Contacts of the helix formed by residues 95 - 107 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LYS* 4.1 9.6 - - + +
15C PHE* 3.7 29.2 - - + +
16C ILE* 3.5 31.9 - - + +
50C PHE* 4.7 6.1 - - + -
53C ILE* 4.1 23.8 - - + -
54C LEU* 4.2 17.5 - - + -
57C GLU* 4.2 19.7 - - + -
92C TYR* 3.1 12.9 + - + +
93C TYR 2.6 4.0 + - - -
94C PRO* 1.3 73.8 - - + +
96C GLN* 1.3 66.0 + - - +
97C ASN* 3.0 4.8 + - - +
98C ALA* 3.2 6.7 + - + +
99C ILE* 2.9 31.7 + - + +
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Residues in contact with GLN 96 (chain C).
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* 5.2 0.2 - - - -
92C TYR* 3.5 33.5 + - - -
93C TYR* 2.8 25.5 + - + +
94C PRO 3.5 0.8 - - - -
95C LEU* 1.3 77.9 - - - +
97C ASN* 1.3 55.6 + - - +
99C ILE* 3.5 11.3 + - - +
100C ILE* 2.7 61.1 + - - +
157C ASN* 2.9 33.4 + - - +
160C VAL* 5.8 0.4 - - + -
161C THR* 3.4 31.0 - - + +
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Residues in contact with ASN 97 (chain C).
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* 3.5 25.7 - - - +
104A THR* 3.7 25.7 - - + +
15C PHE 5.6 0.7 - - - +
16C ILE 4.9 10.9 - - - +
19C GLY* 5.5 4.9 - - - -
94C PRO 5.4 3.2 - - - +
95C LEU* 4.2 1.8 - - - +
96C GLN* 1.3 75.3 - - - +
98C ALA* 1.3 68.9 + - - +
100C ILE* 2.8 18.8 + - - +
101C GLU* 3.1 13.3 + - - +
161C THR* 4.9 17.2 + - - +
164C HIS* 3.5 27.8 + - - -
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 3.9 17.4 + - + +
19C GLY* 4.1 2.3 - - - -
20C TYR* 3.7 21.7 - - + +
50C PHE* 3.6 26.2 - - + -
95C LEU* 3.2 7.8 + - + +
97C ASN* 1.3 78.2 - - - +
99C ILE* 1.3 58.3 + - - +
100C ILE 3.1 0.2 + - - -
101C GLU* 3.2 12.2 + - - +
102C PHE* 2.8 33.8 + - - +
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C PHE* 4.3 8.3 - - + -
54C LEU* 4.3 17.3 - - + -
92C TYR* 3.7 46.0 - - + +
95C LEU* 2.9 32.4 + - + +
96C GLN* 3.6 20.6 - - - +
97C ASN 3.1 0.2 + - - -
98C ALA* 1.3 77.3 - - - +
100C ILE* 1.3 64.7 + - + +
102C PHE* 4.4 1.8 - - - -
103C TYR* 2.9 29.7 + - + +
116C MET* 3.5 19.0 - - + +
120C GLU* 5.9 2.9 - - - +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASN* 4.5 16.2 - - + +
100A ILE* 4.9 17.3 - - + -
161A THR* 5.5 4.3 - - - +
162A PHE* 3.4 39.7 - - + -
96C GLN* 2.7 41.3 - - - +
97C ASN* 2.8 16.1 + - - +
99C ILE* 1.3 77.2 - - + +
101C GLU* 1.3 65.2 + - - +
103C TYR* 3.3 4.2 + - + +
104C THR* 2.9 42.4 + - + +
161C THR* 6.2 0.7 - - - -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN* 4.8 0.4 + - - -
97A ASN* 6.1 0.4 - - - -
101A GLU* 4.0 38.6 - - + +
104A THR* 4.5 11.0 + - + +
18C ASN 4.4 2.4 - - - +
19C GLY* 3.5 10.4 - - - -
20C TYR* 3.0 26.6 + - + -
21C ASN* 2.3 42.1 + - - +
22C ALA* 5.1 0.9 + - - +
97C ASN 3.1 4.4 + - - +
98C ALA* 3.4 17.7 + - - +
100C ILE* 1.3 79.5 - - - +
102C PHE* 1.3 63.5 + - - +
104C THR* 2.8 21.6 + - - -
105C GLU* 3.3 15.2 + - - +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.4 48.5 - + + -
47C GLU* 3.5 25.6 - - + -
50C PHE* 3.5 30.7 - + + -
51C LEU* 4.8 5.2 - - + -
98C ALA 2.8 18.5 + - - +
99C ILE 3.8 3.4 - - - +
101C GLU* 1.3 77.6 - - - +
103C TYR* 1.3 63.6 + - - +
105C GLU* 3.3 2.8 + - - +
106C TYR* 3.0 46.9 + + - +
112C ILE* 3.2 28.5 - - + -
116C MET* 3.3 18.6 - - + -
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Residues in contact with TYR 103 (chain C).
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* 5.8 8.5 - - + -
165A GLU* 4.6 13.0 - - - +
99C ILE* 2.9 22.1 + - + +
100C ILE* 3.7 5.6 - - + +
102C PHE* 1.3 77.2 - - - +
104C THR* 1.3 63.5 + - + +
105C GLU 3.0 0.3 + - - -
106C TYR 5.3 0.4 - - - -
107C TYR* 2.8 52.9 + + + +
112C ILE* 5.1 1.6 - - - -
113C ASN* 2.8 34.2 + - - -
116C MET* 3.5 44.5 - - + +
117C ASN* 3.5 14.0 + - - -
120C GLU* 4.6 9.4 + - - -
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Residues in contact with THR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS 4.1 7.8 - - - +
18A ASN* 4.1 11.3 + - - +
19A GLY* 5.1 0.2 - - - -
97A ASN* 3.6 37.9 + - + +
101A GLU* 4.3 8.1 + - - -
100C ILE* 2.9 29.9 + - + +
101C GLU* 2.8 25.7 + - - -
103C TYR* 1.3 81.8 - - + +
105C GLU* 1.3 56.4 + - - +
107C TYR* 3.0 26.7 - - - -
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Residues in contact with GLU 105 (chain C).
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* 4.3 7.0 - - - +
22A ALA* 3.2 35.9 - - + +
20C TYR* 4.6 1.6 - - - -
21C ASN* 3.3 31.3 + - - +
101C GLU 3.3 13.0 + - - +
102C PHE* 3.9 2.4 - - - +
103C TYR 3.1 0.8 - - - -
104C THR* 1.3 81.0 + - - +
106C TYR* 1.3 95.9 + - + +
107C TYR* 3.2 6.5 + - - -
108C LYS* 3.2 20.3 + - - +
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.6 24.3 + + - -
21C ASN* 5.3 0.7 + - - -
47C GLU* 4.4 15.0 - - + -
102C PHE* 3.0 54.7 + + + +
103C TYR* 3.6 1.8 - - - -
105C GLU* 1.3 106.3 + - + +
107C TYR* 1.3 61.9 + - - +
108C LYS* 3.1 21.5 + - + +
109C THR 3.6 2.4 - - - +
112C ILE* 3.1 44.5 - - + +
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.7 31.3 + - - +
18A ASN* 5.1 2.5 - - - -
103C TYR* 2.8 41.4 + + + +
104C THR* 3.0 28.5 - - - -
105C GLU 3.2 5.1 - - - -
106C TYR* 1.3 77.2 - - - +
108C LYS* 1.3 83.9 + - + +
109C THR 3.6 5.7 - - - +
112C ILE* 5.6 0.4 - - - -
113C ASN* 4.1 21.9 - - + +
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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