Contacts of the helix formed by residues 164 - 170 (chain A) in PDB entry 4RTL
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 SER 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.1 14.5 - - - +
163A GLU* 1.3 77.2 - - - +
165A TYR* 1.3 81.5 + - - +
166A ALA* 3.3 4.5 + - - +
167A ASP* 3.1 23.8 + - - +
168A SER* 3.4 11.0 + - - -
205A GLN* 5.6 0.7 + - - -
301A SFG 3.4 23.1 + - - -
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Residues in contact with TYR 165 (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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34A PRO* 4.4 8.7 - - + -
35A PHE* 3.9 26.5 - + + -
164A SER* 1.3 91.2 + - - +
166A ALA* 1.3 67.9 + - + +
168A SER* 3.8 7.2 - - - -
169A MET* 3.1 36.5 + - - +
201A PHE* 4.3 20.6 - + - -
205A GLN* 3.9 35.4 + - - +
208A HIS* 3.1 33.0 + + - +
209A LEU* 4.1 28.3 - - + -
212A ILE* 4.3 9.2 - - + -
301A SFG 3.6 17.9 + + + +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 3.2 3.6 + - - +
165A TYR* 1.3 92.2 - - + +
167A ASP* 1.3 67.7 + - - +
169A MET* 3.8 2.1 + - - +
170A ALA* 3.6 19.9 + - - +
208A HIS* 4.9 7.6 - - + -
212A ILE* 4.2 22.6 - - + +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 3.8 21.7 - - + +
164A SER* 3.1 20.1 + - - +
166A ALA* 1.3 83.6 - - - +
168A SER* 1.3 63.4 + - - +
170A ALA* 3.6 14.6 + - - +
171A ARG* 4.0 9.5 + - - +
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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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32A VAL* 4.4 15.2 - - - +
33A GLU 6.1 0.2 - - - -
34A PRO* 3.6 23.6 + - - +
51A ILE* 5.6 3.7 - - - +
53A ALA* 4.0 20.8 - - - +
163A GLU* 3.3 22.2 + - - -
164A SER 3.4 7.8 + - - -
165A TYR* 3.5 9.9 + - - -
167A ASP* 1.3 73.7 - - - +
169A MET* 1.3 67.7 + - - +
170A ALA 3.1 2.0 - - - -
171A ARG* 3.1 24.1 + - - +
172A ALA 4.4 0.5 + - - -
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Residues in contact with MET 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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32A VAL* 5.3 4.0 - - - -
34A PRO* 3.7 25.8 - - + -
165A TYR* 3.1 27.1 + - - +
166A ALA 4.3 3.6 - - - +
168A SER* 1.3 76.4 + - - +
170A ALA* 1.3 58.5 + - - +
171A ARG 3.2 1.7 + - - -
172A ALA* 3.5 19.7 + - - +
178A VAL* 4.7 9.4 - - + -
180A CYS* 4.1 18.2 - - - -
209A LEU* 3.8 25.1 - - + +
212A ILE* 3.6 33.4 - - + -
213A ALA* 4.7 10.3 - - + +
216A LEU* 4.1 30.0 - - + +
223A VAL* 5.2 1.8 - - + -
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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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166A ALA 3.6 15.6 + - - +
167A ASP* 3.8 9.6 - - - +
168A SER 3.1 1.2 - - - -
169A MET* 1.3 75.8 - - - +
171A ARG* 1.3 61.0 + - - +
172A ALA 3.3 5.1 + - - +
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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