Contacts of the helix formed by residues 136 - 151 (chain J) in PDB entry 3J7Y
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 136 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134J ASP* 3.7 11.5 - - + +
135J VAL* 1.4 97.7 - - + +
137J LEU* 1.3 61.7 + - - +
138J SER* 4.1 9.4 - - - +
139J SER* 4.0 20.0 - - - +
140J VAL* 3.5 18.9 + - - +
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Residues in contact with LEU 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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118J TYR* 3.7 34.3 - - + +
121J ALA* 3.6 30.3 - - + -
122J ARG* 3.7 42.2 - - - +
136J PRO* 1.3 72.4 - - - +
138J SER* 1.3 61.4 + - - +
139J SER 3.2 0.9 - - - -
140J VAL* 3.2 10.0 + - + +
141J VAL* 2.9 25.4 + - + +
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Residues in contact with SER 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J TYR* 5.6 5.4 + - - -
136J PRO* 3.4 8.3 - - - +
137J LEU* 1.3 79.2 - - - +
139J SER* 1.3 62.1 + - - +
141J VAL* 3.2 15.8 - - - +
142J ARG* 3.1 20.6 + - - +
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Residues in contact with SER 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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2192A A 2.9 28.6 + - - +
2193A U 3.1 10.9 + - - -
134J ASP* 2.6 27.3 + - - -
136J PRO* 4.0 23.0 + - - +
137J LEU 3.2 0.4 - - - -
138J SER* 1.3 77.7 - - - +
140J VAL* 1.3 63.1 + - - +
142J ARG* 3.2 20.3 + - - +
143J SER* 3.7 4.2 + - - -
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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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121J ALA* 3.9 29.6 - - + +
124J LYS* 6.0 0.7 - - + -
125J ALA* 5.9 6.7 - - + +
132J LEU* 4.6 30.2 - - + +
134J ASP* 3.6 23.8 + - + +
136J PRO 3.5 18.4 - - - +
137J LEU* 3.2 14.7 + - + +
139J SER* 1.3 78.1 - - - +
141J VAL* 1.3 61.6 + - - +
142J ARG 3.3 0.5 + - - -
143J SER* 3.3 16.4 + - - -
144J ILE* 3.4 13.3 + - + +
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Residues in contact with VAL 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J LEU* 5.3 6.7 - - + -
117J VAL* 3.6 25.1 - - + -
118J TYR* 3.7 38.8 - - + +
137J LEU* 2.9 14.5 + - + +
138J SER* 3.2 18.8 + - - +
140J VAL* 1.3 77.7 - - - +
142J ARG* 1.3 59.4 + - - +
144J ILE* 3.0 13.4 - - + +
145J ILE* 2.9 39.2 + - + +
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Residues in contact with ARG 142 (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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2190A C 5.0 0.3 + - - -
2191A A 3.2 61.7 + - - +
2192A A 4.8 7.9 + - - +
138J SER 3.1 11.1 + - - +
139J SER* 3.2 12.9 + - - +
141J VAL* 1.3 79.2 - - + +
143J SER* 1.3 57.0 + - - +
145J ILE* 3.2 10.7 + - + +
146J GLY* 2.9 26.3 + - - -
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Residues in contact with SER 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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2169A A 6.0 1.4 - - - -
2170A G 2.8 44.1 + - - +
2191A A 2.8 26.9 + - - -
2192A A 3.2 20.8 + - - -
132J LEU* 5.3 9.9 - - - +
139J SER 3.7 1.6 + - - -
140J VAL* 3.3 9.6 + - - -
141J VAL 3.3 0.2 - - - -
142J ARG* 1.3 77.1 - - - +
144J ILE* 1.3 61.5 + - - +
146J GLY* 3.2 1.9 + - - +
147J SER* 2.9 13.2 + - - -
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Residues in contact with ILE 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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2170A G 5.2 4.5 - - - +
87J VAL* 3.9 13.7 - - + -
91J LEU* 4.3 4.6 - - + +
117J VAL* 3.1 45.1 - - + +
120J ILE* 3.5 26.0 - - + -
121J ALA* 3.4 22.9 - - + -
124J LYS* 4.9 8.5 - - + -
132J LEU* 5.3 3.6 - - + -
140J VAL* 3.4 9.6 + - + +
141J VAL* 3.0 24.5 - - - +
143J SER* 1.3 80.5 - - - +
145J ILE* 1.3 54.2 + - - +
147J SER* 3.2 7.7 + - - +
148J ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 145 (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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2190A C 5.7 0.9 - - - +
114J LEU* 4.2 17.3 - - + -
117J VAL* 4.2 12.1 - - + -
141J VAL* 2.9 28.1 + - + +
142J ARG* 3.4 12.6 - - + +
144J ILE* 1.3 75.9 - - - +
146J GLY* 1.3 57.7 + - - +
148J ALA* 3.2 7.1 + - - +
149J ARG* 2.9 44.6 + - - +
155J VAL* 3.8 37.1 - - + +
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Residues in contact with GLY 146 (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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2190A C 3.1 40.6 - - - -
2191A A 5.1 0.2 - - - -
2198A A 3.7 1.6 + - - -
142J ARG 2.9 12.3 + - - -
143J SER 3.2 4.0 + - - -
145J ILE* 1.3 77.0 - - - +
147J SER* 1.3 53.1 - - - +
149J ARG* 3.2 9.0 + - - +
150J SER* 2.6 30.9 + - - -
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Residues in contact with SER 147 (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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2170A G 2.7 33.6 + - - +
2171A U 4.2 7.0 + - - +
2173A G 5.4 0.5 + - - -
2198A A 4.2 0.9 - - - +
87J VAL* 3.9 26.3 - - - +
88J SER* 5.7 1.6 - - - -
91J LEU* 4.4 7.4 - - - -
143J SER 2.9 9.0 + - - -
144J ILE* 3.4 10.7 - - - +
146J GLY* 1.3 75.9 - - - +
148J ALA* 1.3 60.6 + - - +
150J SER* 2.8 25.9 + - - -
151J LEU* 3.3 13.4 + - - +
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Residues in contact with ALA 148 (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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91J LEU* 4.0 19.4 - - + +
112J VAL* 6.2 0.7 - - + -
117J VAL* 5.6 3.8 - - + -
144J ILE 2.9 13.0 + - - +
145J ILE* 3.3 11.2 - - - +
147J SER* 1.3 77.1 - - - +
149J ARG* 1.3 61.9 - - - +
151J LEU* 3.0 19.9 + - - +
153J ILE* 3.3 27.5 - - + +
155J VAL* 3.7 24.5 - - + -
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Residues in contact with ARG 149 (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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2188A A 4.4 10.3 + - - +
2189A C 5.4 8.1 - - - +
2190A C 4.5 28.0 + - - +
104J THR* 5.1 3.1 - - - -
105J GLY* 5.7 3.3 - - - -
145J ILE* 2.9 26.6 + - - +
146J GLY 3.3 10.1 - - - +
148J ALA* 1.3 76.6 - - - +
150J SER* 1.3 60.0 + - - +
151J LEU 3.4 6.8 - - - +
153J ILE 4.1 8.4 - - - +
154J ARG* 6.1 5.6 - - - +
155J VAL* 5.9 6.5 - - + +
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Residues in contact with SER 150 (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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2173A G 2.4 47.5 + - - +
2174A G 5.0 0.2 - - - -
2188A A 4.6 6.7 - - - -
2198A A 2.5 46.0 + - - -
104J THR* 3.5 9.7 + - - +
146J GLY 2.6 16.3 + - - -
147J SER* 2.8 12.2 + - - -
149J ARG* 1.3 76.2 - - - +
151J LEU* 1.3 57.1 + - - +
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Residues in contact with LEU 151 (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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2173A G 4.2 7.0 - - - +
2174A G 3.4 35.7 - - - +
88J SER* 3.2 41.7 - - - +
91J LEU* 4.2 8.7 - - + -
92J LYS* 3.7 28.9 - - + +
104J THR* 3.6 9.3 - - - +
105J GLY* 5.8 0.5 - - - -
147J SER 3.6 13.0 - - - +
148J ALA 3.0 11.6 + - - +
149J ARG 3.4 7.6 - - - +
150J SER* 1.3 80.6 - - - +
152J GLY* 1.3 54.7 + - - +
153J ILE* 2.7 34.0 + - + +
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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