A LYS* 3.5 32.0 + - + +
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Residues in contact with MET 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A PHE* 6.1 0.2 - - + -
736A PHE* 4.0 24.7 - - + -
737A PRO* 3.2 9.4 + - + +
739A TYR* 1.3 83.0 - - - +
741A VAL* 1.3 65.0 + - - +
743A HIS* 3.1 6.5 + - - +
744A ILE* 3.0 35.0 + - + +
759A VAL* 5.3 1.6 - - + -
763A LEU* 4.5 5.4 - - + -
791A TYR* 3.7 34.9 + - + +
797A ALA* 3.5 37.0 - - + +
800A LEU* 4.0 24.5 - - + -
801A MET* 3.9 16.6 - - + -
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Residues in contact with VAL 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A VAL* 4.0 19.1 - - + -
731A LEU 5.0 1.8 - - - +
732A PHE* 3.5 29.6 - - + +
733A THR* 3.7 31.4 - - + +
736A PHE* 3.5 19.3 - - + +
737A PRO 3.0 18.1 + - - +
738A LEU* 3.6 13.0 - - + +
740A MET* 1.3 75.4 - - - +
742A PHE* 1.3 65.2 + - + +
744A ILE* 3.2 9.8 + - - +
745A ILE* 3.0 25.6 + - + +
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Residues in contact with PHE 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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569A GLU* 3.3 27.1 - - - -
572A ARG* 3.4 24.7 - - - +
576A TRP* 3.6 10.1 - + + -
617A HIS* 6.0 0.2 - - - -
657A VAL* 3.8 21.1 - - + -
660A LEU* 4.1 13.7 - - + -
661A HIS* 3.5 30.1 - + - -
738A LEU* 2.8 63.0 + - + +
739A TYR* 3.9 8.5 - + - +
741A VAL* 1.3 73.7 - - + +
743A HIS* 1.4 58.6 + - - +
745A ILE* 3.2 2.2 + - - -
746A ASP* 3.0 31.4 + - - +
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Residues in contact with HIS 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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563A VAL 3.7 2.2 + - - -
564A ARG 2.9 29.5 + - - -
565A ASN* 3.8 5.6 - - - -
566A GLY* 3.6 20.0 + - - -
572A ARG* 3.7 5.3 + - - +
739A TYR* 3.5 18.2 + - + +
740A MET* 3.1 11.2 + - - +
742A PHE* 1.4 76.3 - - - +
744A ILE* 1.3 64.9 + - - +
746A ASP* 3.2 17.3 - - - +
747A LEU* 3.1 33.9 + - + +
797A ALA 5.5 0.4 + - - -
798A LYS* 5.5 13.0 - - + +
801A MET* 3.7 32.6 - - + +
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Residues in contact with ILE 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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731A LEU 4.1 16.6 - - - +
732A PHE* 3.8 39.0 - - + -
740A MET* 3.0 34.2 + - + +
741A VAL* 3.5 14.1 - - + +
743A HIS* 1.3 76.2 - - - +
745A ILE* 1.3 60.7 + - + +
747A LEU* 3.1 5.1 + - - +
748A LEU* 2.8 30.3 + - + +
755A VAL* 4.6 2.0 - - + +
756A ILE* 4.4 11.0 - - + -
759A VAL* 4.0 19.7 - - + -
801A MET* 3.8 24.7 - - + -
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Residues in contact with ILE 745 (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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576A TRP* 3.8 24.2 - - + -
654A LEU* 4.1 22.0 - - + -
657A VAL* 4.2 17.3 - - + -
658A LEU* 4.9 6.7 - - + -
674A ILE* 5.3 3.1 - - + -
731A LEU* 4.4 23.8 - - + +
733A THR* 4.5 8.7 - - + -
741A VAL* 3.0 17.4 + - + +
742A PHE 3.2 6.3 + - - +
744A ILE* 1.3 74.2 - - + +
746A ASP* 1.3 68.1 + - - +
748A LEU* 4.2 7.2 - - + -
749A LEU* 2.8 50.3 + - + +
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Residues in contact with ASP 746 (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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563A VAL* 3.5 18.7 - - + +
566A GLY* 3.6 3.6 - - - -
567A VAL* 2.8 35.6 + - + +
572A ARG* 2.8 35.3 + - - -
576A TRP* 2.7 34.6 + - - +
579A LEU* 3.9 5.2 - - - +
742A PHE 3.0 16.1 + - - +
743A HIS* 3.2 15.1 - - + +
745A ILE* 1.3 79.6 - - - +
747A LEU* 1.3 60.1 + - - +
749A LEU 3.6 0.2 + - - -
750A CYS* 3.2 15.1 + - - +
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Residues in contact with LEU 747 (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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560A SER 5.8 0.2 - - - +
563A VAL* 4.1 11.9 - - + +
564A ARG* 3.9 23.1 - - + +
743A HIS* 3.1 20.2 + - + +
744A ILE* 3.6 6.3 - - - +
746A ASP* 1.3 79.2 - - - +
748A LEU* 1.3 57.9 + - - +
750A CYS* 3.3 0.8 + - - -
751A GLU* 2.8 44.7 + - + +
755A VAL* 4.2 15.9 - - + -
759A VAL* 5.4 3.1 - - + -
801A MET* 3.2 35.4 - - + -
804A ALA* 5.6 1.1 - - + -
805A CYS* 3.9 30.7 - - - -
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Residues in contact with LEU 748 (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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674A ILE* 4.9 4.9 - - + -
678A TYR* 3.4 26.2 - - + -
731A LEU* 3.7 45.1 - - + -
744A ILE* 2.8 22.1 + - + +
745A ILE* 3.9 10.1 - - + +
747A LEU* 1.3 74.0 - - - +
749A LEU* 1.3 70.8 + - + +
752A GLY* 2.8 39.2 + - - +
753A ILE* 4.0 16.6 - - + -
755A VAL* 3.5 14.1 - - + +
756A ILE* 3.8 18.6 - - + -
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Residues in contact with LEU 749 (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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555A ARG* 3.3 10.6 + - - -
576A TRP* 3.6 45.1 - - + +
579A LEU* 3.8 18.6 - - + +
580A ALA* 4.5 7.2 - - + -
658A LEU* 5.3 0.2 - - + -
670A VAL* 4.6 8.7 - - + -
674A ILE* 3.7 31.0 - - + -
678A TYR* 2.6 43.7 + - + +
745A ILE* 2.8 34.5 + - + +
748A LEU* 1.3 78.3 - - + +
750A CYS* 1.3 59.8 + - - +
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Residues in contact with CYS 750 (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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555A ARG* 2.8 38.5 + - - +
559A LEU* 4.7 4.0 - - - -
560A SER* 3.7 15.9 - - - -
563A VAL* 3.8 26.2 - - + -
579A LEU* 3.9 17.4 - - + +
746A ASP 3.2 17.5 + - - +
747A LEU 3.8 2.7 - - - +
748A LEU 3.2 0.2 - - - -
749A LEU* 1.3 76.0 - - - +
751A GLU* 1.3 82.2 + - + +
752A GLY 3.7 0.2 - - - -
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Residues in contact with GLU 751 (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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560A SER* 2.7 34.4 + - - +
563A VAL* 6.2 0.2 - - + -
747A LEU* 2.8 29.9 + - + +
750A CYS* 1.3 88.7 - - + +
752A GLY* 1.3 59.1 + - - +
754A SER* 5.4 1.9 + - - -
755A VAL* 3.6 18.2 - - + +
808A LYS* 5.8 5.5 - - + +
811A GLN* 5.6 4.0 + - - -
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Residues in contact with GLY 752 (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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678A TYR* 4.3 11.6 - - - -
748A LEU* 2.8 20.1 + - - +
749A LEU 4.6 0.4 - - - -
750A CYS 3.7 1.2 - - - -
751A GLU* 1.3 79.1 - - - +
753A ILE* 1.3 63.7 + - - -
754A SER* 3.1 5.6 + - - -
755A VAL* 3.2 24.8 + - - +
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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
------------------------------------------------------------
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