Contacts of the helix formed by residues 151 - 157 (chain B) in PDB entry 2Q06
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 THR 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ASN* 6.0 0.4 - - - +
149B GLN* 3.5 23.2 + - - +
150B ARG* 1.3 79.3 + - - +
152B ARG* 1.3 71.1 + - + +
153B ALA 3.2 3.2 + - - -
154B LEU* 3.2 18.6 + - - +
155B VAL* 3.3 17.0 + - + +
161B PRO* 3.9 26.9 - - + +
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Residues in contact with ARG 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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289A TYR* 4.2 27.5 - - - -
305A ARG* 3.8 25.5 - - - +
309A ASN* 3.1 45.8 - - - +
150B ARG* 3.3 33.6 - - - +
151B THR* 1.3 79.9 - - - +
153B ALA* 1.3 55.3 + - - +
155B VAL* 2.9 16.8 - - + +
156B ARG* 2.6 39.6 - - + +
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Residues in contact with ALA 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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150B ARG* 3.3 31.6 - - + +
151B THR 3.2 0.8 - - - -
152B ARG* 1.3 80.6 - - - +
154B LEU* 1.3 67.2 + - + +
156B ARG* 3.0 18.5 + - - +
157B THR* 3.3 10.5 + - - +
167B MET* 6.2 0.7 - - + -
191B MET* 4.2 20.4 - - - -
195B ARG* 5.4 2.7 - - - +
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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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150B ARG* 3.5 25.6 - - + +
151B THR 3.2 6.7 + - - +
153B ALA* 1.3 81.6 - - + +
155B VAL* 1.3 64.5 + - - +
157B THR* 3.0 14.5 + - - -
159B MET* 3.0 48.5 + - + +
160B ASP 3.5 12.1 - - - +
161B PRO* 3.2 34.5 - - + +
163B MET* 4.7 3.4 - - + +
164B CYS* 5.1 2.0 - - + +
167B MET* 3.5 43.5 - - + -
191B MET* 4.8 2.0 - - - -
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Residues in contact with VAL 155 (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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309A ASN* 5.2 2.9 - - - +
151B THR* 4.0 8.5 - - + +
152B ARG* 2.9 39.5 - - + +
154B LEU* 1.3 76.7 - - - +
156B ARG* 1.3 68.1 + - + +
158B GLY* 3.6 8.5 + - - -
159B MET 3.7 8.1 - - - +
161B PRO* 3.7 30.1 - - + -
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Residues in contact with ARG 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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466A LEU* 4.4 5.3 + - - +
467A SER* 3.5 43.9 + - - +
469A GLU* 5.4 5.1 + - - +
152B ARG* 2.6 35.6 + - + +
153B ALA* 3.0 9.4 + - - +
154B LEU 3.0 0.2 + - - -
155B VAL* 1.3 83.8 - - - +
157B THR* 1.3 63.7 + - + +
158B GLY* 3.1 5.4 + - - -
198B LYS* 4.6 9.2 + - - -
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Residues in contact with THR 157 (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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153B ALA 3.5 6.1 + - - +
154B LEU 3.0 9.3 + - - -
156B ARG* 1.3 82.2 - - + +
158B GLY* 1.3 59.1 + - - +
159B MET* 3.3 12.5 + - - +
191B MET* 3.4 28.0 - - + +
194B ILE* 3.9 35.1 - - + +
195B ARG* 4.0 33.0 - - + +
198B LYS* 4.6 16.9 - - + +
253B ILE* 5.2 1.6 - - - +
257B ILE* 4.6 2.3 - - - +
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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