Contacts of the strand formed by residues 947 - 957 (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 GLY 947 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904N ARG* 3.5 11.9 - - - +
905N VAL* 2.6 43.4 + - - +
946N ASN* 1.3 80.0 - - - +
948N ILE* 1.3 64.6 + - - -
968N VAL* 4.2 2.7 - - - -
969N ARG 4.0 7.6 - - - -
970N THR* 4.4 5.4 - - - -
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Residues in contact with ILE 948 (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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901N PRO 3.9 1.3 - - - +
902N GLY* 3.4 15.3 - - - +
903N VAL 3.3 13.9 - - - +
904N ARG* 3.8 28.7 - - + +
905N VAL* 4.9 0.2 - - - -
947N GLY* 1.3 78.6 - - - +
949N VAL* 1.3 80.2 + - - +
950N ASP* 4.1 0.3 - - - +
968N VAL* 3.4 5.0 - - - +
969N ARG* 2.7 58.5 + - - +
60O ASP* 5.5 0.9 - - - +
61O GLU* 4.8 2.9 - - - +
60X ARG* 6.3 0.4 - - - +
65X VAL* 5.4 1.6 - - + -
67X PHE* 3.2 43.1 - - + -
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Residues in contact with VAL 949 (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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899N ILE* 3.4 34.1 - - + +
900N ALA 3.7 2.9 - - - +
901N PRO* 2.7 37.3 - - + +
903N VAL 2.9 14.3 + - - +
905N VAL* 3.8 16.0 - - + +
948N ILE* 1.3 84.5 - - - +
950N ASP* 1.3 62.8 + - - +
951N GLN 4.1 1.3 - - - +
952N VAL* 3.9 24.0 - - + -
966N VAL* 4.2 8.5 - - + -
967N ARG 3.8 9.9 - - - +
968N VAL* 4.0 7.8 - - + +
969N ARG* 4.4 2.8 + - - -
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Residues in contact with ASP 950 (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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856N PHE* 3.2 7.6 - - - -
901N PRO* 4.2 11.6 - - - +
949N VAL* 1.3 76.5 - - - +
951N GLN* 1.3 68.5 + - - +
967N ARG* 2.7 56.5 + - - +
968N VAL 4.3 0.2 - - - -
969N ARG* 3.3 49.7 + - + +
59O ALA* 5.3 1.6 - - - +
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Residues in contact with GLN 951 (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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786N ASN 4.2 9.7 + - - -
787N VAL* 5.2 9.5 - - - +
789N MET* 3.5 31.0 - - - +
901N PRO* 4.0 9.0 - - + -
949N VAL* 4.1 2.8 - - - +
950N ASP* 1.3 85.1 - - - +
952N VAL* 1.3 72.6 + - - +
953N LEU* 5.0 1.7 - - - +
967N ARG* 3.0 52.9 + - - +
57X LEU* 3.6 40.0 - - + +
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Residues in contact with VAL 952 (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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898N LEU* 3.8 34.5 - - + -
899N ILE 2.9 27.6 - - - +
901N PRO* 4.1 9.2 - - + +
949N VAL* 3.9 8.5 - - + -
951N GLN* 1.3 84.6 - - - +
953N LEU* 1.3 76.2 + - - +
954N VAL* 5.0 0.2 - - + -
964N VAL* 4.4 2.2 - - + -
965N LYS 3.6 5.6 - - - +
966N VAL* 3.9 31.4 - - + +
57X LEU* 3.5 16.4 - - - -
58X LYS* 3.7 19.8 + - + -
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Residues in contact with LEU 953 (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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119N LEU* 4.4 28.7 - - + +
789N MET* 3.5 24.5 - - + -
951N GLN* 5.0 1.6 - - - +
952N VAL* 1.3 82.4 - - - +
954N VAL* 1.3 62.7 + - - +
955N THR* 4.2 13.7 - - - +
963N PHE* 3.8 2.2 - - + +
964N VAL* 3.4 7.8 - - - +
965N LYS* 2.9 62.4 + - + +
55X ILE* 5.0 5.8 - - + +
56X LEU 3.3 13.5 - - - +
57X LEU* 4.1 18.2 - - + +
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Residues in contact with VAL 954 (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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896N ASP* 6.0 0.2 - - + -
898N LEU* 3.6 31.4 - - + -
952N VAL* 5.0 0.7 - - + -
953N LEU* 1.3 73.6 - - - +
955N THR* 1.3 66.3 + - - +
962N LYS* 5.0 18.4 - - + -
963N PHE 3.7 2.5 - - - +
964N VAL* 3.8 12.1 - - + -
29X TYR* 4.6 28.3 - - + +
46X VAL* 3.7 18.7 - - + +
54X ARG 3.5 1.6 - - - +
55X ILE 2.3 27.0 - - - +
56X LEU* 3.0 10.9 + - + +
57X LEU 5.1 2.9 - - - +
58X LYS* 5.7 1.6 - - + -
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Residues in contact with THR 955 (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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119N LEU* 5.6 1.6 + - - +
120N ARG* 3.4 33.9 - - + +
953N LEU* 4.2 13.5 - - - +
954N VAL* 1.3 77.9 + - - +
956N THR* 1.3 81.8 + - - +
962N LYS* 3.4 5.2 - - - +
963N PHE* 2.4 58.9 + - - -
46X VAL* 4.3 6.7 - - - -
54X ARG* 3.1 18.1 + - + +
55X ILE* 3.4 12.6 + - - +
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Residues in contact with THR 956 (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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120N ARG* 3.2 23.1 + - - +
955N THR* 1.3 87.2 - - - +
957N ASN* 1.3 73.8 + - - +
958N GLN 4.9 0.7 - - - +
960N GLY* 3.4 34.8 - - - +
961N LEU 3.2 4.7 - - - +
962N LYS* 4.8 0.4 - - - +
963N PHE* 4.3 2.9 - - - +
46X VAL* 3.3 30.8 + - - +
54X ARG* 3.9 34.9 + - - +
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Residues in contact with ASN 957 (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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120N ARG* 4.4 13.5 - - - +
121N ASN* 4.7 4.5 - - - +
122N LEU* 4.5 5.9 - - - +
862N GLN* 3.8 23.4 - - - +
956N THR* 1.3 78.4 - - - +
958N GLN* 1.3 62.9 + - - +
959N ASP* 2.4 41.0 + - - -
960N GLY 2.5 15.4 + - - -
961N LEU* 3.0 27.7 + - + +
963N PHE* 4.4 13.7 - - + -
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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