Contacts of the helix formed by residues 138 - 148 (chain B) in PDB entry 2R28
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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.7 2.2 - - - -
99B GLY 3.7 8.7 - - - +
100B TYR* 3.6 26.7 + - + -
132B ASP* 3.5 21.7 + - - +
134B ASP* 5.5 0.4 - - - +
136B GLN 3.8 1.4 + - - +
137B VAL* 1.3 75.8 - - - +
139B TYR* 1.3 65.2 + - - +
140B GLU* 3.2 16.6 + - - +
141B GLU* 2.9 40.3 + - - +
142B PHE* 3.0 21.1 + - - +
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Residues in contact with TYR 139 (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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83B GLU* 4.1 14.7 + - - +
86B ILE* 4.4 6.4 - - + +
87B ARG* 3.6 58.9 + - + +
90B PHE* 3.8 38.7 - + + -
99B GLY 4.1 2.9 + - - +
138B ASN* 1.3 75.0 - - - +
140B GLU* 1.3 66.0 + - + +
142B PHE* 3.0 3.8 + - + +
143B VAL* 2.8 58.1 + - + +
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Residues in contact with GLU 140 (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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138B ASN* 3.2 14.3 + - - +
139B TYR* 1.3 82.2 - - + +
141B GLU* 1.3 57.4 + - + +
143B VAL* 3.5 8.8 + - - +
144B GLN* 2.9 29.7 + - - +
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Residues in contact with GLU 141 (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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129B ALA* 3.3 22.0 - - - +
130B ASP* 4.0 0.4 - - - -
131B ILE* 3.1 20.7 + - + +
132B ASP* 2.9 30.5 + - - +
136B GLN 3.0 3.8 - - - +
137B VAL* 3.3 7.9 - - + -
138B ASN* 2.9 39.6 + - - +
140B GLU* 1.3 75.6 - - + +
142B PHE* 1.3 59.7 + - - +
144B GLN* 3.7 7.2 + - - +
145B MET* 2.9 31.2 + - - +
1004B CA 2.4 30.4 - - - -
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Residues in contact with PHE 142 (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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86B ILE* 3.5 27.4 - - + -
89B ALA* 4.0 8.3 - - + -
90B PHE* 3.5 45.8 - + + -
93B PHE* 4.4 12.3 - + - -
101B ILE* 3.6 24.9 - - + -
137B VAL* 3.8 9.4 - - + +
138B ASN 3.0 13.7 + - - +
139B TYR* 3.0 8.5 + + - +
141B GLU* 1.3 76.8 - - - +
143B VAL* 1.3 62.8 + - - +
145B MET* 3.2 28.6 + - + +
146B MET* 3.1 33.6 + - + +
400D ILE* 3.7 25.6 - - + -
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Residues in contact with VAL 143 (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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86B ILE* 4.0 18.8 - - + -
139B TYR* 2.8 57.8 + - + +
140B GLU* 3.5 10.1 - - - +
142B PHE* 1.3 73.0 - - - +
144B GLN* 1.3 56.8 + - - +
146B MET* 3.0 3.1 + - - +
147B THR* 2.7 52.3 + - + +
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Residues in contact with GLN 144 (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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129B ALA* 5.7 0.8 + - - +
131B ILE* 4.4 24.0 - - + +
140B GLU 2.9 18.3 + - - +
141B GLU* 3.7 7.8 + - - +
143B VAL* 1.3 80.0 - - - +
145B MET* 1.3 63.3 + - - +
147B THR* 3.8 7.1 - - + +
148B ALA 2.8 51.9 + - - +
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Residues in contact with MET 145 (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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129B ALA* 4.4 23.8 - - + -
137B VAL* 5.6 0.7 - - + -
141B GLU 2.9 20.2 + - - +
142B PHE* 3.4 41.3 - - + +
144B GLN* 1.3 79.3 - - - +
146B MET* 1.3 73.4 + - + +
148B ALA* 4.0 1.7 + - - +
396D ILE* 6.6 0.4 - - - -
397D ARG* 2.9 48.3 + - + -
400D ILE* 4.2 13.5 - - + -
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Residues in contact with MET 146 (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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86B ILE* 4.2 30.0 - - + +
89B ALA* 5.9 1.1 - - + -
142B PHE* 3.2 30.7 - - + +
143B VAL 3.0 4.3 + - - +
145B MET* 1.3 98.8 - - + +
147B THR* 1.3 56.1 + - - +
148B ALA 3.3 4.5 - - - -
397D ARG* 3.8 15.0 - - - +
400D ILE* 3.7 31.2 - - + -
401D ARG* 3.3 59.2 + - + +
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Residues in contact with THR 147 (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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82B SER* 5.4 0.9 + - - -
86B ILE* 4.3 10.6 - - - +
143B VAL* 2.7 34.5 + - + +
144B GLN* 4.2 7.6 - - + +
146B MET* 1.3 73.2 - - - +
148B ALA* 1.3 66.4 + - - +
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Residues in contact with ALA 148 (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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144B GLN* 2.8 41.5 + - - +
145B MET* 4.3 1.4 - - - +
146B MET 3.3 3.4 - - - -
147B THR* 1.3 85.3 - - - +
397D ARG* 3.3 26.7 - - - +
401D ARG* 5.9 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