Contacts of the strand formed by residues 165 - 168 (chain A) in PDB entry 4AFZ
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 GLN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A THR 4.3 7.1 + - - -
86A LEU 4.2 12.3 + - - -
87A HIS* 3.6 27.9 + - + +
88A HIS 5.9 1.3 - - - +
158A ARG 5.5 0.4 + - - -
160A PHE* 3.4 32.2 - - + +
161A ASP 2.7 36.4 + - - +
162A HIS* 3.4 17.5 - - - +
163A ASN 3.7 0.8 - - - -
164A LEU* 1.3 86.5 - - + +
166A LEU* 1.3 63.7 + - - +
197A SER* 5.5 0.2 + - - -
198A TYR* 4.3 5.1 + - - -
208A VAL* 3.4 25.6 - - + +
209A PHE 3.2 9.6 - - - +
210A THR* 4.9 2.9 - - + -
211A ARG* 3.7 8.3 + - - +
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Residues in contact with LEU 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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117A VAL* 4.0 12.8 - - + +
148A LEU* 4.4 10.8 - - + -
160A PHE* 3.6 10.2 - - - -
162A HIS* 6.1 0.4 - - - -
165A GLN* 1.3 75.7 - - - +
167A CYS* 1.3 60.3 + - - +
168A VAL* 3.8 10.8 - - + -
186A LEU* 3.6 29.4 - - + -
193A GLN* 3.8 9.2 - - + +
194A GLY* 3.8 20.6 - - - -
208A VAL* 3.6 1.7 - - - -
209A PHE* 2.7 33.6 + - + +
211A ARG* 3.3 56.5 - - + +
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Residues in contact with CYS 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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148A LEU* 3.6 4.6 - - - +
149A MET* 2.7 54.9 + - - +
150A ASP 3.9 5.8 - - - +
151A PRO* 4.5 1.8 - - + -
153A ALA 3.9 0.7 - - - -
154A CYS* 2.1 58.8 - - + -
160A PHE* 3.7 11.6 - - + -
166A LEU* 1.3 73.5 - - - +
168A VAL* 1.3 59.6 + - - +
206A PRO* 3.6 12.8 - - - -
207A ALA 3.9 0.2 - - - -
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Residues in contact with VAL 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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123A CYS* 5.9 0.4 - - + -
146A LEU* 3.7 36.0 - - + +
147A ARG 3.7 5.6 - - - +
148A LEU* 3.7 20.0 - - + -
166A LEU* 3.8 11.4 - - + -
167A CYS* 1.3 77.7 - - - +
169A GLY* 1.3 61.8 + - - +
176A SER* 5.3 1.2 + - - -
186A LEU* 4.0 18.8 - - + -
205A PRO* 4.7 0.5 - - - +
206A PRO* 3.2 4.0 - - - +
207A ALA* 2.8 38.4 + - - +
209A PHE* 3.5 39.3 - - + -
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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