Contacts of the helix formed by residues 64 - 68 (chain A) in PDB entry 1JS6
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 ILE 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.6 3.1 + - - -
38A LEU* 4.5 14.1 - - + -
59A ASP 4.1 0.2 - - - +
60A VAL* 3.2 22.2 + - + +
63A ILE* 1.3 82.8 - - + +
65A MET* 1.3 57.8 + - + +
67A GLY* 2.7 31.5 + - - -
68A VAL* 3.5 11.6 - - + +
98B ILE* 4.7 8.7 - - + -
110B ALA* 3.7 3.4 - - + +
114B LEU* 4.3 19.7 - - + -
357B PHE* 3.7 31.9 - - + -
360B LEU* 4.8 3.4 - - + -
363B TRP* 3.6 38.8 - - + -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.7 22.2 - - + +
20A TYR* 3.4 42.6 - - + -
27A ARG* 3.9 23.3 - - - +
60A VAL* 3.0 22.2 + - + +
61A GLU* 3.4 23.8 - - - +
64A ILE* 1.3 77.9 - - - +
66A PRO* 1.3 63.3 - - + +
67A GLY 3.0 1.0 + - - -
68A VAL* 3.0 30.3 + - - +
70A HIS* 4.0 18.2 + - + -
98B ILE* 4.3 19.3 - - + -
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Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 3.3 21.0 - - - +
32A ASP 4.7 0.3 + - - -
33A VAL* 3.6 22.8 + - + +
37A TYR* 4.9 2.2 - - + -
61A GLU 3.5 9.4 - - - +
62A LYS* 3.4 17.9 - - - +
63A ILE* 3.5 15.5 - - - +
64A ILE 3.4 4.5 - - - -
65A MET* 1.3 93.7 - - + +
67A GLY* 1.3 55.6 + - - +
68A VAL 3.4 0.2 - - - -
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.4 1.6 - - - -
33A VAL* 4.2 6.7 - - - -
37A TYR* 3.4 27.1 + - - -
64A ILE 2.7 13.1 + - - -
66A PRO* 1.3 80.6 - - - +
68A VAL* 1.3 56.0 + - - -
108B SER 3.5 1.2 - - - -
109B PRO* 3.1 16.3 - - - +
110B ALA* 2.9 25.6 + - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 4.5 1.1 - - - +
28A GLN 4.9 0.7 - - - +
29A VAL 3.9 0.7 - - - +
31A PRO* 3.8 14.2 - - - +
64A ILE* 3.5 29.2 - - + +
65A MET* 3.0 24.7 + - - +
66A PRO 3.4 0.4 - - - -
67A GLY* 1.3 80.3 - - - +
69A THR* 1.3 71.9 + - - +
70A HIS* 3.7 36.6 + - + +
98B ILE* 3.8 31.0 - - + +
108B SER* 3.7 7.4 - - - +
110B ALA* 4.7 3.4 - - + -
357B PHE* 4.8 3.4 - - + -
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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