Contacts of the helix formed by residues 742 - 755 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739B VAL* 4.5 16.1 + - + +
740B PRO 4.0 2.6 + - - -
741B LYS* 1.3 76.1 - - - +
743B SER* 1.3 66.7 + - - +
744B LEU* 3.1 6.7 - - + +
745B VAL* 3.0 31.2 + - + +
746B TYR* 3.5 5.4 + - - +
772B LEU* 5.8 0.2 - - - -
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Residues in contact with SER 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B LYS 4.3 0.4 - - - -
742B GLU* 1.3 70.4 - - - +
744B LEU* 1.3 64.3 + - - +
746B TYR* 3.1 3.7 + - - +
747B PHE* 3.1 19.1 + - - +
769B ALA* 3.2 41.4 - - - +
772B LEU* 4.5 11.0 - - - +
773B ASP* 3.9 19.1 - - - -
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Residues in contact with LEU 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B PRO* 5.6 10.5 - - + +
742B GLU* 4.8 6.5 - - + -
743B SER* 1.3 78.8 - - - +
745B VAL* 1.3 61.0 + - - +
747B PHE* 3.2 9.9 - - - +
748B LEU* 3.1 22.5 + - - +
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Residues in contact with VAL 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B LEU 6.0 0.9 - - - +
736B LYS* 5.7 12.1 - - + -
739B VAL* 5.8 3.8 - - + +
742B GLU* 3.0 21.0 + - + +
744B LEU* 1.3 77.7 - - - +
746B TYR* 1.3 62.4 + - - +
748B LEU* 3.5 8.1 + - - +
749B ILE* 3.3 19.2 + - - +
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Residues in contact with TYR 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B GLU 3.5 4.9 + - - +
743B SER* 3.1 3.3 + - - +
745B VAL* 1.3 75.5 - - - +
747B PHE* 1.3 65.9 + - - +
749B ILE* 3.3 5.8 + - - -
750B GLY 3.2 6.4 + - - -
765B ASN* 3.1 49.1 - - + +
766B PHE 4.1 0.2 + - - -
768B TRP* 4.4 7.2 - - + -
769B ALA* 3.6 16.8 - - + +
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Residues in contact with PHE 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B SER 3.1 11.1 + - - +
744B LEU* 3.2 13.2 - - - +
746B TYR* 1.3 76.8 - - - +
748B LEU* 1.3 57.6 + - - +
749B ILE 3.0 0.2 - - - -
750B GLY* 3.0 5.4 + - - -
751B LYS* 2.8 27.2 + - - +
765B ASN 5.1 0.2 - - - -
766B PHE* 5.2 5.8 - - - +
769B ALA* 3.8 9.7 - - + +
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Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B SER* 5.8 3.8 - - - +
720B PHE* 5.6 3.0 - - + -
744B LEU 3.1 12.0 + - - +
745B VAL* 3.9 8.3 - - - +
746B TYR 3.4 0.4 - - - -
747B PHE* 1.3 77.0 - - - +
749B ILE* 1.3 60.1 + - - +
751B LYS* 3.5 12.4 - - - +
752B VAL* 3.3 21.3 + - - +
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Residues in contact with ILE 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B VAL 3.3 11.6 + - - +
746B TYR* 3.3 13.2 + - - +
747B PHE 3.0 0.8 - - - -
748B LEU* 1.3 75.8 - - - +
750B GLY* 1.3 59.7 + - - +
752B VAL* 3.2 7.1 + - - +
753B TYR* 2.9 28.6 + - - +
761B LEU* 5.1 1.7 - - - +
765B ASN* 3.9 11.4 - - + -
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Residues in contact with GLY 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746B TYR 3.2 6.3 + - - -
747B PHE* 3.0 7.0 + - - -
749B ILE* 1.3 78.5 - - - +
751B LYS* 1.3 61.0 + - - +
753B TYR 3.3 8.0 + - - -
754B LYS* 3.3 13.0 + - - +
762B ALA* 3.6 39.5 - - - +
765B ASN* 3.9 1.6 - - - +
766B PHE* 4.9 4.0 - - - -
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Residues in contact with LYS 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B VAL* 6.0 3.8 - - + -
720B PHE* 3.6 31.2 - - + -
747B PHE 2.8 13.2 + - - +
748B LEU* 3.5 17.0 - - - +
750B GLY* 1.3 78.1 - - - +
752B VAL* 1.3 58.8 + - - +
754B LYS* 3.8 15.5 - - - +
755B LYS* 4.3 2.1 + - - +
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Residues in contact with VAL 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B PHE* 3.8 22.7 - - + -
725B TYR* 5.3 15.1 - - + +
728B ALA* 6.2 2.9 - - + -
729B LEU* 6.0 5.6 - - + +
748B LEU 3.3 10.5 + - - +
749B ILE* 3.2 9.9 + - - +
751B LYS* 1.3 77.4 - - - +
753B TYR* 1.3 63.0 + - - +
754B LYS 3.3 0.7 - - - -
755B LYS* 3.3 9.9 + - - +
756B LEU* 3.3 17.3 + - - +
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Residues in contact with TYR 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B ILE 2.9 13.8 + - - +
750B GLY 3.3 0.8 + - - +
752B VAL* 1.3 73.6 - - - +
754B LYS* 1.3 58.6 + - - +
755B LYS 3.2 1.8 - - - -
756B LEU* 3.1 9.7 - - + +
757B GLY 2.8 28.1 + - - -
758B GLN 3.9 7.1 + - - +
761B LEU* 3.7 15.7 - - + -
762B ALA* 3.2 41.2 - - + +
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Residues in contact with LYS 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750B GLY 3.3 8.6 + - - +
751B LYS* 3.8 13.0 - - - +
752B VAL 3.3 0.6 - - - -
753B TYR* 1.3 73.9 - - - +
755B LYS* 1.3 62.4 + - - +
756B LEU 2.9 5.5 + - - -
757B GLY* 3.7 7.3 + - - -
762B ALA* 4.4 4.9 - - + +
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Residues in contact with LYS 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B PHE* 5.1 1.8 - - + -
725B TYR* 3.8 47.0 - - + +
751B LYS 4.3 2.4 + - - +
752B VAL* 3.3 15.0 + - - +
753B TYR 3.2 0.2 - - - -
754B LYS* 1.3 77.6 - - - +
756B LEU* 1.3 59.7 + - - +
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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