Contacts of the strand formed by residues 1086 - 1092 (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 PHE1086 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663M SER* 3.1 7.3 + - - +
664M THR 3.2 23.6 - - - +
665M GLY* 3.5 13.9 - - - -
666M ILE* 3.2 28.3 - - + -
825N VAL* 4.5 0.7 - - - +
826N ALA* 4.2 0.7 + - - -
827N ILE* 3.5 38.0 + - + +
1025N HIS* 6.2 0.2 - + - -
1026N LEU* 3.2 33.7 - - + -
1029N CYS* 3.1 35.7 - - + -
1030N LEU* 4.2 9.6 - - + -
1067N ARG 3.5 16.6 - - - -
1068N GLY* 4.5 3.6 - - - -
1069N PHE* 4.2 9.4 - + + +
1085N ILE* 1.3 75.4 - - - +
1087N PHE* 1.3 58.4 + - - +
1088N GLY 4.1 0.5 + - - -
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Residues in contact with PHE1087 (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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824N ILE* 2.9 30.3 - - + -
825N VAL 3.1 13.9 - - - -
826N ALA* 4.6 4.0 - - + +
1000N PRO 4.9 0.2 - - - -
1002N THR* 3.7 26.2 - - + -
1006N ILE* 4.5 3.1 - - + -
1007N VAL* 3.6 11.0 - - - -
1008N PRO* 3.5 33.4 - - + -
1029N CYS* 4.1 5.5 - - - -
1033N LYS* 3.4 23.0 + - - +
1068N GLY* 3.5 7.4 + - - +
1070N GLU* 4.1 21.3 - - + -
1072N MET* 3.3 39.5 - - + -
1085N ILE* 3.3 3.4 + - + -
1086N PHE* 1.3 75.6 - - - +
1088N GLY* 1.3 78.5 + - - +
44V TYR* 4.3 7.6 - - - -
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Residues in contact with GLY1088 (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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824N ILE* 4.5 1.6 - - - -
825N VAL* 3.2 22.2 + - - +
1029N CYS* 3.3 15.3 - - - -
1033N LYS* 4.1 8.1 - - - -
1087N PHE* 1.3 88.9 - - - +
1089N PRO* 1.3 80.8 - - - +
44V TYR* 4.4 2.0 - - - -
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Residues in contact with PRO1089 (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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803N LEU* 3.5 31.0 - - + -
822N ASN* 4.9 5.2 - - + -
823N ALA 3.3 12.3 - - - +
824N ILE* 3.8 19.2 - - + -
1029N CYS* 3.3 17.7 - - - -
1032N SER* 3.6 4.4 - - - +
1033N LYS* 3.5 30.7 - - + +
1036N ALA* 4.3 4.7 - - + -
1088N GLY* 1.3 87.0 - - - +
1090N THR* 1.3 66.4 + - - +
44V TYR* 3.8 16.4 - - + -
48V ARG* 5.2 1.8 - - + +
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Residues in contact with THR1090 (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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822N ASN* 4.1 4.4 + - - +
823N ALA* 2.7 29.4 + - - +
825N VAL* 3.7 21.3 - - - +
982N SER* 4.6 3.6 - - - -
1025N HIS* 4.3 27.1 + - + +
1028N GLU* 3.1 21.8 - - + +
1029N CYS* 3.9 13.3 - - - +
1032N SER* 4.9 2.7 - - - -
1088N GLY 3.7 4.7 + - - -
1089N PRO* 1.3 82.9 + - - +
1091N TYR* 1.3 75.9 + - - +
1092N TYR* 3.4 8.0 + - + -
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Residues in contact with TYR1091 (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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755N ILE* 5.9 0.2 - - + -
800N GLN 3.0 23.5 + - - -
802N PRO* 3.3 30.5 - - + -
803N LEU 5.4 0.2 - - - +
804N GLY 5.9 0.2 - - - +
814N PHE* 3.9 20.4 - + - -
818N PRO* 3.1 4.2 - - - +
819N ALA 2.9 13.7 + - - -
820N GLY* 2.6 50.4 + - - -
821N GLN* 3.0 18.2 - - - -
822N ASN* 3.7 10.8 + - - +
982N SER* 3.8 13.5 - - - -
983N ARG* 3.2 46.0 - - + +
1028N GLU* 2.5 10.4 + - - +
1032N SER* 5.5 0.2 + - - -
1090N THR* 1.3 82.6 - - - +
1092N TYR* 1.3 58.4 + - - +
1093N GLN* 5.1 5.8 - - + -
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Residues in contact with TYR1092 (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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820N GLY* 4.3 0.7 - - - -
821N GLN 2.9 31.9 + - - +
823N ALA* 4.7 1.6 - - + -
825N VAL* 3.3 31.2 - - + -
839N MET* 4.3 10.3 - - + -
851N PHE* 3.0 24.9 - - + -
980N PHE* 5.0 0.4 - - + -
981N ALA* 3.1 16.2 - - - -
982N SER* 2.9 44.3 - - - -
986N GLN* 4.4 10.2 + - - +
1010N LEU* 3.2 28.3 - - + -
1012N ILE* 3.3 37.1 - - + +
1025N HIS* 3.5 6.5 + - - -
1090N THR* 3.4 9.6 + - + +
1091N TYR* 1.3 76.0 - - - +
1093N GLN* 1.3 62.6 + - - +
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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