Contacts of the helix formed by residues 1083 - 1093 (chain C) in PDB entry 6JOD
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 LYS1083 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023C ALA* 5.5 0.2 - - - -
1078C LEU* 3.7 10.6 + - + +
1081C GLU* 3.5 29.4 + - + +
1082C GLY* 1.3 72.5 - - - +
1084C VAL* 1.3 61.0 + - - +
1085C LYS 3.5 1.6 - - - -
1086C GLU* 3.3 32.9 + - + +
1087C ALA* 2.9 29.5 + - - +
66L SER* 4.0 16.1 + - - +
69L SER* 4.8 16.2 + - - -
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Residues in contact with VAL1084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021C ASP 5.1 1.6 - - - +
1022C ASN* 3.6 30.1 - - + +
1023C ALA* 3.6 27.4 - - + +
1026C VAL* 4.7 2.2 - - + +
1082C GLY 2.9 14.5 + - - +
1083C LYS* 1.3 72.1 - - - +
1085C LYS* 1.3 63.8 + - + +
1087C ALA* 3.2 6.7 + - - +
1088C GLN* 2.9 51.9 + - + +
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Residues in contact with LYS1085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C LYS 3.5 0.4 - - - -
1084C VAL* 1.3 79.7 - - + +
1086C GLU* 1.3 57.2 + - - +
1088C GLN* 3.3 18.3 + - - +
1089C ALA* 3.0 26.3 + - - +
65L GLY 5.4 0.7 - - - -
66L SER* 4.8 13.7 - - - -
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Residues in contact with GLU1086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078C LEU* 4.7 20.9 - - + +
1083C LYS* 3.3 36.6 + - + +
1084C VAL 3.3 0.6 - - - -
1085C LYS* 1.3 79.1 - - - +
1087C ALA* 1.3 57.4 + - - +
1089C ALA* 3.3 6.1 + - - +
1090C ALA* 3.0 27.0 + - - +
64L SER* 3.5 20.0 + - - +
65L GLY* 3.4 26.8 - - - +
66L SER* 3.3 25.8 + - - +
69L SER* 4.4 5.2 - - - +
70L TYR* 5.7 0.2 - - - -
71L SER* 5.2 2.8 + - - -
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Residues in contact with ALA1087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023C ALA* 6.3 0.2 - - + -
1026C VAL* 4.1 15.7 - - + +
1075C ALA* 4.5 3.3 - - - +
1078C LEU* 3.8 13.2 - - + +
1079C ALA* 3.8 31.2 - - + +
1083C LYS 2.9 20.1 + - - +
1084C VAL* 3.6 5.2 - - - +
1086C GLU* 1.3 74.8 - - - +
1088C GLN* 1.3 59.8 + - - +
1090C ALA* 3.3 2.8 + - - +
1091C ALA* 2.9 31.0 + - - +
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Residues in contact with GLN1088 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C ILE* 3.2 45.6 + - + +
1018C GLU* 5.1 3.1 + - - -
1020C ALA* 3.6 25.1 + - - +
1026C VAL* 4.3 10.8 - - + -
1084C VAL* 2.9 30.1 + - - +
1085C LYS* 3.3 21.5 + - - +
1087C ALA* 1.3 76.2 - - - +
1089C ALA* 1.3 56.7 + - - +
1091C ALA 3.4 0.5 + - - -
1092C GLU* 3.0 29.6 + - - +
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Residues in contact with ALA1089 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1085C LYS 3.0 13.3 + - - +
1086C GLU* 3.6 10.5 - - - +
1087C ALA 3.3 0.2 - - - -
1088C GLN* 1.3 76.1 - - - +
1090C ALA* 1.3 63.0 + - - +
1092C GLU* 3.4 8.1 + - - +
1093C GLN* 3.4 19.4 + - - +
51L SER* 4.0 28.5 - - - +
63L GLY 5.2 2.5 - - - +
64L SER* 4.8 10.3 - - - +
65L GLY 5.6 1.6 - - - +
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Residues in contact with ALA1090 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075C ALA* 4.3 13.8 - - + +
1078C LEU* 3.5 31.4 - - + -
1086C GLU 3.0 11.3 + - - +
1087C ALA* 3.7 4.7 - - - +
1088C GLN 3.3 0.2 - - - -
1089C ALA* 1.3 78.5 - - - +
1091C ALA* 1.3 59.7 + - - +
1093C GLN* 3.1 29.3 + - - +
64L SER* 5.1 6.2 + - - +
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Residues in contact with ALA1091 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014C LEU* 3.4 13.7 - - - +
1017C ILE* 3.5 29.2 - - + -
1030C LEU* 3.6 28.5 - - + -
1033C MET* 5.6 6.2 - - - +
1075C ALA* 4.5 5.8 - - + +
1087C ALA 2.9 17.2 + - - +
1090C ALA* 1.3 74.3 - - - +
1092C GLU* 1.3 64.6 + - - +
1093C GLN 3.4 4.0 + - - -
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Residues in contact with GLU1092 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A CYS 5.5 2.8 + - - -
1014C LEU* 3.7 23.0 - - - +
1017C ILE* 3.3 17.4 - - + +
1018C GLU* 3.1 26.5 - - - +
1088C GLN 3.0 17.0 + - - +
1089C ALA* 3.7 9.2 - - - +
1090C ALA 3.3 0.2 - - - -
1091C ALA* 1.3 77.4 - - - +
1093C GLN* 1.3 64.1 + - - +
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Residues in contact with GLN1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071C GLN* 5.4 16.5 - - - +
1089C ALA 3.4 8.0 + - - +
1090C ALA* 3.1 24.1 + - - +
1091C ALA 4.2 4.3 - - - -
1092C GLU* 1.3 82.9 - - - +
18L LYS* 6.2 2.0 - - - +
62L SER* 3.9 28.6 + - - -
64L SER* 6.0 1.7 - - - -
73L THR* 5.6 4.9 - - - +
75L SER* 6.0 4.2 - - - -
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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