Contacts of the helix formed by residues 122 - 133 (chain Q) in PDB entry 3H1J
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 GLY 122 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Q PRO* 4.7 7.2 - - - -
120Q ARG 3.2 0.4 + - - -
121Q HIS* 1.3 73.2 - - - +
123Q GLY* 1.3 66.1 + - - +
124Q GLU* 3.3 1.0 + - - +
125Q ASP* 3.0 24.3 + - - +
126Q TYR* 3.2 11.1 + - - -
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Residues in contact with GLY 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q VAL* 3.1 31.9 - - - -
120Q ARG* 3.0 10.5 + - - -
121Q HIS 3.3 1.2 + - - -
122Q GLY* 1.3 75.8 - - - +
124Q GLU* 1.3 61.6 + - - -
126Q TYR* 2.9 6.9 + - - +
127Q VAL* 2.7 34.5 + - - +
191Q ARG* 4.7 2.7 - - - -
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Residues in contact with GLU 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q TRP* 3.3 44.1 - - + +
14Q HIS* 2.6 31.1 + - - +
117Q VAL* 4.0 7.4 - - + +
122Q GLY 3.3 0.6 + - - +
123Q GLY* 1.3 72.5 - - - -
125Q ASP* 1.3 58.2 + - - +
127Q VAL* 4.2 7.9 - - - -
128Q PHE* 2.7 35.0 + - - +
187Q CYS* 3.9 17.3 - - + +
191Q ARG* 2.8 41.6 + - - +
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Residues in contact with ASP 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q PRO* 4.0 6.3 - - + -
8Q PRO 3.3 21.0 - - - +
9Q ALA* 3.3 20.1 - - - +
10Q PHE* 3.2 18.3 + - - +
12Q TRP* 2.5 35.9 + - - -
122Q GLY* 3.0 13.4 + - - +
124Q GLU* 1.3 79.1 - - - +
126Q TYR* 1.3 56.8 + - - +
128Q PHE* 4.0 0.9 - - - +
129Q SER* 2.8 34.0 + - - -
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Residues in contact with TYR 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q PRO* 3.7 22.2 - - + +
120Q ARG* 4.1 27.5 - - + -
121Q HIS 3.5 24.0 - - - +
122Q GLY* 3.2 6.5 + - - -
123Q GLY 2.9 7.4 + - - +
125Q ASP* 1.3 78.0 - - - +
127Q VAL* 1.3 77.2 + - + +
129Q SER* 3.4 1.4 + - - -
130Q LEU* 3.0 41.7 + - + +
152Q TYR* 3.5 28.5 - - + -
153Q PHE* 3.8 15.1 - - - -
154Q PRO* 3.8 9.9 - - + +
501Q HEC 2.7 31.0 + - + -
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Residues in contact with VAL 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Q ILE* 4.7 11.7 - - + +
117Q VAL* 4.6 14.6 - - + -
120Q ARG* 5.6 1.1 - - + -
123Q GLY* 2.7 25.7 + - - +
124Q GLU* 4.2 1.1 - - - -
126Q TYR* 1.3 84.2 - - + +
128Q PHE* 1.3 61.5 + - - +
130Q LEU* 3.4 5.7 + - - +
131Q LEU* 3.0 36.6 + - + +
187Q CYS* 3.4 21.1 - - - -
190Q LEU* 4.1 18.2 - - + -
501Q HEC 4.2 23.8 - - + -
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Residues in contact with PHE 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 3.3 41.3 - + - -
12Q TRP* 3.9 13.0 - + + -
124Q GLU 2.7 23.5 + - - +
125Q ASP 4.0 2.5 - - - +
127Q VAL* 1.3 73.5 - - - +
129Q SER* 1.3 63.8 + - - +
130Q LEU 3.1 1.0 + - - -
131Q LEU* 3.2 4.8 + - - +
132Q THR* 3.1 42.6 + - + +
180Q SER* 3.5 13.0 - - - -
183Q ALA* 3.4 24.7 - - + -
184Q LYS* 3.3 32.5 - - + -
187Q CYS* 3.3 9.5 - - - -
17U LEU* 5.8 0.9 - - + -
73U LEU* 4.1 19.7 - - + -
74U PHE* 4.1 8.3 - + - -
77U LEU* 4.8 0.7 - - + -
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Residues in contact with SER 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q PRO* 3.2 22.8 - - - +
8Q PRO* 3.5 12.3 - - - +
10Q PHE* 3.6 9.7 - - - -
125Q ASP 2.8 21.3 + - - -
126Q TYR 3.9 2.0 - - - -
128Q PHE* 1.3 80.6 - - - +
130Q LEU* 1.3 52.7 + - - +
132Q THR* 3.6 5.3 + - - -
133Q GLY* 2.6 35.0 + - - -
152Q TYR* 3.3 26.8 - - - -
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Residues in contact with LEU 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Q TYR* 3.0 41.3 + - + +
127Q VAL* 3.6 4.3 - - - +
128Q PHE 3.1 0.2 - - - -
129Q SER* 1.3 74.7 - - - +
131Q LEU* 1.3 68.2 + - + +
132Q THR 3.2 0.9 + - - -
133Q GLY 3.3 4.7 + - - -
134Q TYR* 3.7 3.0 - - - +
150Q ASN* 2.8 57.9 + - - +
152Q TYR* 4.2 5.1 - - + +
153Q PHE* 3.6 28.7 - - + +
158Q ILE* 4.3 14.4 - - + -
160Q MET* 4.5 7.9 - - + -
501Q HEC 4.0 33.2 - - + -
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Residues in contact with LEU 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q VAL* 3.0 27.1 + - + +
128Q PHE 3.2 4.2 + - - +
130Q LEU* 1.3 82.8 - - + +
132Q THR* 1.3 58.0 + - - +
134Q TYR* 3.5 19.3 - - - -
160Q MET* 4.5 8.1 - - + -
162Q PRO* 5.4 0.2 - - - +
163Q PRO* 3.7 30.1 - - + +
164Q ILE* 4.4 15.1 - - + +
179Q MET* 4.4 12.4 - - - +
183Q ALA* 4.2 18.4 - - + -
186Q VAL* 3.8 29.4 - - + -
187Q CYS* 4.7 1.6 - - - -
501Q HEC 4.1 31.9 - - + -
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Residues in contact with THR 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Q PHE* 3.1 35.0 + - + +
129Q SER* 3.6 6.2 + - - -
131Q LEU* 1.3 76.9 - - - +
133Q GLY* 1.3 60.3 + - - +
134Q TYR* 2.9 16.5 + - - +
179Q MET* 4.2 18.5 - - - +
180Q SER* 4.3 11.2 - - - -
183Q ALA* 3.8 22.7 - - + -
17U LEU* 4.0 9.1 - - + +
21U ARG* 3.2 30.3 + - - -
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Residues in contact with GLY 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q SER 2.6 26.2 + - - -
130Q LEU 3.3 1.7 + - - -
132Q THR* 1.3 71.5 + - - +
134Q TYR* 1.3 61.9 + - - +
135Q CYS* 4.3 2.1 - - - +
150Q ASN* 4.1 6.3 - - - -
151Q PRO* 3.0 29.8 - - - +
152Q TYR* 4.0 13.0 - - - -
21U ARG* 4.6 5.4 - - - -
62U LEU* 6.1 0.2 - - - +
65U ARG* 5.9 2.0 - - - -
66U ASP* 6.5 0.4 - - - -
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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