Contacts of the helix formed by residues 95 - 106 (chain A) in PDB entry 1JT0
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.7 24.2 - - + +
15A PHE* 4.8 5.4 - - + -
16A ILE* 3.5 34.5 - - + +
50A PHE* 4.0 14.4 - - + -
53A ILE* 4.3 12.3 - - + -
54A LEU* 3.1 35.0 - - + -
57A GLU* 4.3 10.5 - - + +
92A TYR* 3.4 13.2 + - - +
93A TYR 3.2 0.8 - - - -
94A PRO* 1.3 76.8 - - + +
96A GLN* 1.3 58.4 + - - +
97A ASN* 3.5 7.2 - - - -
98A ALA* 3.8 8.1 - - + +
99A ILE* 2.8 31.4 + - + +
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Residues in contact with GLN 96 (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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92A TYR* 3.3 39.3 + - - -
93A TYR* 3.0 28.7 + - - +
94A PRO 3.1 2.6 + - - +
95A LEU* 1.3 74.4 - - - +
97A ASN* 1.3 66.8 + - - +
99A ILE* 2.9 22.6 + - - +
100A ILE* 3.0 22.0 + - + +
120A GLU* 4.4 5.9 - - - +
157A ASN* 3.5 18.1 + - - +
161A THR* 3.3 33.2 - - + -
164A HIS* 6.4 1.6 - - + -
162C PHE* 3.7 19.1 - - + -
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Residues in contact with ASN 97 (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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15A PHE 3.7 14.3 + - - -
16A ILE 4.0 10.9 + - - +
19A GLY* 4.0 8.5 - - - +
94A PRO 3.2 21.3 - - - +
95A LEU* 4.0 1.1 - - - +
96A GLN* 1.3 74.4 - - - +
98A ALA* 1.3 78.6 + - - +
100A ILE* 2.7 31.3 + - - +
101A GLU* 2.9 15.6 + - - +
161A THR* 5.2 5.6 - - - +
164A HIS* 4.8 11.9 - - + -
100C ILE* 4.5 9.1 - - + +
101C GLU* 6.1 1.0 - - - -
104C THR* 3.6 33.0 + - + +
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Residues in contact with ALA 98 (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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15A PHE* 4.1 10.3 - - + +
19A GLY 4.5 0.4 - - - -
20A TYR* 4.1 21.6 - - + +
50A PHE* 3.9 22.2 - - + -
95A LEU* 3.8 13.5 - - + +
96A GLN 3.3 0.2 - - - -
97A ASN* 1.3 92.1 - - - +
99A ILE* 1.3 52.6 + - - +
101A GLU* 3.5 9.4 - - - +
102A PHE* 2.7 37.1 + - - +
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Residues in contact with ILE 99 (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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50A PHE* 4.2 8.1 - - + -
54A LEU* 4.2 6.1 - - + -
92A TYR* 3.6 50.7 - - + +
95A LEU* 2.8 37.5 - - + +
96A GLN* 2.9 26.2 + - - +
98A ALA* 1.3 74.7 - - - +
100A ILE* 1.3 60.4 + - + +
102A PHE* 3.6 5.8 - - - +
103A TYR* 2.9 30.7 + - + +
116A MET* 3.4 21.2 - - + +
120A GLU* 4.8 10.5 - - - +
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Residues in contact with ILE 100 (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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96A GLN* 3.0 26.9 + - + +
97A ASN* 2.7 20.8 + - - +
99A ILE* 1.3 70.6 - - + +
101A GLU* 1.3 58.0 + - - +
102A PHE 2.9 0.7 + - - -
103A TYR* 3.0 4.9 + - - +
104A THR* 2.6 41.1 + - + +
161A THR* 6.1 1.1 - - + +
162A PHE* 6.1 1.6 - - + -
97C ASN* 3.5 32.8 - - - +
100C ILE* 4.9 18.4 - - + -
161C THR* 5.8 4.3 - - - +
162C PHE* 4.1 32.5 - - + -
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Residues in contact with GLU 101 (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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18A ASN 4.8 0.9 - - - +
19A GLY* 3.7 9.5 - - - -
20A TYR* 3.3 19.0 + - + -
21A ASN* 2.6 52.3 + - - +
22A ALA* 3.9 3.3 + - - +
97A ASN* 2.9 11.1 + - - +
98A ALA* 3.5 9.1 + - - +
100A ILE* 1.3 77.2 - - - +
102A PHE* 1.3 59.0 + - - +
104A THR* 2.3 24.7 + - - -
105A GLU* 3.8 11.8 - - - +
21C ASN* 5.0 1.5 + - - -
101C GLU* 4.0 40.5 - - + +
104C THR* 4.3 6.9 + - - -
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Residues in contact with PHE 102 (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* 3.7 32.1 - + + -
47A GLU* 4.3 8.1 - - + -
50A PHE* 3.5 35.0 - + + -
51A LEU* 3.7 26.9 - - + -
98A ALA 2.7 21.8 + - - +
99A ILE* 3.6 4.5 - - - +
100A ILE 2.9 0.6 + - - -
101A GLU* 1.3 71.9 - - - +
103A TYR* 1.3 65.5 + - - +
104A THR 3.1 1.9 + - - -
105A GLU* 3.4 2.7 + - - -
106A TYR* 3.1 60.6 + + - +
112A ILE* 3.3 32.8 - - + -
116A MET* 3.6 19.1 - - - -
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Residues in contact with TYR 103 (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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99A ILE* 2.9 21.5 + - + +
100A ILE* 3.8 3.8 - - - +
102A PHE* 1.3 74.0 - - - +
104A THR* 1.3 68.5 + - + +
106A TYR* 4.8 3.1 - - - +
107A TYR* 2.8 66.7 + + - +
113A ASN* 2.7 32.3 + - - -
116A MET* 3.7 38.1 - - + -
117A ASN* 2.8 30.5 + - - -
120A GLU* 4.8 11.9 - - - -
164C HIS* 6.0 4.7 - - + -
165C GLU* 3.3 14.2 + - - -
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Residues in contact with THR 104 (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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100A ILE* 2.6 34.8 + - + +
101A GLU* 2.3 36.0 + - - +
103A TYR* 1.3 76.2 - - - +
105A GLU* 1.3 61.6 + - - +
107A TYR* 3.8 9.6 - - - +
17C LYS 4.6 10.3 - - - +
18C ASN 4.8 10.8 + - - -
19C GLY* 5.5 1.1 - - - -
97C ASN* 3.7 42.2 - - + +
101C GLU* 4.5 10.1 + - + +
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Residues in contact with GLU 105 (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* 4.8 0.2 - - - -
21A ASN* 2.5 39.7 + - - +
101A GLU 3.8 7.0 - - - +
102A PHE 3.8 3.1 - - - +
104A THR* 1.3 79.2 + - - +
106A TYR* 1.3 103.2 + - + +
107A TYR* 2.8 12.7 + - - +
108A LYS* 3.9 8.7 + - - +
18C ASN* 4.2 19.3 - - + +
22C ALA* 4.3 18.1 + - + +
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Residues in contact with TYR 106 (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* 3.7 18.7 + + - -
21A ASN* 5.1 2.6 + - - -
47A GLU* 3.3 33.9 + - - -
102A PHE* 3.1 46.7 + + - +
103A TYR* 3.8 4.2 - - - -
105A GLU* 1.3 103.2 + - + +
107A TYR* 1.3 58.4 + - - +
108A LYS 3.2 2.2 - - - +
109A THR* 3.0 41.0 + - + +
112A ILE* 3.8 22.3 - - + +
113A ASN* 4.3 2.4 + - - -
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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