Contacts of the helix formed by residues 132 - 144 (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 ASP 132 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126J TYR* 3.7 6.6 - - - -
130J ILE* 3.4 22.6 + - - +
131J GLY* 1.3 75.6 - - - +
133J ILE* 1.3 80.5 + - - +
134J SER* 2.9 30.0 + - - -
135J GLU* 3.5 26.9 + - + +
136J LEU 3.5 7.8 + - - -
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Residues in contact with ILE 133 (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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115J MET* 3.4 42.0 - - + +
118J ALA* 3.8 13.7 - - + -
119J MET* 3.5 33.7 - - + +
126J TYR* 3.3 39.4 - - + +
130J ILE* 4.8 0.9 - - - -
132J ASP* 1.3 80.9 + - - +
134J SER* 1.3 63.3 + - - +
135J GLU 3.3 0.4 - - - -
136J LEU* 3.1 8.6 + - + +
137J TYR* 2.8 42.8 + - + +
166J VAL* 5.4 1.6 - - + -
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Residues in contact with SER 134 (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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119J MET* 5.4 1.9 - - - +
132J ASP* 2.9 17.9 + - - -
133J ILE* 1.3 79.0 - - - +
135J GLU* 1.3 64.6 + - - +
137J TYR* 3.1 32.0 + - - +
138J LEU* 3.3 10.0 + - - +
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Residues in contact with GLU 135 (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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562I LEU 3.7 20.4 - - - +
563I GLY* 4.6 6.7 - - - -
565I LEU* 5.7 2.8 - - - +
130J ILE 4.0 16.1 - - - +
131J GLY* 5.2 0.3 - - - -
132J ASP* 3.5 28.3 + - + +
134J SER* 1.3 79.4 - - - +
136J LEU* 1.3 60.1 + - - +
138J LEU* 3.3 24.8 - - + +
139J ARG* 4.0 5.0 + - - +
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Residues in contact with LEU 136 (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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115J MET* 3.7 25.1 - - + -
130J ILE* 3.7 32.5 - - + +
132J ASP 3.5 2.8 + - - +
133J ILE* 3.1 14.4 + - + +
135J GLU* 1.3 74.8 - - - +
137J TYR* 1.3 59.7 + - - +
138J LEU 3.1 0.7 - - - -
139J ARG* 3.0 11.9 + - + +
140J VAL* 2.9 30.5 + - + +
159J TRP* 5.0 4.9 - - + -
162J LEU* 4.1 20.6 - - + -
163J ILE* 3.7 29.4 - - + -
166J VAL* 3.8 23.3 - - + -
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Residues in contact with TYR 137 (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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112J PHE* 4.2 24.0 - + + -
115J MET* 3.0 60.6 + - + -
116J ASN* 3.2 22.2 + - - -
119J MET* 3.3 19.9 - - + +
133J ILE* 2.8 26.8 + - + +
134J SER* 3.1 25.9 + - - +
136J LEU* 1.3 74.4 - - - +
138J LEU* 1.3 59.1 - - - +
140J VAL* 3.8 5.8 - - + +
141J GLU* 2.9 36.5 + - + +
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564I SER* 5.4 4.7 - - - +
134J SER 3.3 7.7 + - - +
135J GLU* 3.3 19.3 - - + +
136J LEU 3.1 0.4 - - - -
137J TYR* 1.3 77.2 - - - +
139J ARG* 1.3 84.5 + - - +
141J GLU* 4.0 3.2 - - + +
142J GLN* 3.0 57.6 + - + +
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Residues in contact with ARG 139 (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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563I GLY* 3.8 1.7 - - - -
564I SER* 2.4 43.6 + - - +
135J GLU 4.8 5.8 - - - +
136J LEU* 3.0 11.3 + - + +
138J LEU* 1.3 108.4 - - - +
140J VAL* 1.3 52.3 + - - +
142J GLN* 3.2 17.1 + - - +
143J TYR 2.6 30.5 + - - -
146J ARG* 2.7 34.1 + - - +
159J TRP* 3.3 62.2 - - + +
163J ILE* 4.2 13.0 - - + -
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Residues in contact with VAL 140 (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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111J SER* 4.5 4.7 - - - -
112J PHE* 3.6 30.1 - - + -
115J MET* 4.7 9.4 - - + -
136J LEU* 2.9 27.3 + - + +
137J TYR* 4.2 3.4 - - + -
139J ARG* 1.3 72.4 - - - +
141J GLU* 1.3 63.8 + - - +
143J TYR* 3.3 18.8 + - + +
144J TRP* 3.5 13.4 - - - +
163J ILE* 3.8 28.5 - - + -
167J PHE* 3.7 30.5 - - + -
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Residues in contact with GLU 141 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108J LYS* 3.7 22.1 + - - -
112J PHE* 3.0 33.6 - - + -
137J TYR* 2.9 24.3 + - + +
138J LEU* 4.0 3.8 - - + +
140J VAL* 1.3 77.0 - - - +
142J GLN* 1.3 60.3 + - + +
143J TYR 3.3 0.7 + - - -
144J TRP* 3.4 17.4 + - - +
145J ASP* 4.2 5.2 + - - +
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Residues in contact with GLN 142 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J LEU* 3.0 43.9 + - + +
139J ARG* 3.2 27.2 + - - +
141J GLU* 1.3 74.9 - - + +
143J TYR* 1.3 59.8 + - - +
144J TRP 3.2 0.4 - - - -
145J ASP* 3.0 30.2 + - + +
146J ARG* 3.1 25.7 + - - +
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Residues in contact with TYR 143 (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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103J MET* 3.3 13.7 - - - +
139J ARG 2.6 18.9 + - - +
140J VAL* 3.3 10.8 - - - +
141J GLU 3.1 0.8 - - - -
142J GLN* 1.3 76.0 - - - +
144J TRP* 1.3 73.5 + + - +
145J ASP 3.1 0.4 - - - -
146J ARG* 3.4 15.5 - - - +
147J ARG* 2.4 82.9 + - + +
160J ASP* 3.2 31.9 - - - -
163J ILE* 3.6 17.0 - - + -
164J TRP* 2.8 38.7 + + - -
167J PHE* 4.8 6.7 - + - -
219J GLN* 3.8 0.9 + - - -
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Residues in contact with TRP 144 (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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103J MET 5.3 2.2 - - - -
106J LEU* 3.2 27.8 - - + -
107J GLN* 3.4 33.0 - - + -
108J LYS* 3.9 21.2 - - + +
111J SER* 3.6 22.4 + - - -
112J PHE* 3.8 14.4 - + - -
140J VAL* 3.5 16.9 + - - +
141J GLU* 3.4 9.1 + - - +
142J GLN 3.2 0.6 - - - -
143J TYR* 1.3 90.5 - + - +
145J ASP* 1.3 63.8 + - - +
146J ARG 3.3 1.3 - - - -
147J ARG* 4.2 25.5 - - + +
148J ALA* 4.6 11.0 + - - +
164J TRP* 6.3 0.7 - + - -
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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