Contacts of the helix formed by residues 165 - 170 (chain A) in PDB entry 3JRQ
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LEU* 5.9 0.7 - - - +
163A ARG* 3.5 16.4 + - + +
164A PHE* 1.3 84.5 - - - +
166A PRO* 1.3 73.5 - - - +
167A GLN* 3.0 43.6 + - - +
168A SER* 2.9 29.4 + - - +
169A ALA 4.6 0.3 + - - -
207A LEU* 4.9 1.2 - - - +
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE* 4.0 30.7 - - + +
165A ASP* 1.3 93.2 - - - +
167A GLN* 1.3 59.0 + - - +
168A SER 3.3 0.2 - - - -
169A ALA* 3.3 22.2 - - - +
207A LEU* 3.7 24.7 - - + -
250A PHE* 5.1 1.3 - - - -
251A PRO* 5.0 5.9 - - - +
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.1 12.4 - - + +
165A ASP* 3.0 30.3 + - - +
166A PRO* 1.3 74.1 - - - +
168A SER* 1.3 58.1 + - - +
169A ALA 3.0 6.3 - - - -
170A ALA* 2.8 31.7 + - - +
200A ILE* 5.3 1.6 - - - +
205A PRO* 3.0 28.9 + - - +
206A MET* 4.7 0.2 - - - +
207A LEU* 4.3 15.7 - - + +
213A TRP* 3.0 20.3 + - + +
217A TRP* 2.6 32.2 + - - -
250A PHE* 3.6 17.6 - - + -
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.3 35.8 + - - +
152A LEU* 4.1 20.6 - - - +
153A GLN* 3.1 33.2 + - - -
165A ASP* 2.9 22.7 + - - +
167A GLN* 1.3 74.5 - - - +
169A ALA* 1.3 54.0 + - - +
170A ALA 3.0 6.0 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A SER* 4.6 6.1 - - - +
150A ARG* 3.7 23.0 - - - +
166A PRO 3.3 17.7 + - - +
167A GLN 3.0 0.8 - - - -
168A SER* 1.3 77.6 + - - +
170A ALA* 1.3 63.3 + - - +
171A HIS* 3.1 26.9 + - - -
249A VAL 4.0 2.2 - - - +
251A PRO* 4.0 25.3 - - + +
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.2 20.8 - - - -
151A PHE* 3.2 30.6 + - + -
152A LEU* 4.6 2.4 + - + -
167A GLN 2.8 17.3 + - - +
168A SER 3.0 1.6 - - - -
169A ALA* 1.3 75.6 - - - +
171A HIS* 1.3 58.1 + - - +
217A TRP* 4.5 2.5 - - + -
248A VAL* 3.9 4.9 - - + -
249A VAL 3.5 7.6 - - - -
250A PHE* 3.5 28.0 - - + -
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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