Contacts of the helix formed by residues 95 - 105 (chain B) in PDB entry 1JT6
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 LEU 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LYS* 4.5 6.1 - - + +
15B PHE* 3.8 27.1 - - + -
16B ILE* 3.4 29.8 - - + +
50B PHE* 4.8 4.0 - - + -
53B ILE* 3.9 16.8 - - + -
54B LEU* 4.1 21.8 - - + -
57B GLU* 3.8 34.5 - - + +
92B TYR* 2.8 12.2 + - - +
94B PRO* 1.3 81.0 - - + +
96B GLN* 1.3 58.0 + - - +
97B ASN 3.3 2.9 - - - -
98B ALA* 3.0 14.3 + - + +
99B ILE* 2.8 30.6 + - + +
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Residues in contact with GLN 96 (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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162A PHE* 3.3 20.2 - - + -
92B TYR* 3.3 32.5 + - - +
93B TYR* 3.2 23.5 + - + +
94B PRO 3.4 0.4 - - - -
95B LEU* 1.3 77.0 - - - +
97B ASN* 1.3 63.7 + - - +
99B ILE* 3.1 30.0 + - - +
100B ILE* 3.0 28.2 + - - +
123B TYR* 5.1 1.0 - - - -
157B ASN* 2.7 41.0 + - - +
161B THR* 3.6 18.4 - - + +
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Residues in contact with ASN 97 (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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103A TYR* 4.4 1.1 - - - -
104A THR* 3.7 23.3 - - + +
107A TYR* 3.1 44.0 + - - +
201A DEQ 3.3 37.8 + - - -
94B PRO 4.9 4.0 + - - +
95B LEU 3.3 1.0 - - - -
96B GLN* 1.3 76.1 - - - +
98B ALA* 1.3 63.8 + - - +
100B ILE* 3.0 9.3 + - - +
101B GLU* 3.0 22.9 + - - +
161B THR* 3.8 10.6 + - - +
164B HIS* 5.9 3.8 - - - +
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Residues in contact with ALA 98 (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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15B PHE* 3.6 24.7 - - + +
19B GLY* 4.8 1.6 - - - -
20B TYR* 3.8 11.3 - - - +
50B PHE* 3.8 20.4 - - + -
94B PRO 5.4 1.0 + - - +
95B LEU* 3.0 18.4 + - + +
97B ASN* 1.3 79.3 - - - +
99B ILE* 1.3 57.1 - - - +
101B GLU* 3.6 12.4 - - - +
102B PHE* 2.9 28.2 + - - +
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Residues in contact with ILE 99 (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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162A PHE* 5.7 4.0 - - + -
50B PHE* 3.8 21.8 - - + -
54B LEU* 3.8 28.0 - - + -
92B TYR* 4.3 13.0 - - + +
95B LEU* 2.8 25.6 + - + +
96B GLN* 3.3 39.3 - - - +
97B ASN 3.0 0.2 - - - -
98B ALA* 1.3 77.1 - - - +
100B ILE* 1.3 60.0 + - - +
102B PHE* 3.5 2.3 - - + +
103B TYR* 3.0 27.8 + - + +
116B MET* 3.8 32.8 - - + -
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Residues in contact with ILE 100 (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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100A ILE* 3.4 35.9 - - + -
161A THR* 3.9 27.4 - - + +
162A PHE* 3.7 26.5 - - + -
201A DEQ 4.1 16.6 - - + -
96B GLN 3.0 21.0 + - - +
97B ASN* 3.5 23.8 - - - +
99B ILE* 1.3 73.6 - - - +
101B GLU* 1.3 68.4 + - - +
103B TYR* 3.2 6.8 + - - +
104B THR* 3.2 25.9 + - + +
161B THR* 4.6 2.7 - - + -
162B PHE* 4.7 1.3 - - + -
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Residues in contact with GLU 101 (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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100A ILE* 3.9 10.2 - - + +
101A GLU* 5.8 4.3 - - - -
104A THR* 3.8 27.5 + - - +
19B GLY* 3.4 11.4 - - - -
20B TYR* 2.8 24.1 + - + -
21B ASN* 2.6 44.8 + - - +
22B ALA* 4.3 2.3 + - - +
97B ASN 3.0 9.1 + - - +
98B ALA* 3.6 9.9 - - - +
100B ILE* 1.3 76.5 - - - +
102B PHE* 1.3 65.6 + - - +
104B THR* 2.7 26.9 + - - +
105B GLU* 3.4 12.4 + - - +
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Residues in contact with PHE 102 (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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20B TYR* 3.3 45.0 - + + +
47B GLU* 3.8 20.2 - - + -
50B PHE* 3.5 32.1 - + + -
51B LEU* 4.4 15.7 - - + -
54B LEU* 5.7 0.2 - - + -
98B ALA 2.9 20.0 + - - +
99B ILE* 3.5 7.0 - - + +
100B ILE 3.3 0.2 - - - -
101B GLU* 1.3 75.3 - - - +
103B TYR* 1.3 69.1 + - + +
105B GLU* 3.1 14.1 + - - -
106B TYR* 3.5 29.3 + + + +
112B ILE* 4.0 33.2 - - + -
116B MET* 4.9 14.8 - - + -
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Residues in contact with TYR 103 (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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164A HIS* 3.5 47.4 + + + -
165A GLU* 4.6 9.2 - - + -
99B ILE* 3.0 17.3 + - + +
100B ILE* 3.9 5.6 - - - +
102B PHE* 1.3 82.6 - - + +
104B THR* 1.3 65.9 + - + +
105B GLU 3.2 0.7 + - - -
106B TYR* 4.8 1.3 - - - +
107B TYR* 3.2 46.3 + + + +
112B ILE* 4.3 18.4 - - + -
113B ASN* 3.2 24.6 + - - -
116B MET* 4.1 31.4 - - + -
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Residues in contact with THR 104 (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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96A GLN* 6.4 0.2 - - + -
97A ASN* 4.0 21.4 + - - +
100A ILE* 3.9 30.6 - - + +
100B ILE* 3.2 16.1 + - + +
101B GLU* 2.7 23.4 + - - +
103B TYR* 1.3 80.6 - - + +
105B GLU* 1.3 67.9 + - - +
107B TYR* 2.9 29.3 - - + -
108B LYS* 5.6 1.0 - - - +
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Residues in contact with GLU 105 (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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101A GLU* 5.9 3.8 - - - +
20B TYR* 3.8 7.6 - - - -
21B ASN* 2.1 51.0 + - - +
101B GLU* 3.7 14.5 - - - +
102B PHE 3.1 6.8 + - - +
104B THR* 1.3 91.9 + - - +
106B TYR* 1.3 79.1 + - + +
108B LYS* 5.3 4.9 - - - -
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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