Contacts of the helix formed by residues 137 - 156 (chain C) in PDB entry 4A9J
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 ALA 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C GLN* 5.4 2.2 - - - +
79C LEU* 3.8 15.3 - - - +
135C TYR* 3.9 1.4 - - - +
136C TRP* 1.3 81.7 - - + +
138C ALA* 1.3 65.8 + - - +
139C SER* 3.3 20.3 + - - +
140C GLU* 3.3 22.2 + - - +
141C CYS 3.8 1.6 + - - -
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Residues in contact with ALA 138 (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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78C GLN* 3.6 41.0 + - + +
79C LEU* 4.0 7.8 - - - +
82C LEU* 3.5 25.7 - - + +
137C ALA* 1.3 73.2 - - - +
139C SER* 1.3 62.2 + - - +
141C CYS* 3.1 5.2 + - - +
142C MET* 2.9 26.9 + - - +
180C MET* 4.0 12.6 - - + -
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA* 3.8 14.9 - - - +
138C ALA* 1.3 77.4 - - - +
140C GLU* 1.3 64.5 + - - +
142C MET* 3.3 13.6 + - - +
143C GLN* 2.8 42.8 + - - +
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Residues in contact with GLU 140 (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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134C TYR* 4.8 7.8 - - - +
135C TYR* 3.6 20.7 - - + -
136C TRP* 3.7 36.4 + - - +
137C ALA* 3.3 9.5 + - - +
138C ALA 3.2 0.6 - - - -
139C SER* 1.3 87.5 + - - +
141C CYS* 1.3 58.5 + - - +
143C GLN* 3.3 9.6 + - - +
144C ASP* 3.0 31.2 + - - +
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Residues in contact with CYS 141 (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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79C LEU* 4.3 4.3 - - + -
82C LEU* 3.8 24.9 - - + -
126C ILE* 4.0 7.9 - - - -
130C LEU* 4.0 12.3 - - - -
135C TYR* 3.5 40.1 - - + -
137C ALA 3.8 0.4 + - - -
138C ALA 3.1 8.6 + - - +
140C GLU* 1.3 75.0 - - - +
142C MET* 1.3 64.8 + - - +
144C ASP* 3.1 4.3 + - - +
145C PHE* 3.1 43.9 + - - -
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Residues in contact with MET 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.5 8.3 - - + -
138C ALA* 2.9 24.0 + - - +
139C SER* 3.5 12.8 - - - +
141C CYS* 1.3 76.3 - - - +
143C GLN* 1.3 57.5 + - + +
145C PHE* 3.4 4.9 + - - +
146C ASN* 2.9 27.8 + - - +
173C PHE* 3.8 28.7 - - + -
177C VAL* 3.7 29.2 - - + -
180C MET* 3.7 24.9 - - + -
1186C SO4 4.8 2.5 - - - +
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Residues in contact with GLN 143 (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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139C SER* 2.8 37.2 + - - +
140C GLU* 3.5 10.3 - - - +
142C MET* 1.3 73.3 - - - +
144C ASP* 1.3 59.0 + - - +
146C ASN* 3.2 16.2 + - - +
147C THR* 2.8 36.5 + - - +
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Residues in contact with ASP 144 (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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121C MET* 3.3 28.6 - - + +
126C ILE* 3.8 13.2 - - + -
129C ARG* 2.8 25.2 + - - -
135C TYR* 2.5 33.0 + - - +
140C GLU 3.0 13.3 + - - +
141C CYS 3.1 8.7 + - - +
143C GLN* 1.3 75.1 - - - +
145C PHE* 1.3 65.2 + - - +
147C THR* 3.3 6.8 + - - -
148C MET* 3.0 19.6 + - - +
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Residues in contact with PHE 145 (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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82C LEU* 5.3 1.6 - - + -
86C VAL* 4.4 10.8 - - + -
87C MET* 3.4 35.4 - - + -
90C LEU* 3.4 32.3 - - + -
123C MET* 4.2 13.7 - - + -
126C ILE* 3.6 23.2 - - + +
130C LEU* 5.3 0.7 - - + -
141C CYS* 3.1 33.3 + - - -
142C MET 3.5 7.0 - - - +
144C ASP* 1.3 75.1 - - - +
146C ASN* 1.3 62.1 + - - +
148C MET* 3.2 19.7 + - + +
149C PHE* 3.1 34.1 + + + -
173C PHE* 3.4 33.7 - + + -
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Residues in contact with ASN 146 (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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142C MET 2.9 14.4 + - - +
143C GLN* 3.2 21.8 + - - +
145C PHE* 1.3 76.4 - - - +
147C THR* 1.3 57.1 + - - +
149C PHE* 3.3 2.1 + - - +
150C THR* 2.8 53.4 + - - +
170C GLU* 3.8 20.4 - - - +
173C PHE* 5.0 4.6 - - + -
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Residues in contact with THR 147 (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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119C GLN* 3.1 45.0 + - + +
121C MET* 4.1 9.6 - - + -
143C GLN* 2.8 28.0 + - - +
144C ASP* 3.5 9.6 + - - -
146C ASN* 1.3 76.3 + - - +
148C MET* 1.3 58.2 + - - +
150C THR* 4.5 3.8 - - - -
151C ASN* 2.9 42.9 + - - +
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Residues in contact with MET 148 (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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99C PHE* 3.9 26.7 - - + -
121C MET* 3.5 29.4 - - + +
122C ASP* 3.7 3.1 - - - -
123C MET* 3.5 49.8 - - + -
126C ILE* 4.7 1.8 - - - -
144C ASP 3.0 13.3 + - - +
145C PHE* 3.4 16.4 - - + +
147C THR* 1.3 78.2 - - - +
149C PHE* 1.3 99.8 + - + +
151C ASN* 3.6 5.9 + - - +
152C CYS* 3.4 18.4 + - - +
169C LEU* 5.7 0.2 - - + -
1184C TYL 5.5 3.3 - - + +
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Residues in contact with PHE 149 (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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90C LEU* 4.8 3.8 - - + -
99C PHE* 5.0 3.4 - + - -
123C MET* 5.9 0.4 - - - -
145C PHE* 3.1 37.8 + + + -
146C ASN 3.8 3.1 - - - +
148C MET* 1.3 103.2 - - + +
150C THR* 1.3 64.5 + - - +
152C CYS* 3.1 10.4 + - - +
153C TYR* 3.1 29.0 + - + -
166C ALA* 3.7 23.1 - - + -
169C LEU* 3.6 30.7 - - + -
170C GLU* 3.5 60.3 - - + +
173C PHE* 4.3 10.5 - + + -
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Residues in contact with THR 150 (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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146C ASN* 2.8 41.7 + - - +
147C THR* 3.9 5.2 - - - -
149C PHE* 1.3 70.2 - - - +
151C ASN* 1.3 68.0 + - - +
153C TYR* 3.1 14.7 + - + +
154C ILE* 2.9 47.4 + - + +
170C GLU* 5.5 0.5 + - - -
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Residues in contact with ASN 151 (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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113C TYR* 4.0 13.9 + - - +
117C ILE* 3.4 37.7 - - + +
118C LYS 5.4 0.3 + - - -
119C GLN 2.9 28.5 + - - +
120C PRO* 3.6 9.1 - - - +
121C MET 3.7 8.5 + - - +
147C THR* 2.9 29.8 + - - +
148C MET* 3.7 6.7 - - - +
149C PHE 3.3 0.2 - - - -
150C THR* 1.3 76.4 - - - +
152C CYS* 1.3 58.2 + - - +
154C ILE* 4.7 2.5 - - - +
155C TYR* 2.9 35.0 + - - +
1184C TYL 6.3 0.7 - - + -
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Residues in contact with CYS 152 (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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99C PHE* 4.0 13.0 - - + -
148C MET 3.4 9.2 + - - +
149C PHE 3.1 11.3 + - - +
151C ASN* 1.3 79.0 - - - +
153C TYR* 1.3 61.9 + - - +
156C ASN* 3.0 48.9 + - - +
162C ILE* 3.7 42.0 - - - -
163C VAL* 4.3 4.5 - - - +
166C ALA* 3.9 13.2 - - + -
1184C TYL 4.3 8.2 - - + +
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Residues in contact with TYR 153 (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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149C PHE* 3.1 23.2 + - + +
150C THR* 3.1 12.3 + - + +
152C CYS* 1.3 78.3 - - - +
154C ILE* 1.3 65.6 + - + +
156C ASN 3.6 11.6 - - - +
163C VAL* 3.8 31.5 - - + +
166C ALA* 3.4 27.7 + - + +
167C GLN* 3.3 34.9 + - + +
170C GLU* 3.1 29.5 + - - +
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Residues in contact with ILE 154 (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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116C ILE* 4.2 22.2 - - + +
117C ILE* 4.3 8.1 - - + -
150C THR* 2.9 40.9 + - + +
151C ASN* 3.9 6.3 - - - +
153C TYR* 1.3 80.0 - - + +
155C TYR* 1.3 64.4 + - - +
156C ASN 4.2 2.3 - - - +
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Residues in contact with TYR 155 (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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110C LEU* 3.3 39.5 - - + +
112C ASP* 2.7 30.4 + - - -
113C TYR* 3.7 43.3 - + + -
116C ILE* 3.8 30.3 - - + +
117C ILE* 4.1 10.3 - - + -
151C ASN 2.9 16.8 + - - +
154C ILE* 1.3 82.0 - - - +
156C ASN* 1.3 83.6 + - - +
157C LYS* 5.7 0.2 - - - +
1184C TYL 4.5 2.0 - + - -
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Residues in contact with ASN 156 (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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152C CYS* 3.0 36.5 + - - +
153C TYR 3.6 13.2 - - - +
154C ILE 4.2 2.3 - - - +
155C TYR* 1.3 89.7 - - - +
157C LYS* 1.3 63.8 + - - +
158C PRO* 3.8 2.4 - - - +
160C ASP* 3.5 13.8 - - - +
162C ILE* 3.6 11.9 - - + +
163C VAL* 3.9 14.8 - - + +
1184C TYL 3.0 51.6 + - - -
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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
------------------------------------------------------------
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