Contacts of the helix formed by residues 96 - 106 (chain J) in PDB entry 6GYS
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 THR 96 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93I ASP* 5.4 7.4 - - + -
95J ASP* 1.3 84.4 - - + +
97J GLU* 1.3 68.6 + - - +
98J GLU 3.4 2.7 - - - -
99J CYS* 2.9 5.5 + - - +
100J MET* 2.4 55.4 + - + +
218J PHE* 3.6 28.9 - - + -
222J GLN* 5.0 2.2 - - - +
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Residues in contact with GLU 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J THR* 3.4 11.4 - - + -
95J ASP* 3.2 23.4 + - - +
96J THR* 1.3 86.0 + - - +
98J GLU* 1.3 64.1 + - - +
100J MET* 4.2 6.3 - - + +
101J PHE* 3.2 28.4 + - + +
191J TYR* 3.1 21.9 + - + +
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Residues in contact with GLU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J THR* 4.3 19.5 + - - +
95J ASP 5.8 0.4 - - - +
96J THR 3.4 0.4 - - - -
97J GLU* 1.3 75.7 - - - +
99J CYS* 1.3 60.6 + - - +
102J TRP* 3.1 30.0 + - - -
191J TYR* 3.0 32.6 + - - +
192J LEU* 4.9 2.4 - - - +
211J ASN* 2.7 47.9 - - - +
214J ARG* 3.7 37.5 - - + -
215J CYS* 3.3 7.6 - - - -
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Residues in contact with CYS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ASP 5.3 0.4 + - - -
96J THR* 2.9 8.9 + - - +
98J GLU* 1.3 80.4 - - - +
100J MET* 1.3 60.6 + - + +
102J TRP 3.5 1.0 + - - -
103J MET* 2.9 55.3 + - - +
214J ARG 5.1 0.4 - - - +
215J CYS* 3.3 38.4 - - - +
218J PHE* 3.6 34.5 - - + -
219J GLN* 4.1 3.6 - - - -
222J GLN* 4.0 8.5 - - - -
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Residues in contact with MET 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I LEU* 5.1 6.7 - - + -
96J THR* 2.4 49.1 + - + +
97J GLU* 4.5 4.3 - - + -
99J CYS* 1.3 69.1 - - + +
101J PHE* 1.3 59.5 + - - +
103J MET* 3.3 33.7 + - + +
104J ASN* 2.8 42.3 + - - +
147J ARG* 4.3 16.4 - - - +
222J GLN* 3.4 28.9 - - - +
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Residues in contact with PHE 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J GLU* 3.2 18.1 + - + +
100J MET* 1.3 77.8 - - - +
102J TRP* 1.3 78.0 + + + +
104J ASN* 3.3 8.4 + - + +
105J TYR* 2.9 33.1 + + + +
187J PRO* 3.8 19.3 - - + -
188J LEU* 4.0 24.0 - - + -
190J GLU* 5.8 1.6 - - + -
191J TYR* 3.6 38.4 - + + -
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Residues in contact with TRP 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J GLU* 3.1 35.8 + - - -
99J CYS 3.5 1.2 + - - -
100J MET 3.3 0.4 - - - -
101J PHE* 1.3 88.1 - + + +
103J MET* 1.3 63.1 + - - +
105J TYR* 4.0 4.9 - + - +
106J LEU* 3.5 16.6 + - - +
164J TRP* 3.7 2.5 - - - -
188J LEU* 3.6 53.2 - - + -
191J TYR* 3.5 21.4 - + - -
192J LEU* 3.6 23.8 - - + -
204J MET* 5.1 5.6 - - + -
208J MET* 3.5 24.9 - - + -
211J ASN* 3.9 18.6 - - + -
212J PHE* 3.5 42.8 - + + -
215J CYS* 3.6 16.2 - - - -
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Residues in contact with MET 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J CYS* 2.9 39.4 + - - +
100J MET* 3.6 18.6 - - + +
102J TRP* 1.3 79.0 - - - +
104J ASN* 1.3 60.0 + - - +
106J LEU 3.6 15.0 - - - +
143J TYR* 3.3 22.2 - - - +
144J TRP* 5.3 1.7 - - - -
147J ARG* 3.4 47.3 + - - +
157J LYS* 5.1 7.4 - - - +
160J ASP* 6.4 0.2 - - - -
164J TRP* 3.6 29.0 - - + -
215J CYS* 4.9 2.2 - - + -
219J GLN* 3.4 21.5 - - + +
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Residues in contact with ASN 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J MET* 2.8 33.6 + - - +
101J PHE* 3.3 8.9 + - + +
103J MET* 1.3 75.5 - - - +
105J TYR* 1.3 63.4 + - - +
106J LEU 4.5 1.8 - - - +
107J GLN* 4.5 10.7 + - - +
147J ARG* 2.5 25.6 + - - +
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Residues in contact with TYR 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J PHE* 2.9 23.4 + + + +
102J TRP* 4.5 10.8 - + - +
104J ASN* 1.3 76.3 - - - +
106J LEU* 1.3 63.8 + - + +
107J GLN* 3.1 13.3 + - - +
110J GLN* 2.9 48.8 + - - +
183J PHE* 3.5 19.3 - + - -
184J SER* 2.8 39.7 + - - -
187J PRO* 4.2 22.0 - - + -
188J LEU* 3.5 39.7 - - + -
212J PHE* 5.4 0.4 - + - -
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J TRP 3.5 16.2 + - - +
103J MET 3.6 10.4 + - - +
104J ASN 3.5 1.2 - - - +
105J TYR* 1.3 77.2 - - - +
107J GLN* 1.3 59.9 + - - +
110J GLN* 3.3 36.1 - - + +
111J SER* 3.7 22.7 - - - -
114J LEU* 4.5 1.6 - - + -
143J TYR* 6.1 0.2 - - + -
144J TRP* 3.2 20.6 - - + -
164J TRP* 3.7 27.3 - - + -
167J PHE* 4.3 19.1 - - + -
183J PHE* 4.1 2.2 - - + -
212J PHE* 3.6 34.8 - - + -
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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