Contacts of the helix formed by residues 146 - 156 (chain B) in PDB entry 2H8R
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 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B GLY 4.3 0.2 + - - -
145B LEU* 1.3 75.1 - - - +
147B GLN* 1.3 68.8 + - - +
148B SER* 3.3 9.6 + - - +
149B HIS* 2.7 39.3 + - + +
150B LEU* 2.8 12.6 + - - +
7E T 2.8 66.3 + - - +
8E A 4.0 21.8 + - - -
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Residues in contact with GLN 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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136B GLN* 2.8 25.7 + - + +
137B ARG* 6.2 0.4 - - - -
140B VAL* 3.6 28.0 - - + +
145B LEU 3.3 3.2 + - - -
146B ASN* 1.3 76.9 - - - +
148B SER* 1.3 70.2 + - - +
150B LEU* 3.8 2.2 - - - +
151B SER* 3.3 17.6 + - - -
9E A 4.2 3.8 + - - -
12F T 4.0 20.3 - - + +
13F A 3.4 42.2 + - - -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 3.3 13.2 + - - +
147B GLN* 1.3 88.5 + - - +
149B HIS* 1.3 66.3 + - - +
150B LEU 3.0 1.0 + - - -
151B SER* 3.6 1.4 + - - -
152B GLN* 3.4 25.6 + - - +
7E T 3.7 8.8 + - - +
8E A 3.5 16.7 + - - -
9E A 4.1 6.3 - - - -
14F T 3.3 29.3 + - - +
15F T 3.4 15.2 + - - -
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 5.7 1.3 - - + -
146B ASN* 2.7 33.5 + - + +
148B SER* 1.3 77.5 - - - +
150B LEU* 1.3 62.3 + - - +
152B GLN* 4.3 2.4 - - - +
153B HIS* 3.3 19.2 + - - +
158B THR* 4.1 8.5 + - + +
159B PRO 3.4 24.0 - - - -
160B MET* 2.9 35.6 - - + +
164B LYS* 4.8 5.4 - - + -
5E G 4.4 0.9 - - + +
6E T 3.0 59.4 + - + +
7E T 3.6 17.3 - - + +
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Residues in contact with LEU 150 (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 MET* 6.2 0.4 - - - -
136B GLN* 4.2 20.6 - - + -
139B VAL* 3.8 26.9 - - + -
140B VAL* 4.3 13.5 - - + -
143B THR* 5.2 2.9 - - - +
145B LEU* 4.6 14.4 - - + -
146B ASN 2.8 13.1 + - - +
147B GLN* 4.1 3.8 - - - +
148B SER 3.0 0.2 - - - -
149B HIS* 1.3 78.7 - - - +
151B SER* 1.4 58.2 + - - +
152B GLN 2.9 0.9 + - - -
153B HIS* 3.1 4.1 + - - +
154B LEU* 2.7 57.1 + - + +
160B MET* 4.5 14.1 - - - -
168B LEU* 4.4 19.5 - - + -
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Residues in contact with SER 151 (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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136B GLN* 3.4 17.5 - - - +
147B GLN* 3.3 22.4 + - - -
148B SER 3.8 4.9 - - - -
150B LEU* 1.4 79.1 - - - +
152B GLN* 1.3 57.6 + - - +
154B LEU* 3.6 2.4 + - - -
155B ASN* 2.9 32.4 + - - +
13F A 2.5 31.1 + - - +
14F T 3.7 17.2 - - - +
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Residues in contact with GLN 152 (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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148B SER* 3.4 17.0 + - - +
149B HIS* 4.3 2.2 - - - +
150B LEU 2.9 4.8 + - - -
151B SER* 1.3 72.2 - - - +
153B HIS* 1.3 64.1 + - - +
154B LEU 2.8 0.7 - - - -
155B ASN* 4.8 0.7 - - + -
156B LYS* 2.5 60.8 + - + +
157B GLY 2.6 6.1 + - - -
158B THR* 3.5 20.9 + - - +
6E T 5.7 5.5 + - - +
7E T 4.2 13.7 + - - +
14F T 4.4 13.4 - - + +
15F T 4.2 30.7 + - - +
16F A 5.5 0.8 - - - +
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Residues in contact with HIS 153 (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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118B PRO* 4.3 17.1 + - + +
119B TRP* 4.6 1.3 - + - -
122B ALA* 4.1 21.5 - - + +
149B HIS* 3.3 15.3 + - + +
150B LEU* 3.1 4.2 + - - +
152B GLN* 1.3 81.6 - - - +
154B LEU* 1.3 69.1 + - + +
157B GLY* 3.4 15.3 + - - -
158B THR 2.6 35.6 + - - +
159B PRO* 4.3 2.0 - - + -
160B MET* 3.6 34.5 - - + -
165B ARG* 3.7 22.9 - - - -
168B LEU* 4.3 20.5 - - + +
169B TYR* 4.5 6.1 - + - -
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Residues in contact with LEU 154 (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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119B TRP* 4.9 5.4 + - - -
122B ALA* 3.8 39.7 - - + +
123B LYS* 5.9 0.2 - - - -
125B ILE* 4.7 8.1 - - + -
126B LYS* 3.9 18.5 + - + +
129B MET* 4.0 30.7 - - + -
136B GLN* 5.7 3.4 - - + +
139B VAL* 6.4 0.2 - - + -
150B LEU* 2.7 39.8 + - + +
151B SER* 4.3 3.4 - - - +
152B GLN 2.8 1.2 - - - -
153B HIS* 1.3 89.0 - - - +
155B ASN* 1.3 69.2 + - - +
156B LYS 3.4 0.2 - - - -
157B GLY 4.4 0.8 + - - -
168B LEU* 4.5 18.8 - - + -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TRP* 5.5 4.3 - - - -
126B LYS* 3.0 43.5 + - - +
136B GLN* 4.8 1.2 + - - -
151B SER* 2.9 21.7 + - - +
152B GLN* 4.8 0.2 - - - -
154B LEU* 1.3 82.5 + - - +
156B LYS* 1.3 72.0 + - + +
157B GLY 3.8 0.2 - - - -
13F A 3.3 32.5 + - + +
14F T 5.7 4.0 - - - +
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Residues in contact with LYS 156 (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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306A GLU* 3.4 48.1 + - - +
308A ALA 3.7 28.5 + - - +
119B TRP* 4.3 6.0 + - - -
152B GLN* 2.5 47.3 + - + +
155B ASN* 1.3 85.7 - - + +
157B GLY* 1.3 59.8 + - - +
158B THR* 3.3 4.2 - - - +
14F T 4.6 15.3 - - - +
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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