Contacts of the helix formed by residues 728 - 740 (chain A) in PDB entry 4C2M
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 GLY 728 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680A LEU* 3.2 36.4 + - - +
681A THR* 4.7 1.8 - - - -
682A SER 5.2 1.0 + - - -
685A SER* 3.4 11.3 + - - -
687A PHE* 3.6 14.8 - - - -
727A THR* 1.3 73.0 - - - +
729A LYS* 1.3 54.6 + - - +
731A ILE* 2.8 31.2 + - - +
732A ILE* 3.3 5.1 + - - +
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Residues in contact with LYS 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU 4.4 1.0 + - - -
681A THR* 2.6 36.7 + - - +
682A SER 4.4 0.9 - - - +
683A LYS* 4.3 10.1 - - - +
727A THR* 3.4 9.6 + - - +
728A GLY* 1.3 75.4 - - - +
730A GLN* 1.3 56.8 + - + +
732A ILE* 3.3 6.4 + - - +
733A THR* 3.1 29.2 + - - -
766A GLU* 2.9 31.7 + - - -
776A LEU* 3.6 44.9 - - + +
777A LEU 4.6 3.8 - - - +
778A CYS* 3.9 8.7 - - - +
779A GLY 3.2 26.7 + - - +
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Residues in contact with GLN 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 4.4 2.7 - - + -
715A LEU* 4.0 18.6 - - + +
716A PRO 2.8 29.1 + - - -
717A PRO 3.9 0.4 - - - -
718A THR* 2.8 27.7 + - - +
726A TRP* 3.2 22.9 - - + -
727A THR* 2.7 43.9 + - - +
729A LYS* 1.3 75.0 - - - +
731A ILE* 1.3 55.3 + - - +
733A THR* 3.8 7.1 - - - +
734A THR* 2.7 38.3 + - - -
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Residues in contact with ILE 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 4.4 8.5 - - + -
687A PHE* 3.8 33.2 - - + -
692A TYR* 3.9 24.9 - - + -
695A TYR* 4.0 27.1 - - + -
696A ILE* 4.0 15.0 - - + +
727A THR 3.9 7.4 - - - +
728A GLY* 2.8 18.6 + - - +
730A GLN* 1.3 72.9 - - - +
732A ILE* 1.3 56.7 + - - +
734A THR* 3.4 2.1 + - - -
735A VAL* 2.9 29.9 + - + +
816A LEU* 3.7 34.3 - - + -
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Residues in contact with ILE 732 (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* 4.5 2.0 - - + -
681A THR* 4.0 22.0 - - + -
728A GLY 3.8 10.8 - - - +
729A LYS 3.3 7.2 + - - +
730A GLN 3.2 0.4 - - - -
731A ILE* 1.3 74.9 - - - +
733A THR* 1.3 65.7 + - - +
734A THR 3.1 0.2 + - - -
735A VAL* 3.2 6.7 + - + +
736A LEU* 3.0 30.5 + - + +
771A PHE* 4.4 18.4 - - + -
776A LEU* 4.3 8.1 - - + -
781A LEU* 3.9 26.9 - - + -
793A ILE* 6.2 0.4 - - + -
813A LEU* 4.0 28.0 - - + -
816A LEU* 4.3 14.6 - - + -
817A PHE* 4.5 7.6 - - + -
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Residues in contact with THR 733 (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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715A LEU* 3.8 26.9 - - + -
729A LYS 3.1 12.5 + - - -
730A GLN* 3.8 8.6 - - - +
732A ILE* 1.3 77.7 - - - +
734A THR* 1.3 56.7 + - - +
736A LEU* 3.6 3.4 + - - +
737A LEU* 2.9 30.9 + - + +
771A PHE* 6.1 0.2 - - - -
774A GLY 3.7 11.6 - - - +
775A ALA* 3.2 27.2 - - + +
776A LEU* 2.8 28.2 + - - +
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Residues in contact with THR 734 (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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692A TYR* 2.5 29.1 + - + +
696A ILE* 3.6 25.1 - - + -
713A VAL 3.5 24.9 - - - +
714A THR* 4.3 3.1 - - + -
715A LEU* 3.7 9.6 - - - +
730A GLN 2.7 22.0 + - - -
731A ILE 3.7 3.6 - - - -
733A THR* 1.3 75.4 - - - +
735A VAL* 1.3 65.9 + - - +
737A LEU* 3.2 8.4 + - + +
738A ASN* 2.9 33.0 + - - +
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Residues in contact with VAL 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A ILE* 4.6 6.7 - - + -
699A CYS* 3.7 30.5 - - - -
700A ILE* 4.2 9.0 - - + -
731A ILE 2.9 18.1 + - - +
732A ILE* 3.2 9.8 + - + +
734A THR* 1.3 74.7 - - - +
736A LEU* 1.3 75.7 + - + +
738A ASN* 2.9 11.8 + - - -
739A VAL* 3.1 22.3 + - + +
809A VAL* 5.2 2.7 - - + -
812A VAL* 3.5 24.7 - - + -
813A LEU* 4.6 14.1 - - + -
816A LEU* 4.7 11.4 - - + -
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Residues in contact with LEU 736 (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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732A ILE* 3.0 24.9 + - + +
733A THR 3.9 3.8 - - - +
735A VAL* 1.3 83.1 - - + +
737A LEU* 1.3 59.0 + - - +
739A VAL* 4.5 2.2 - - - +
740A THR* 2.8 44.9 + - + +
747A ILE* 4.6 7.0 - - + -
771A PHE* 4.0 25.1 - - + -
774A GLY* 3.9 21.1 - - - +
793A ILE* 4.7 3.4 - - + -
797A LEU* 3.7 39.3 - - + -
809A VAL* 4.0 21.1 - - + -
813A LEU* 6.0 1.1 - - + -
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Residues in contact with LEU 737 (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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709A ARG* 3.0 41.4 + - - +
713A VAL* 3.8 32.8 - - + +
714A THR 5.2 0.2 - - - -
715A LEU* 4.1 28.0 - - + -
733A THR* 2.9 22.7 + - + +
734A THR* 3.3 8.7 - - - +
735A VAL 3.1 0.2 - - - -
736A LEU* 1.3 78.3 - - - +
738A ASN* 1.3 60.9 + - - +
739A VAL 3.7 0.2 + - - -
740A THR* 4.1 6.9 + - - +
774A GLY 5.4 0.2 + - - -
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Residues in contact with ASN 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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696A ILE* 4.4 4.6 - - - +
700A ILE* 4.1 22.0 - - + +
706A HIS* 4.5 2.6 - - - +
708A THR* 3.2 24.8 + - - +
709A ARG* 4.7 7.3 - - + +
711A LYS 4.4 1.4 - - - +
712A ILE* 3.7 17.9 - - - +
713A VAL* 2.8 53.8 + - - +
734A THR* 2.9 30.5 + - - +
735A VAL 2.9 5.9 + - - +
737A LEU* 1.3 79.8 - - - +
739A VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 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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700A ILE* 3.8 21.1 - - + -
706A HIS* 3.5 21.3 + - + -
708A THR* 3.9 7.4 - - - +
735A VAL* 3.1 21.7 + - + +
736A LEU* 4.3 4.0 - - - +
738A ASN* 1.3 82.8 - - - +
740A THR* 1.3 67.2 + - + +
741A PRO* 4.3 0.2 - - - +
805A VAL* 4.0 10.4 - - + +
808A LYS* 4.2 22.2 - - + -
809A VAL* 3.6 31.6 - - + +
812A VAL* 4.2 15.7 - - + -
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Residues in contact with THR 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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708A THR* 3.7 13.4 + - - -
709A ARG* 4.4 1.6 + - - -
736A LEU* 2.8 37.3 + - + +
737A LEU* 4.1 10.7 + - - +
739A VAL* 1.3 83.1 - - + +
741A PRO* 1.3 78.3 + - - +
742A PRO* 3.5 2.6 - - - +
744A MET 5.1 1.9 + - - -
746A GLY* 5.5 3.5 - - - -
797A LEU* 4.5 6.3 - - + -
801A TYR* 3.8 37.1 + - + +
805A VAL* 4.3 9.6 - - + -
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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