Contacts of the helix formed by residues 1011 - 1017 (chain B) in PDB entry 5JPM
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 GLY1011 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010B CYS* 1.3 73.1 - - - +
1012B GLU* 1.3 66.5 + - - +
1014B THR* 3.0 23.5 + - - -
1015B MET* 3.9 0.3 - - - +
1056B ILE* 3.4 13.6 - - - +
1059B PHE* 3.8 24.1 - - - -
1068B ALA* 3.2 22.8 + - - +
1078B LEU* 4.6 6.1 - - - -
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Residues in contact with GLU1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B CYS* 4.4 0.2 - - - +
1011B GLY* 1.3 75.1 - - - +
1013B GLN* 1.3 75.7 + - - +
1014B THR 3.1 2.0 + - - -
1015B MET* 3.2 19.7 + - - +
1016B ILE 4.6 0.3 + - - -
1068B ALA* 5.6 0.4 - - - +
1077B TRP* 3.6 29.8 - - + -
1078B LEU* 3.8 23.1 - - + +
1081B PHE* 3.6 10.9 - - + -
1123B VAL* 4.7 12.9 - - + +
1124B LEU* 5.1 3.5 - - + +
1302B THR* 2.9 32.1 + - - -
1303B GLN* 3.1 28.7 + - - +
1306B VAL* 5.1 1.6 - - - +
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Residues in contact with GLN1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B PRO 4.4 3.4 - - - +
1008B ARG* 3.8 31.9 - - + +
1010B CYS* 1.8 64.1 - - - +
1011B GLY 3.2 0.6 - - - -
1012B GLU* 1.3 91.4 + - - +
1014B THR* 1.3 63.2 + - - +
1015B MET 3.2 0.2 - - - -
1016B ILE* 3.1 26.7 + - - +
1017B TYR* 4.5 0.7 - - - -
1302B THR* 4.0 21.1 - - + +
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Residues in contact with THR1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B CYS 3.8 3.9 + - - -
1011B GLY* 3.0 18.0 + - - -
1012B GLU 3.1 0.6 - - - -
1013B GLN* 1.3 78.7 - - - +
1015B MET* 1.3 57.0 + - - +
1016B ILE 3.1 0.2 - - - -
1017B TYR* 3.0 32.7 + - + +
1018B LEU* 4.0 3.9 + - + +
1052B GLY* 3.3 29.8 - - - +
1055B ARG* 3.0 36.1 + - + +
1056B ILE* 3.6 25.6 - - + +
1059B PHE* 4.4 1.7 - - - -
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Residues in contact with MET1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B GLY 3.9 12.1 - - - +
1012B GLU* 3.2 23.7 + - - +
1013B GLN 3.2 1.0 - - - -
1014B THR* 1.3 74.7 - - - +
1016B ILE* 1.3 58.3 + - - +
1017B TYR 3.1 0.7 - - - -
1018B LEU* 2.9 21.8 + - + -
1019B ALA* 2.8 31.2 + - + +
1020B PRO* 3.2 2.9 - - - +
1056B ILE* 4.0 17.0 - - + -
1078B LEU* 4.1 2.5 - - + -
1081B PHE* 3.5 43.5 - - + -
1082B VAL* 4.0 28.3 - - + -
1085B VAL* 3.7 29.8 - - + -
1086B LEU* 5.8 0.7 - - - -
1306B VAL* 4.4 3.1 - - + -
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Residues in contact with ILE1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000B VAL* 3.3 24.6 + - + +
1001B ALA* 3.8 27.2 + - + -
1004B LEU* 3.8 29.8 - - + -
1008B ARG* 3.9 14.1 - - + -
1012B GLU 4.6 0.2 + - - -
1013B GLN* 3.1 22.1 + - - +
1014B THR 3.1 1.6 - - - -
1015B MET* 1.3 77.5 - - - +
1017B TYR* 1.3 64.7 + - + +
1018B LEU 3.3 0.2 - - - -
1020B PRO* 3.3 23.2 - - + +
1021B THR* 4.6 1.7 + - - -
1302B THR* 4.1 14.1 - - + +
1305B THR* 3.9 11.0 - - + -
1306B VAL* 3.6 22.8 - - + +
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Residues in contact with TYR1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B GLY 5.0 3.8 - - - -
1001B ALA* 3.6 21.3 - - + -
1008B ARG* 2.8 33.9 + - + +
1013B GLN 4.7 0.9 - - - -
1014B THR* 3.0 33.1 + - + +
1016B ILE* 1.3 86.0 - - + +
1018B LEU* 1.3 55.6 + - - +
1021B THR* 2.9 23.6 + - - -
1048B LEU* 3.6 42.7 - - + +
1049B ILE 4.1 0.5 + - - -
1051B LYS* 4.0 39.8 + - + -
1052B GLY* 3.9 12.3 - - - -
1055B ARG* 4.4 19.2 - - - -
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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