Contacts of the helix formed by residues 123 - 132 (chain B) in PDB entry 1C3Q
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 ASN 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ARG* 4.1 2.9 - - - +
122B GLY* 1.3 75.3 - - - -
124B ALA* 1.3 64.7 + - - +
125B ALA* 3.1 10.2 + - - +
126B GLU* 2.8 60.4 + - - +
127B ILE* 3.1 12.3 + - - +
167B ILE* 4.0 1.8 - - - -
168B THR 3.8 15.7 - - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASN* 1.3 74.0 - - - +
125B ALA* 1.3 59.0 + - - +
127B ILE* 3.2 3.3 + - - +
128B ALA* 2.9 30.9 + - - +
150B ILE* 3.8 29.2 - - + -
153B LEU* 3.7 11.6 - - + +
167B ILE* 3.5 18.8 - - + +
168B THR 4.8 0.8 + - - -
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 4.6 1.6 - - - +
123B ASN* 3.1 9.2 + - - +
124B ALA* 1.3 79.0 - - - +
126B GLU* 1.3 64.4 + - + +
128B ALA* 3.8 5.3 - - - +
129B HIS* 3.0 44.5 + - + +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASP* 4.6 2.4 - - - +
95B PRO* 3.6 30.5 - - + +
96B VAL* 3.5 8.3 - - - +
97B GLY* 2.9 21.9 + - - +
98B ALA* 3.7 20.6 - - + +
121B ARG* 5.3 0.9 + - - -
122B GLY* 3.5 8.8 - - - -
123B ASN* 2.8 55.6 + - - +
125B ALA* 1.3 73.2 - - + +
127B ILE* 1.3 61.1 + - - +
130B THR* 2.7 33.7 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PRO* 4.4 10.1 - - + -
120B ILE* 3.6 34.1 - - + +
122B GLY 4.5 10.3 - - - +
123B ASN 3.1 13.6 + - - +
124B ALA 3.7 5.8 - - - +
126B GLU* 1.3 77.0 - - - +
128B ALA* 1.3 63.8 + - - +
130B THR* 3.3 4.8 + - - -
131B VAL* 3.0 27.7 + - + +
153B LEU* 4.5 7.0 - - + -
157B ALA* 4.0 26.7 - - + -
165B ILE* 4.3 18.2 - - + -
167B ILE* 4.0 26.7 - - + -
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA 2.9 17.7 + - - +
125B ALA* 3.8 6.3 - - - +
127B ILE* 1.3 78.1 - - - +
129B HIS* 1.3 57.9 + - + +
131B VAL* 4.0 1.4 - - - +
132B GLY* 2.7 40.2 + - - +
133B VAL* 4.7 12.3 - - + +
153B LEU* 4.1 25.1 - - + +
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 4.6 1.1 - - - +
99B GLY* 4.1 31.4 - - - +
105B THR* 3.6 11.7 - - + +
109B ARG* 3.2 18.0 + - - -
125B ALA* 3.0 38.2 + - + +
126B GLU 4.5 1.3 - - - +
128B ALA* 1.3 75.7 - - + +
130B THR* 1.3 63.7 + - - +
132B GLY* 3.8 4.2 + - - +
133B VAL* 4.0 23.7 - - + +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 5.9 0.2 - - + -
95B PRO* 4.2 7.1 - - + +
98B ALA* 3.3 19.8 - - - +
105B THR* 4.5 4.0 - - - +
108B ALA* 4.0 17.2 - - + +
109B ARG* 2.8 35.9 + - + +
112B ILE* 3.5 33.0 - - + -
126B GLU 2.7 23.9 + - - -
127B ILE* 3.8 5.2 - - - -
129B HIS* 1.3 76.9 - - - +
131B VAL* 1.3 64.3 + - + +
161B LEU* 5.6 0.7 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 4.2 2.5 + - - -
127B ILE* 3.0 19.5 + - + +
128B ALA* 4.1 2.7 - - - +
130B THR* 1.3 78.3 - - - +
132B GLY* 1.3 65.8 + - - +
153B LEU* 6.0 3.1 - - + -
157B ALA* 3.9 23.6 - - + -
160B LYS* 3.6 38.6 + - + +
161B LEU* 3.8 33.7 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 3.9 14.4 - - - -
128B ALA 2.7 18.4 + - - +
129B HIS* 3.8 3.3 + - - -
130B THR 3.3 2.4 - - - -
131B VAL* 1.3 85.8 - - - +
133B VAL* 1.3 64.7 + - - -
134B THR* 3.2 10.5 + - - -
160B LYS* 4.5 1.7 + - - -
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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