Contacts of the helix formed by residues 1058 - 1060 (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 GLN1058 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASN* 3.3 19.7 + - - +
182A HIS* 5.7 3.1 + - - -
186A VAL* 3.5 24.5 - - - +
205A PRO* 3.8 19.3 - - + +
207A ILE* 4.0 15.9 - - + -
208A SER* 4.2 7.9 + - - +
209A GLU 5.1 1.9 + - - -
213A TRP* 3.7 24.4 - - - -
1054B MET 3.1 19.8 + - - +
1055B ARG 3.4 15.7 - - - +
1056B ILE 3.1 0.8 - - - -
1057B GLN* 1.3 78.1 - - - +
1059B PHE* 1.3 59.9 + - + +
1060B ARG 3.3 3.5 + - - +
1070B LEU* 3.9 21.9 - - + +
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Residues in contact with PHE1059 (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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207A ILE* 4.0 20.0 - - + -
1009B GLY 4.2 12.1 - - - -
1010B CYS 4.4 0.4 - - - -
1011B GLY* 3.8 22.9 - - - -
1014B THR* 4.4 7.4 - - - -
1055B ARG* 3.6 22.7 - - + -
1056B ILE* 3.1 20.2 + - + +
1058B GLN* 1.3 76.7 - - - +
1060B ARG* 1.3 63.2 + - - +
1061B LYS* 3.4 3.8 + - - +
1066B TYR* 3.7 9.7 - - + -
1067B ALA* 3.4 45.3 + - - +
1068B ALA 3.4 18.2 - - - -
1069B TRP* 3.9 17.5 - + - -
1070B LEU* 3.6 28.9 - - + +
1078B LEU* 5.6 0.7 - - + -
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Residues in contact with ARG1060 (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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182A HIS* 5.2 7.4 + - - -
184A LEU* 3.6 25.8 - - + +
1057B GLN* 3.3 20.1 + - - +
1058B GLN 3.3 3.8 - - - +
1059B PHE* 1.3 77.7 - - - +
1061B LYS* 1.3 73.9 + - - +
1064B GLY* 3.6 10.0 - - - -
1065B SER 3.6 7.0 - - - +
1066B TYR* 3.1 40.6 + - + +
1099B LYS* 2.8 49.1 + - - +
1100B LEU* 5.2 2.4 - - - +
1102B GLU* 2.9 28.3 + - - +
1103B THR* 2.8 23.5 + - - -
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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