Contacts of the helix formed by residues 826 - 835 (chain A) in PDB entry 4ZGA
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 ARG 826 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 3.1 21.3 + - - -
432A ARG* 6.1 0.2 - - + -
434A HIS* 5.0 0.8 + - - -
505A GLU* 3.5 31.1 + - - -
507A ILE* 4.8 4.0 - - - +
508A GLU* 4.3 4.9 + - - -
525A ASN 5.1 2.4 + - - -
527A THR* 4.6 1.4 + - - -
793A SER* 4.7 0.7 - - - -
825A ALA* 1.3 76.2 - - - +
827A VAL* 1.3 66.0 + - - +
828A ARG* 3.5 38.5 - - - +
829A ASP* 2.6 52.0 + - - +
830A ILE* 3.3 8.3 + - - +
832A HIS* 4.4 5.9 + - - -
853A LYS 3.6 11.4 - - - +
854A THR* 3.3 36.9 - - - +
855A TYR 3.5 15.5 - - - +
856A LEU* 4.0 13.0 - - + -
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Residues in contact with VAL 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A ILE* 3.8 13.5 - - + -
791A VAL* 4.0 23.8 - - + -
793A SER* 3.8 18.8 - - - +
825A ALA 4.0 0.6 + - - -
826A ARG* 1.3 72.1 - - - +
828A ARG* 1.3 58.4 + - - +
830A ILE* 2.9 11.9 + - - +
831A GLU* 2.8 26.3 + - + +
838A PHE* 3.7 26.2 - - + -
839A PHE* 4.2 16.2 - - + -
852A LEU 4.7 0.7 - - - +
853A LYS* 3.3 33.9 + - + +
855A TYR 4.5 1.5 + - - +
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Residues in contact with ARG 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASN 5.9 0.4 - - - +
526A GLY 5.7 0.8 + - - -
527A THR* 3.1 45.3 + - - +
826A ARG* 3.5 27.4 - - - +
827A VAL* 1.3 75.6 - - - +
829A ASP* 1.3 66.8 + - - +
831A GLU* 2.9 53.4 + - - +
832A HIS* 3.1 45.4 + - - +
837A ASP* 5.4 2.0 + - - -
853A LYS* 3.0 26.2 + - - +
854A THR* 5.0 1.1 - - - -
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Residues in contact with ASP 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS* 6.0 0.9 - - + -
432A ARG* 4.0 17.4 - - - +
434A HIS* 2.7 33.2 + - + +
795A ILE* 4.1 16.6 - - + -
825A ALA* 4.2 1.4 - - - +
826A ARG* 2.6 66.0 + - - +
828A ARG* 1.3 81.5 - - - +
830A ILE* 1.3 63.3 + - - +
832A HIS* 3.2 15.5 + - - +
833A LEU* 3.2 17.4 + - + +
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Residues in contact with ILE 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A ILE* 4.8 2.0 - - + -
769A TYR* 3.9 35.2 - - + -
770A SER 4.0 2.5 - - - +
771A ILE* 3.6 27.1 - - + -
793A SER* 4.0 17.9 - - - -
794A PHE 4.0 4.5 - - - +
795A ILE* 3.8 24.2 - - + -
825A ALA 5.4 0.2 - - - +
826A ARG 3.3 6.2 + - - +
827A VAL* 2.9 10.1 + - - +
829A ASP* 1.3 77.6 - - - +
831A GLU* 1.3 54.6 + - - +
833A LEU* 3.4 4.8 + - - +
834A THR* 2.4 39.5 + - + +
838A PHE* 3.7 25.8 - - + -
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Residues in contact with GLU 831 (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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605A LEU* 5.7 1.0 - - + +
827A VAL* 2.8 14.2 + - - +
828A ARG* 2.9 40.2 + - - +
830A ILE* 1.3 75.6 - - - +
832A HIS* 1.3 55.2 + - - +
834A THR* 3.4 6.1 - - - -
835A SER* 2.5 35.5 + - - -
836A LEU 3.3 17.4 - - - +
837A ASP* 3.4 4.7 - - - +
838A PHE* 3.1 33.5 + - + -
853A LYS* 2.8 48.0 + - - +
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Residues in contact with HIS 832 (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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222A TYR* 5.1 3.0 + - - -
434A HIS* 5.1 4.0 - + + -
525A ASN* 5.0 11.1 + - - -
745A GLY 3.4 14.6 - - - +
746A LEU* 3.5 14.0 - - + +
747A HIS* 3.0 14.9 + - - +
826A ARG* 4.4 9.0 + - - -
828A ARG* 3.1 64.0 + - + +
829A ASP* 3.2 12.1 + - - +
831A GLU* 1.3 77.2 - - - +
833A LEU* 1.3 64.8 + - - +
834A THR 3.1 1.0 + - - -
835A SER* 3.7 5.1 + - - +
1B NAG 3.7 28.8 + - + +
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Residues in contact with LEU 833 (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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431A LYS* 4.0 23.3 - - + -
434A HIS* 6.1 3.4 - - + -
738A ILE* 4.1 28.7 - - + +
739A PHE 4.6 4.5 + - - +
740A ASP* 3.5 32.3 - - + +
745A GLY* 3.2 34.8 - - - +
746A LEU 4.0 1.6 - - - +
747A HIS* 3.0 24.3 - - - +
795A ILE* 3.9 29.2 - - + -
829A ASP* 3.2 13.0 + - + +
830A ILE 3.9 3.8 - - - +
832A HIS* 1.3 79.6 - - - +
834A THR* 1.3 60.0 + - - +
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Residues in contact with THR 834 (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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606A TYR* 3.6 14.6 + - - -
630A LEU 5.6 0.4 - - - +
737A PRO 4.3 4.5 - - - +
738A ILE* 3.8 22.7 - - + -
747A HIS* 3.9 8.0 - - - -
769A TYR* 4.0 19.5 - - + -
830A ILE* 2.4 30.4 + - + +
831A GLU* 3.4 2.4 + - - -
833A LEU* 1.3 82.2 - - - +
835A SER* 1.3 75.5 + - - +
836A LEU* 3.2 33.2 + - + +
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Residues in contact with SER 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 3.8 1.2 - - - -
605A LEU* 2.8 47.5 + - - -
606A TYR* 3.6 19.5 - - - +
747A HIS* 3.0 25.6 + - - +
831A GLU 2.5 20.0 + - - -
832A HIS 3.7 3.5 + - - -
834A THR* 1.3 77.3 + - - +
836A LEU* 1.3 55.8 + - - +
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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
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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