Contacts of the helix formed by residues 825 - 834 (chain A) in PDB entry 2XR9
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 825 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.1 21.5 + - - -
431A ARG* 6.1 0.4 - - + -
433A HIS* 4.3 0.8 + - - -
504A GLU* 3.8 28.8 + - - +
506A ILE* 4.4 4.4 - - - +
507A GLU* 4.0 9.7 + - - -
524A ASN 5.0 3.2 + - - -
526A THR* 4.7 1.0 + - - -
792A SER* 4.6 2.0 - - - -
824A ALA* 1.3 75.1 - - - +
826A VAL* 1.3 66.2 + - - +
827A ARG* 3.6 28.6 - - - +
828A ASP* 2.9 50.7 + - - +
829A ILE* 3.4 8.1 + - - +
831A HIS* 4.4 7.1 + - - -
852A LYS 3.6 8.5 - - - +
853A THR* 3.2 45.7 - - - +
854A TYR 3.4 15.5 - - - +
855A LEU* 4.1 12.8 - - + -
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Residues in contact with VAL 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A ILE* 3.8 22.2 - - + -
790A VAL* 3.9 18.2 - - + -
792A SER* 3.6 20.3 + - - +
824A ALA 4.2 0.4 + - - -
825A ARG* 1.3 70.9 - - - +
827A ARG* 1.3 63.2 + - - +
829A ILE* 3.0 10.2 + - - +
830A GLU* 3.0 21.6 + - + +
837A PHE* 3.7 27.1 - - + -
838A TYR* 4.1 14.8 - - + -
852A LYS* 3.3 32.1 + - + +
854A TYR 4.5 1.6 + - - -
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Residues in contact with ARG 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ASN 5.8 0.9 - - - +
525A GLY 5.2 3.6 + - - -
526A THR* 2.9 42.5 + - - +
825A ARG* 3.6 27.4 - - - +
826A VAL* 1.3 76.9 - - - +
828A ASP* 1.3 60.7 + - - +
830A GLU* 2.9 46.5 + - - +
831A HIS* 3.2 58.6 + - - +
836A ASP* 5.0 4.2 + - - -
849A LEU* 5.9 1.3 - - - +
852A LYS* 2.9 25.5 + - - +
853A THR* 4.6 3.1 - - - -
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Residues in contact with ASP 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 5.8 0.7 - - + +
431A ARG* 4.1 15.0 - - - +
433A HIS* 2.8 35.1 + - + +
744A GLY 4.7 0.3 - - - +
794A ILE* 3.9 16.2 - - + -
824A ALA* 3.9 5.5 - - - +
825A ARG* 2.9 56.9 + - - +
827A ARG* 1.3 78.6 - - - +
829A ILE* 1.3 62.0 + - - +
831A HIS* 3.5 8.1 + - - +
832A LEU* 3.2 29.0 + - + +
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Residues in contact with ILE 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A ILE* 4.6 1.3 - - + -
768A TYR* 3.7 39.7 - - + -
770A ILE* 3.7 26.0 - - + -
792A SER* 3.8 19.3 - - - -
793A PHE 3.9 15.5 - - - +
794A ILE* 3.6 24.0 - - + -
824A ALA* 4.7 0.2 - - + -
825A ARG 3.4 7.2 + - - +
826A VAL* 3.0 8.2 + - - +
828A ASP* 1.3 74.7 - - - +
830A GLU* 1.3 59.0 + - - +
832A LEU* 3.1 6.5 + - - +
833A THR* 2.7 38.9 + - + +
837A PHE* 4.1 14.1 - - + -
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Residues in contact with GLU 830 (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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826A VAL* 3.0 19.0 + - - +
827A ARG* 2.9 43.6 + - - +
829A ILE* 1.3 74.8 - - - +
831A HIS* 1.3 58.3 + - - +
833A THR* 3.8 2.9 - - - -
834A GLY* 2.8 32.1 + - - -
835A LEU 3.2 21.7 + - - +
836A ASP* 3.3 4.2 - - - +
837A PHE* 3.1 27.2 + - + -
852A LYS* 2.5 46.2 + - - +
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Residues in contact with HIS 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 5.4 2.3 + - - -
433A HIS* 5.2 2.7 - + - -
524A ASN* 5.2 8.4 + - - +
744A GLY 3.3 15.3 - - - +
745A LEU* 3.4 15.6 - - + +
746A ARG* 3.1 20.4 + - - +
825A ARG* 4.4 7.7 + - - -
827A ARG* 3.2 60.9 + - + +
828A ASP* 3.7 9.4 - - - +
830A GLU* 1.3 77.1 - - - +
832A LEU* 1.3 59.9 + - - +
833A THR 3.4 0.7 + - - -
834A GLY* 4.1 1.0 + - - -
1B NAG 3.6 30.5 + - + -
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Residues in contact with LEU 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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430A LYS* 4.1 18.6 - - + -
433A HIS* 6.2 2.7 - - + -
737A ILE* 3.9 34.1 - - + +
738A PHE 4.4 4.3 + - - +
739A ASP* 3.2 42.4 - - + +
744A GLY* 3.4 22.9 - - - +
745A LEU 3.8 1.8 - - - +
746A ARG* 3.4 19.4 - - - +
794A ILE* 3.9 25.4 - - + -
828A ASP* 3.2 17.6 + - + +
829A ILE 3.1 5.4 + - - +
831A HIS* 1.3 81.4 - - - +
833A THR* 1.3 60.0 + - - +
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Residues in contact with THR 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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605A TYR* 3.5 10.0 + - - -
629A LEU* 5.4 2.6 - - - +
736A PRO 4.0 5.8 - - - +
737A ILE* 3.6 22.7 - - + -
746A ARG* 3.5 20.3 - - - +
768A TYR* 3.9 21.5 - - + -
829A ILE* 2.7 27.3 + - + +
830A GLU* 3.6 0.7 + - - -
832A LEU* 1.3 80.8 - - - +
834A GLY* 1.3 63.5 + - - +
835A LEU* 3.3 33.4 + - + +
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Residues in contact with GLY 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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603A VAL* 3.8 1.0 - - - -
604A LEU* 2.8 43.0 + - - +
605A TYR* 3.8 14.7 - - - -
746A ARG* 4.1 7.4 - - - +
830A GLU 2.8 16.3 + - - -
831A HIS 4.1 3.6 + - - -
832A LEU 3.9 0.4 - - - -
833A THR* 1.3 72.3 - - - +
835A LEU* 1.3 56.2 + - - +
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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