Contacts of the strand formed by residues 792 - 803 (chain A) in PDB entry 1JV2
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 LYS 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790A PHE* 3.5 3.6 - - - -
791A SER* 1.3 82.2 + - - +
793A ALA* 1.3 62.4 - - - +
886A VAL 3.6 15.5 - - - +
887A GLY* 3.9 6.1 - - - -
928A VAL* 3.8 2.6 - - - +
929A ILE* 2.9 20.0 + - + -
930A GLU* 2.6 69.3 + - + +
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Residues in contact with ALA 793 (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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782A LEU* 4.7 7.4 - - + -
790A PHE* 3.6 26.2 - - + -
792A LYS* 1.3 76.4 - - - +
794A MET* 1.3 71.8 + - - +
886A VAL* 3.0 36.6 + - + +
926A PHE* 5.1 1.6 - - + -
927A ASN 3.1 15.9 - - - +
928A VAL* 3.7 11.2 - - + -
929A ILE* 3.9 3.5 - - - +
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Residues in contact with MET 794 (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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782A LEU* 5.8 0.4 - - - -
793A ALA* 1.3 83.6 - - - +
795A LEU* 1.3 59.5 + - - +
796A HIS* 4.0 20.7 + - + +
883A VAL* 4.0 22.7 - - + -
884A CYS 3.5 16.8 - - - +
885A GLN* 4.0 23.8 - - + +
886A VAL* 5.2 1.3 - - - -
926A PHE* 2.9 29.6 - - - +
927A ASN* 2.8 22.6 + - + +
929A ILE* 3.5 26.2 - - + -
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Residues in contact with LEU 795 (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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744A ILE* 3.9 24.0 - - + -
780A TYR* 5.4 8.7 - - + +
781A GLU 6.3 0.2 - - - -
782A LEU* 4.8 14.8 - - + +
794A MET* 1.3 72.7 - - - +
796A HIS* 1.3 65.2 + - - +
797A LEU* 5.2 2.5 - - + +
820A MET* 4.0 17.5 - - + -
882A ILE 3.8 0.9 - - - +
883A VAL* 3.5 3.6 - - - +
884A CYS* 2.7 69.1 + - + +
886A VAL* 4.6 9.8 - - + +
897A LEU* 4.3 18.4 - - + -
924A ALA* 4.9 6.1 - - + -
925A SER 3.6 12.8 - - - +
926A PHE* 4.1 7.6 - - + -
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Residues in contact with HIS 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A MET* 4.2 28.5 - - + +
795A LEU* 1.3 76.6 - - - +
797A LEU* 1.3 60.8 + - - +
798A GLN* 4.2 7.3 - - + +
882A ILE 3.9 2.0 - - - -
883A VAL* 3.4 24.8 - - + +
923A SER 4.0 0.2 - - - +
924A ALA* 3.0 4.5 - - - +
925A SER* 2.7 57.2 + - - +
926A PHE* 5.5 1.6 - - - -
927A ASN* 5.8 2.9 - - + -
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Residues in contact with LEU 797 (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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780A TYR* 3.6 17.9 - - + -
795A LEU* 5.5 3.4 - - + -
796A HIS* 1.3 74.7 - - - +
798A GLN* 1.3 76.7 + - - +
799A TRP* 4.5 7.4 - - + +
881A LYS* 3.3 6.6 - - - +
882A ILE* 2.9 62.9 + - + +
897A LEU* 3.9 29.2 - - + -
899A VAL* 4.0 14.6 - - + -
922A SER* 3.4 17.5 - - - +
923A SER 3.3 17.7 - - - +
924A ALA* 4.0 6.7 - - + -
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Residues in contact with GLN 798 (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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796A HIS* 4.2 8.2 - - + +
797A LEU* 1.3 79.6 - - - +
799A TRP* 1.3 61.1 + - - +
874A CYS* 3.9 31.7 + - + +
879A CYS* 4.6 3.9 - - - -
880A LEU 4.2 2.0 - - - -
881A LYS* 3.7 28.3 - - + -
921A LYS 4.8 0.3 - - - +
922A SER* 3.8 2.6 + - - -
923A SER* 2.7 45.3 + - - +
925A SER* 5.6 2.1 + - - -
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Residues in contact with TRP 799 (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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778A HIS* 3.5 47.6 - + + -
797A LEU* 4.6 15.0 - - + -
798A GLN* 1.3 75.2 - - - +
800A PRO* 1.4 106.2 - - + +
801A TYR* 4.2 3.4 - + - -
809A LEU* 2.9 29.9 + - + +
811A ILE* 3.3 28.9 - - + +
874A CYS* 3.4 13.8 - - - -
879A CYS* 3.4 0.9 - - - -
880A LEU* 3.0 38.3 + - + +
882A ILE* 5.3 1.3 - - + -
899A VAL* 3.8 22.7 - - + -
901A SER* 3.2 35.4 - - - -
921A LYS 4.8 0.2 - - - -
922A SER* 3.7 14.6 - - - -
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Residues in contact with PRO 800 (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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799A TRP* 1.4 126.7 - - + +
801A TYR* 1.3 69.0 + - - +
808A LEU* 3.2 29.4 - - + +
809A LEU* 4.3 7.2 - - + -
872A LEU 4.0 11.9 - - - +
874A CYS* 4.7 6.1 - - - +
877A ALA* 5.1 7.4 - - + -
878A GLN 3.9 3.6 - - - +
880A LEU* 3.8 0.7 - - - +
920A LEU 4.2 6.5 - - - -
921A LYS 2.9 31.6 - - - +
922A SER* 4.5 1.8 - - - -
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Residues in contact with TYR 801 (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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799A TRP* 4.3 4.9 - + - +
800A PRO* 1.3 83.5 - - - +
802A LYS* 1.3 106.7 + - + +
807A THR* 3.3 13.9 - - + +
808A LEU* 2.9 29.3 + - - +
809A LEU 5.1 1.9 - - - +
810A TYR* 6.4 4.0 - + - -
826A MET* 3.7 37.6 - - + +
830A PRO* 5.9 6.2 - - + +
878A GLN* 3.1 24.1 + - + +
879A CYS 4.6 0.9 - - - -
880A LEU* 4.0 26.2 - - + -
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Residues in contact with LYS 802 (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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801A TYR* 1.3 124.1 + - + +
803A TYR* 1.3 64.7 - - - +
805A ASN* 3.3 34.6 + - - +
806A ASN 3.0 10.1 - - - +
807A THR* 3.7 24.2 - - - +
808A LEU* 3.9 5.9 - - - +
877A ALA* 2.9 26.3 - - - +
878A GLN* 3.6 20.2 + - - +
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Residues in contact with TYR 803 (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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802A LYS* 1.3 81.0 - - - +
804A ASN* 1.3 97.9 + - + +
806A ASN* 2.8 25.1 + - + +
808A LEU* 3.6 18.8 - - + -
868A ASP* 2.8 41.9 + - - -
872A LEU* 4.3 20.9 - - + -
876A VAL 4.0 18.2 - - - -
877A ALA* 4.3 2.5 - - + -
878A GLN* 3.8 7.3 + - - +
918A TYR* 5.4 11.9 - + - -
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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