Contacts of the strand formed by residues 961 - 972 (chain N) in PDB entry 2JA7
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 LEU 961 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862N GLN* 4.7 12.6 - - + +
863N GLU* 3.2 37.0 - - + +
864N LYS* 5.1 4.0 - - - -
865N LYS* 3.9 28.5 - - + +
871N THR* 6.0 0.7 - - + -
956N THR* 3.2 6.4 - - - -
957N ASN* 3.0 49.5 + - + +
959N ASP* 3.9 27.1 - - + +
960N GLY* 1.3 80.6 - - - +
962N LYS* 1.3 63.9 + - - +
963N PHE 3.2 0.7 + - - -
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Residues in contact with LYS 962 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862N GLN* 3.4 20.8 - - - -
863N GLU* 3.1 37.4 + - - +
873N THR* 6.2 1.4 - - - +
874N PHE* 3.5 27.9 - - + +
954N VAL* 5.0 17.0 - - + -
955N THR 3.5 6.5 - - - +
956N THR* 4.8 0.7 - - - +
960N GLY 4.1 1.7 + - - +
961N LEU* 1.3 69.7 - - - +
963N PHE* 1.3 60.6 + - - +
41X SER 4.6 7.7 + - - -
42X ARG* 4.3 25.5 - - - +
43X THR 5.2 6.3 - - - +
45X ALA 5.9 1.3 - - - -
46X VAL* 5.2 14.1 - - + -
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Residues in contact with PHE 963 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N LEU 3.3 25.8 - - - -
120N ARG* 4.0 13.2 - - + -
121N ASN* 3.0 35.2 - - + -
860N MET* 3.9 18.2 - - + -
861N ASP 3.7 2.9 - - - -
862N GLN* 3.2 35.7 - - + -
953N LEU* 3.8 2.4 - - + +
954N VAL 3.6 0.2 - - - -
955N THR* 2.4 61.9 + - + +
956N THR 4.3 6.7 - - - -
957N ASN* 4.4 7.4 - - + -
961N LEU 3.2 5.5 + - - +
962N LYS* 1.3 72.3 - - - +
964N VAL* 1.3 62.3 + - - +
965N LYS* 3.7 22.0 - - + -
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Residues in contact with VAL 964 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859N TYR 4.3 0.2 - - - +
860N MET* 3.5 2.9 - - - -
861N ASP 2.9 37.3 + - - +
874N PHE* 4.1 23.6 - - + -
898N LEU* 3.6 31.9 - - + -
912N ILE* 4.2 6.9 - - + +
952N VAL* 4.4 0.9 - - + -
953N LEU 3.4 12.8 - - - +
954N VAL* 3.8 26.5 - - + -
962N LYS 4.1 0.2 + - - -
963N PHE* 1.3 80.9 - - - +
965N LYS* 1.3 69.6 + - - +
966N VAL* 4.0 12.1 - - + -
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Residues in contact with LYS 965 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N ARG 4.1 10.3 + - - -
119N LEU 4.0 8.7 - - - +
121N ASN* 3.4 23.0 - - - +
789N MET* 3.0 48.3 + - + +
858N SER* 5.4 3.8 - - - +
859N TYR 3.5 6.1 - - - +
860N MET* 3.8 26.5 - - + +
952N VAL* 3.6 0.3 - - - -
953N LEU* 2.9 46.2 + - + +
963N PHE* 3.7 28.7 - - + -
964N VAL* 1.3 76.9 - - - +
966N VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 966 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789N MET* 4.1 0.7 - - - -
857N ARG 3.8 0.3 - - - +
858N SER* 3.0 3.3 - - - -
859N TYR* 2.8 39.1 + - + +
898N LEU* 4.6 1.3 - - + -
899N ILE* 5.3 1.1 - - + +
911N ILE* 3.3 38.4 - - + +
912N ILE* 3.9 24.0 - - + -
949N VAL* 4.2 13.2 - - + -
951N GLN 3.9 2.2 - - - -
952N VAL* 3.9 28.0 - - + +
964N VAL* 4.0 9.0 - - + -
965N LYS* 1.3 78.4 - - - +
967N ARG* 1.3 64.7 + - - +
968N VAL* 5.1 3.4 - - + -
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Residues in contact with ARG 967 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785N TYR 3.5 15.7 + - - -
786N ASN* 3.4 25.5 + - - +
788N ARG 3.0 31.7 + - - +
789N MET* 3.8 14.3 - - - -
790N ASP 5.5 0.4 - - - -
856N PHE* 3.3 35.8 - - + -
857N ARG 3.0 14.8 - - - +
858N SER* 3.9 9.0 - - - +
949N VAL* 3.7 3.8 - - - +
950N ASP* 2.7 52.4 + - - +
951N GLN* 3.0 44.0 + - - +
966N VAL* 1.3 76.2 - - - +
968N VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 968 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855N PHE 3.5 1.7 - - - +
856N PHE* 3.5 2.9 - - - -
857N ARG* 2.7 36.8 + - + +
859N TYR* 4.4 10.7 - - + -
905N VAL* 4.1 17.9 - - + -
911N ILE* 4.5 5.8 - - + -
941N LEU* 4.2 18.6 - - + -
946N ASN 4.8 1.8 - - - +
947N GLY* 4.2 9.9 - - - +
948N ILE 3.4 23.1 - - - +
949N VAL* 4.0 15.9 - - + -
950N ASP* 4.3 0.7 - - - -
966N VAL* 4.2 4.4 + - + -
967N ARG* 1.3 78.6 - - - +
969N ARG* 1.3 66.9 + - - +
970N THR* 4.5 4.8 + - - +
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Residues in contact with ARG 969 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854N LEU* 4.6 3.6 - - + -
855N PHE 3.4 3.1 - - - -
856N PHE* 3.5 30.1 - - + +
901N PRO 5.7 0.2 + - - -
947N GLY* 4.0 0.2 - - - -
948N ILE* 2.7 72.0 + - - +
949N VAL 4.4 7.4 + - - -
950N ASP* 3.3 39.2 + - + +
968N VAL* 1.3 72.6 - - - +
970N THR* 1.3 70.2 + - - +
59O ALA* 3.7 14.3 - - - +
60O ASP* 2.7 28.9 + - - +
61O GLU* 2.6 54.1 + - - +
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Residues in contact with THR 970 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854N LEU* 3.5 8.3 - - - +
855N PHE* 2.9 53.0 + - - -
945N GLU* 6.0 1.6 - - - +
946N ASN* 3.3 31.4 + - - +
947N GLY* 4.4 3.9 - - - -
968N VAL* 4.5 5.0 + - - +
969N ARG* 1.3 77.5 + - - +
971N THR* 1.3 83.1 + - - +
972N LYS* 4.1 9.6 - - + -
61O GLU* 4.0 5.4 - - - -
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Residues in contact with THR 971 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797N TYR* 2.9 26.7 + - + +
852N ARG* 4.6 10.5 - - - +
853N SER 3.5 7.6 - - - +
854N LEU* 3.7 4.3 - - - +
970N THR* 1.3 83.1 - - - +
972N LYS* 1.3 68.7 + - - +
973N ILE* 4.0 15.3 + - + +
61O GLU* 2.8 38.1 + - + +
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Residues in contact with LYS 972 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794N ASN* 5.1 2.6 + - - +
852N ARG* 4.0 1.6 - - - -
853N SER* 3.2 30.3 + - - +
855N PHE* 3.4 52.5 - - + -
945N GLU* 5.7 2.2 - - - +
970N THR* 4.1 9.1 + - + -
971N THR* 1.3 76.3 - - - +
973N ILE* 1.3 61.7 + - - +
1094N ARG* 3.3 24.8 + - - +
1098N MET* 3.8 23.5 - - + +
1101N ASP* 3.1 35.7 + - - +
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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