Contacts of the helix formed by residues 742 - 755 (chain A) in PDB entry 4RG7
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 GLU 742 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A LEU* 6.6 0.2 - - + -
739A VAL* 4.0 18.9 + - + +
740A PRO 3.6 1.6 - - - -
741A LYS* 1.3 78.1 - - + +
743A SER* 1.3 64.3 + - - +
744A LEU* 3.3 14.9 + - + +
745A VAL* 3.3 19.1 + - + +
746A TYR* 4.0 3.8 + - - +
772A LEU* 5.5 0.7 - - - -
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Residues in contact with SER 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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741A LYS 3.4 3.6 + - - -
742A GLU* 1.3 72.0 - - - +
744A LEU* 1.3 57.6 + - - +
746A TYR* 3.0 5.2 + - - +
747A PHE* 2.9 31.9 + - - +
769A ALA* 3.2 27.9 + - - +
772A LEU* 3.4 9.3 + - - -
773A ASP* 3.2 34.3 + - - -
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Residues in contact with LEU 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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672A PRO* 6.3 2.9 - - + -
710A LEU* 6.1 4.9 - - + -
713A PHE* 3.5 36.8 - - + -
742A GLU* 3.1 10.5 - - + +
743A SER* 1.3 77.7 - - - +
745A VAL* 1.3 60.3 + - - +
747A PHE* 3.6 6.8 + - - +
748A LEU* 3.2 17.7 + - - +
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Residues in contact with VAL 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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713A PHE* 4.3 9.3 - - + -
732A LEU 6.0 0.7 - - - +
735A LEU* 5.4 3.6 - - + +
736A LYS* 4.7 18.9 - - + +
739A VAL* 4.2 17.3 - - + +
742A GLU* 3.3 15.8 + - + +
743A SER 3.1 0.4 - - - -
744A LEU* 1.3 78.9 - - - +
746A TYR* 1.3 60.2 + - - +
748A LEU* 3.5 4.5 + - - +
749A ILE* 3.3 20.1 + - - +
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Residues in contact with TYR 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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742A GLU 4.0 2.6 + - - +
743A SER* 3.0 5.3 + - - +
745A VAL* 1.3 77.9 - - - +
747A PHE* 1.3 60.3 + - - +
748A LEU 3.3 0.2 - - - -
749A ILE* 3.5 8.1 + - - +
750A GLY* 3.0 22.5 + - - -
765A ASN* 3.6 21.3 - - + +
768A TRP* 5.0 3.1 - - + -
769A ALA* 3.4 26.9 - - + +
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Residues in contact with PHE 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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743A SER* 2.9 17.4 + - - +
744A LEU* 3.8 7.6 - - - +
746A TYR* 1.3 77.7 - - - +
748A LEU* 1.3 57.1 + - - +
750A GLY* 3.4 3.0 + - - +
751A LYS* 3.2 23.9 + - - +
766A PHE* 5.4 3.4 - - - +
769A ALA* 3.5 11.4 - - + +
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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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713A PHE* 4.4 15.9 - - + -
716A ALA* 6.6 0.4 - - + -
732A LEU* 6.2 4.0 - - + -
744A LEU 3.2 17.7 + - - +
745A VAL* 3.8 5.4 - - - +
746A TYR 3.3 0.2 - - - -
747A PHE* 1.3 75.6 - - - +
749A ILE* 1.3 60.3 + - - +
751A LYS* 3.2 6.9 + - - +
752A VAL* 2.9 31.7 + - - +
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Residues in contact with ILE 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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745A VAL 3.3 11.8 + - - +
746A TYR* 3.6 11.4 - - - +
748A LEU* 1.3 77.1 - - - +
750A GLY* 1.3 63.3 + - - +
752A VAL* 3.9 6.6 - - - +
753A TYR* 3.0 27.0 + - - +
761A LEU 5.5 0.4 - - - +
765A ASN* 4.3 12.3 - - + -
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Residues in contact with GLY 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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746A TYR 3.0 14.5 + - - -
747A PHE* 3.4 5.8 + - - -
748A LEU 3.2 0.4 - - - -
749A ILE* 1.3 77.9 - - - +
751A LYS* 1.3 60.5 + - - +
754A LYS* 3.3 17.3 + - - +
762A ALA* 3.3 31.7 - - - +
765A ASN* 4.3 3.3 - - - +
766A PHE* 4.8 7.6 - - - -
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Residues in contact with LYS 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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720A PHE* 5.0 18.1 - - + -
747A PHE 3.2 12.7 + - - +
748A LEU* 3.2 9.4 + - - +
750A GLY* 1.3 76.4 - - - +
752A VAL* 1.3 62.7 + - - +
754A LYS* 3.0 17.8 + - - +
755A LYS* 3.2 14.8 + - - +
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Residues in contact with VAL 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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720A PHE* 4.9 16.5 - - + -
725A TYR 5.9 2.9 - - - +
728A ALA* 6.2 4.0 - - + -
729A LEU* 5.7 10.3 - - + -
748A LEU 2.9 21.3 + - - +
749A ILE* 3.9 6.7 - - - +
751A LYS* 1.3 71.9 - - - +
753A TYR* 1.3 59.8 + - - +
755A LYS* 4.0 2.6 + - - +
756A LEU* 3.3 20.3 + - - +
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Residues in contact with TYR 753 (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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749A ILE 3.0 18.5 + - - +
752A VAL* 1.3 76.1 - - - +
754A LYS* 1.3 66.6 + - - +
755A LYS 3.2 0.2 - - - -
756A LEU* 2.9 16.3 + - - +
757A GLY 3.0 10.0 + - - -
758A GLN* 3.3 25.5 + - + +
761A LEU* 4.3 5.2 - - + -
762A ALA* 3.6 24.0 - - + +
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Residues in contact with LYS 754 (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 GLY 3.3 11.1 + - - +
751A LYS* 3.0 12.9 + - - +
753A TYR* 1.3 78.3 - - - +
755A LYS* 1.3 61.4 + - - +
756A LEU 3.4 0.5 + - - -
757A GLY* 3.4 9.5 + - - -
758A GLN 4.7 3.1 - - - -
759A THR* 5.6 1.8 - - - +
762A ALA* 3.7 11.5 - - + +
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Residues in contact with LYS 755 (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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720A PHE* 4.6 20.4 - - + -
725A TYR* 5.1 17.8 - - + -
751A LYS 3.2 11.0 + - - +
752A VAL 4.4 4.3 - - - +
753A TYR 3.2 0.4 - - - -
754A LYS* 1.3 77.2 - - - +
756A LEU* 1.3 59.2 + - - +
757A GLY 3.4 0.2 - - - -
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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