Contacts of the strand formed by residues 838 - 848 (chain A) in PDB entry 1R4X
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 HIS 838 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A VAL* 4.0 1.6 - - - -
834A PHE* 2.9 30.6 + - + +
836A GLY 4.3 11.3 + - - -
837A GLY* 1.3 79.4 + - - +
839A ASP* 1.3 63.7 + - - +
860A SER* 4.2 13.9 + - - +
861A LEU* 3.8 34.8 - - + +
862A GLU* 3.1 37.3 + - + +
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Residues in contact with ASP 839 (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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767A VAL* 4.8 0.5 - - - +
769A LYS* 3.3 34.2 + - - -
775A ALA* 5.7 1.0 - - - +
778A GLU* 5.3 4.7 - - - +
779A VAL* 4.5 21.8 - - + +
832A GLY 3.3 8.7 - - - +
833A VAL* 3.5 20.3 - - - +
837A GLY 3.9 2.5 + - - +
838A HIS* 1.3 70.9 - - - +
840A ILE* 1.3 54.9 + - - +
841A LEU* 4.2 8.4 - - + +
859A ARG 4.7 0.2 - - - -
860A SER* 2.8 34.0 + - - -
861A LEU* 4.4 2.8 + - - +
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Residues in contact with ILE 840 (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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764A ILE* 4.2 14.8 - - + -
810A MET* 3.3 11.6 - - + +
832A GLY 2.8 47.9 + - - +
833A VAL 4.2 1.3 - - - +
834A PHE* 4.0 17.7 - - + +
839A ASP* 1.3 74.5 - - - +
841A LEU* 1.3 71.0 + - - +
842A VAL* 4.3 4.7 - - + -
858A ALA* 4.2 2.7 - - + -
859A ARG 3.6 15.7 - - - +
860A SER* 4.1 3.6 - - - -
865A PRO* 4.0 37.0 - - + +
866A VAL* 4.0 10.1 - - + +
869A ILE* 3.9 23.3 - - + -
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Residues in contact with LEU 841 (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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769A LYS* 4.6 11.4 - - + -
772A PHE* 4.2 9.0 - - + -
775A ALA* 3.6 40.2 - - + +
776A TRP* 3.6 28.3 - - + +
779A VAL* 3.9 16.8 - - + -
830A LEU 3.4 3.6 - - - +
831A ALA* 3.7 24.7 - - + -
832A GLY 4.6 1.1 - - - +
839A ASP* 4.7 10.5 - - + +
840A ILE* 1.3 83.8 - - - +
842A VAL* 1.3 65.5 + - - +
858A ALA* 3.3 4.3 - - - +
859A ARG* 3.0 38.3 + - + +
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Residues in contact with VAL 842 (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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772A PHE* 3.7 4.7 - - - -
804A ILE* 6.2 0.4 - - + -
808A LEU* 4.7 4.7 - - + -
810A MET* 3.7 20.4 - - + -
828A LEU 3.8 0.9 - - - +
829A LEU* 3.5 2.8 - - - -
830A LEU* 2.8 59.6 + - + +
840A ILE* 4.3 1.3 - - + -
841A LEU* 1.3 81.9 - - - +
843A ARG* 1.3 65.8 + - - +
844A SER* 4.8 3.1 - - - +
856A VAL* 3.7 28.3 - - + -
857A THR 3.4 4.5 - - - +
858A ALA* 4.3 3.4 - - + -
869A ILE* 3.8 34.1 - - + -
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Residues in contact with ARG 843 (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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772A PHE* 4.7 2.9 - - + -
776A TRP* 3.7 44.3 - - + +
784A GLU* 4.6 4.6 + - - -
827A THR* 3.8 20.9 - - + -
828A LEU 3.4 3.8 - - - -
829A LEU* 4.0 12.1 - - + -
842A VAL* 1.3 75.2 - - - +
844A SER* 1.3 62.3 + - - +
845A ARG* 3.5 55.0 - - + +
855A GLN 3.5 2.0 + - - +
856A VAL* 3.4 2.6 - - - +
857A THR* 2.8 70.8 + - - +
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Residues in contact with SER 844 (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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804A ILE* 4.9 4.7 - - - -
827A THR* 3.3 4.3 - - - -
828A LEU* 2.9 52.4 + - - -
830A LEU* 6.2 0.6 - - - +
842A VAL* 4.2 3.8 - - - +
843A ARG* 1.3 74.8 - - - +
845A ARG* 1.3 62.3 + - - +
846A LEU* 3.3 13.1 - - - +
854A MET* 3.2 37.2 - - - +
855A GLN 3.3 2.9 - - - -
856A VAL* 3.8 11.9 - - - +
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Residues in contact with ARG 845 (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 HIS 3.7 4.7 - - - +
827A THR* 3.9 21.6 + - + +
843A ARG* 3.5 53.1 - - - +
844A SER* 1.3 71.9 + - - +
846A LEU* 1.3 60.7 + - - +
847A LEU* 5.7 0.2 - - - +
853A THR 4.0 0.2 - - - +
854A MET* 3.2 2.1 - - - -
855A GLN* 2.8 64.8 + - + +
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Residues in contact with LEU 846 (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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797A LEU* 3.9 15.9 - - + -
800A ALA* 3.8 29.4 - - + -
801A VAL* 4.2 20.6 - - + -
804A ILE* 4.5 4.5 - - + -
825A THR* 3.4 7.9 - - - +
826A HIS* 2.8 38.0 + - - +
828A LEU* 4.2 11.0 - - + +
844A SER* 3.3 38.6 - - - +
845A ARG* 1.3 74.0 - - - +
847A LEU* 1.3 60.6 + - - +
852A VAL* 3.8 12.3 - - + -
853A THR 3.4 5.8 - - - +
854A MET* 3.8 17.0 - - + -
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Residues in contact with LEU 847 (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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797A LEU* 4.4 3.4 - - - -
824A ASN* 3.5 25.4 - - - +
825A THR* 3.9 15.0 - - + -
845A ARG 5.7 0.2 - - - +
846A LEU* 1.3 74.9 - - - +
848A LEU* 1.3 60.9 + - - +
849A LEU* 3.9 29.8 + - + +
851A THR 3.7 1.6 - - - +
852A VAL* 3.3 3.3 - - - -
853A THR* 2.9 45.1 + - + +
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Residues in contact with LEU 848 (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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795A LYS 3.6 31.4 - - - +
796A THR* 4.2 9.6 - - - -
797A LEU* 3.9 22.4 - - + +
823A LYS 5.5 1.6 - - - +
824A ASN* 2.8 49.6 + - + +
847A LEU* 1.3 69.2 - - - +
849A LEU* 1.3 62.0 + - - +
850A ASP 3.8 12.8 - - - +
851A THR* 3.6 23.8 - - - -
852A VAL* 3.9 6.5 - - + +
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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