Contacts of the helix formed by residues 131 - 140 (chain J) in PDB entry 6PST
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 PRO 131 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129J ASP 4.8 0.9 - - - +
130J MET* 1.3 97.5 - - + +
132J LEU* 1.3 66.4 + - - +
133J ARG* 4.5 3.6 - - + +
134J ASP* 3.2 35.4 + - + +
135J ILE* 3.2 13.7 + - - +
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Residues in contact with LEU 132 (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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117J LEU* 3.4 35.2 - - + +
118J LYS* 4.8 12.3 - - + -
119J SER 4.9 5.2 - - - +
120J LEU* 5.1 6.3 - - + +
122J SER* 3.7 19.7 - - - +
125J GLY* 5.6 0.4 - - - -
130J MET 3.8 1.6 + - - -
131J PRO* 1.3 74.1 - - - +
133J ARG* 1.3 71.0 + - + +
134J ASP 3.2 0.2 + - - -
135J ILE* 3.3 8.7 + - + +
136J GLU* 2.9 48.1 + - + +
47L MET* 5.5 3.8 - - + -
83L VAL* 4.7 22.7 - - + -
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Residues in contact with ARG 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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118J LYS* 5.0 10.7 - - - +
131J PRO* 3.3 4.3 - - + +
132J LEU* 1.3 83.0 - - + +
134J ASP* 1.3 56.6 + - - +
136J GLU* 2.5 35.5 + - - +
137J ARG* 2.9 51.0 + - - +
312J ARG* 5.3 2.0 - - - +
40L GLN* 5.9 2.0 - - - -
43L ASP* 5.1 13.9 - - - +
47L MET* 4.2 10.3 - - - +
83L VAL* 3.4 35.6 - - + +
86L SER* 5.5 10.3 - - - +
87L VAL* 4.5 14.6 - - + +
90L GLU* 4.1 9.9 - - - +
93L ARG* 3.2 28.2 + - - +
95L THR* 5.6 6.3 - - - +
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Residues in contact with ASP 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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130J MET* 3.0 18.8 - - + +
131J PRO* 3.2 34.4 + - + +
132J LEU 3.1 0.6 - - - -
133J ARG* 1.3 76.3 - - - +
135J ILE* 1.3 65.6 + - - +
137J ARG* 3.1 15.7 + - - +
138J VAL* 3.0 20.6 + - - +
157J GLN 5.4 1.8 - - - +
159J ILE* 2.9 44.3 + - - +
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Residues in contact with ILE 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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117J LEU* 4.0 21.1 - - + -
122J SER* 5.0 2.9 - - - +
124J ILE* 4.3 7.9 - - + +
125J GLY* 3.2 37.5 - - - +
128J LEU* 4.9 1.3 - - + -
130J MET* 3.6 30.7 - - + -
131J PRO 3.2 18.5 + - - +
132J LEU* 3.8 7.9 - - + +
134J ASP* 1.3 75.6 - - - +
136J GLU* 1.3 58.6 + - - +
138J VAL* 3.2 2.8 + - - +
139J LEU* 2.8 30.2 + - + +
185J ILE* 3.5 34.5 - - + -
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Residues in contact with GLU 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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117J LEU* 4.7 11.5 - - + +
118J LYS* 3.5 27.4 - - - +
132J LEU* 2.9 38.6 + - + +
133J ARG* 2.5 41.4 + - - +
134J ASP 3.2 0.2 - - - -
135J ILE* 1.3 75.9 - - - +
137J ARG* 1.3 57.6 + - - +
139J LEU* 3.7 6.5 - - - -
140J TYR* 3.0 45.2 + - + +
312J ARG* 3.5 12.2 + - - -
93L ARG* 3.9 15.8 + - - +
95L THR* 6.0 1.0 - - - +
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Residues in contact with ARG 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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133J ARG* 2.9 40.0 + - - +
134J ASP* 3.1 12.9 + - - +
136J GLU* 1.3 75.2 - - - +
138J VAL* 1.3 61.7 + - - +
139J LEU 3.3 0.2 + - - -
141J PHE 3.4 2.3 + - - -
142J GLU* 2.7 52.8 + - + +
143J SER* 3.3 7.0 + - - +
159J ILE* 4.0 22.8 - - + +
86L SER* 5.6 3.8 + - - -
90L GLU* 3.4 36.5 + - - +
93L ARG* 4.1 15.7 - - - +
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Residues in contact with VAL 138 (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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130J MET* 4.1 8.3 - - + -
134J ASP* 3.0 17.5 + - - +
135J ILE 3.2 5.4 + - - +
137J ARG* 1.3 77.1 - - - +
139J LEU* 1.3 57.3 + - - +
141J PHE* 3.6 5.0 + - - -
143J SER 3.4 20.6 - - - +
145J VAL* 3.8 24.9 - - + -
159J ILE* 4.0 12.8 - - + -
180J MET* 4.0 1.8 - - - +
181J GLY* 2.6 35.9 + - - +
184J ALA* 3.4 31.9 - - + -
185J ILE* 4.1 11.2 - - + -
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Residues in contact with LEU 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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112J ALA* 3.6 19.7 - - + -
117J LEU* 3.6 37.2 - - + -
135J ILE* 2.8 13.3 + - + +
136J GLU* 3.9 5.6 - - - +
137J ARG 3.1 0.2 - - - -
138J VAL* 1.3 75.9 - - - +
140J TYR* 1.3 68.3 + - + +
141J PHE* 3.1 27.2 + - - -
181J GLY* 3.9 3.3 - - - -
182J ALA* 3.5 25.5 + - + +
185J ILE* 3.4 32.8 - - + -
300J GLN* 4.3 21.8 - - - +
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Residues in contact with TYR 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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117J LEU* 5.2 1.8 - - + +
136J GLU* 3.0 35.7 + - + +
139J LEU* 1.3 85.9 - - + +
141J PHE* 1.3 73.6 + - - +
142J GLU* 3.4 5.4 + - + +
297J ARG* 3.0 37.6 + - + -
300J GLN* 4.0 31.5 + - + +
301J GLU* 5.4 4.0 - - + -
304J ASP* 5.2 1.7 + - - +
312J ARG* 2.8 52.6 + - - -
93L ARG* 5.2 3.4 - - - +
95L THR* 5.3 9.2 - - + -
97L PRO* 5.7 7.0 - - + -
100L MET* 3.9 32.6 - - + +
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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