Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 3URF
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 PHE 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLN 4.0 11.2 - - - +
164A PRO* 1.3 75.6 - - - +
166A ALA* 1.3 69.8 + - - +
195A LYS* 3.8 34.1 - - + -
196A ILE* 3.4 9.1 - - - +
197A SER* 2.8 67.5 + - - +
199A MET* 3.5 6.4 - - - +
310A ALA 3.1 12.8 - - - +
311A PHE* 4.0 11.0 - - + -
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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
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165A PHE* 1.3 81.6 - - - +
167A HIS* 1.3 63.2 + - - +
168A LEU* 4.2 7.4 - - + -
195A LYS 3.4 7.6 - - - +
196A ILE* 3.6 20.2 - - + -
199A MET* 3.9 2.9 - - - -
206A LEU* 3.7 29.8 - - + -
217A TYR* 3.8 3.1 + - - -
309A GLY* 3.1 3.7 - - - -
310A ALA 2.8 33.0 + - - +
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Residues in contact with HIS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 5.8 0.2 - - + -
166A ALA* 1.3 75.8 - - - +
168A LEU* 1.3 60.7 + - - +
169A THR* 4.1 10.1 - - + +
193A TRP* 3.1 40.7 - - + +
194A ALA* 3.0 25.5 - - - +
195A LYS* 2.8 33.4 + - + +
217A TYR* 2.8 25.5 + + - +
303A GLN 5.0 1.0 + - - -
307A TYR* 3.4 43.2 - + - -
308A PHE 3.5 3.5 + - - -
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Residues in contact with LEU 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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166A ALA* 4.2 11.2 - - + -
167A HIS* 1.3 87.5 - - - +
169A THR* 1.3 62.2 + - - +
187A TRP* 3.5 14.3 - - + -
188A TYR 3.3 16.8 - - - +
189A HIS* 3.8 20.2 - - + -
195A LYS 4.4 2.5 - - - +
196A ILE* 4.7 4.3 - - + -
201A PHE* 3.6 26.2 - - + -
206A LEU* 4.2 14.4 - - + -
307A TYR* 3.1 5.5 - - - +
308A PHE* 2.8 72.4 + - + +
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Residues in contact with THR 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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167A HIS* 4.1 19.3 + - + +
168A LEU* 1.3 76.6 - - - +
170A ILE* 1.3 63.9 + - - +
187A TRP* 3.4 5.5 - - - -
188A TYR* 2.8 50.9 + - - +
191A ARG 4.5 2.3 + - - -
193A TRP* 4.6 1.1 - - + -
194A ALA* 3.5 20.2 - - + +
303A GLN* 3.8 42.9 + - + +
306A THR 3.6 4.3 - - - -
307A TYR* 4.1 2.2 - - + -
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Residues in contact with ILE 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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169A THR* 1.3 76.5 + - - +
171A ASN* 1.3 67.4 + - - +
172A ALA* 3.8 4.2 + - + +
175A ILE* 4.6 17.9 - - + -
184A LEU* 4.3 16.2 - - + -
186A SER* 3.1 20.4 - - - +
187A TRP* 3.3 26.4 - - + +
188A TYR* 3.6 11.4 - - - -
299A LEU* 5.0 5.6 - - + -
300A ASP 3.8 3.4 - - - +
301A PRO* 3.6 34.4 - - + +
302A ASP 4.4 2.2 - - - +
303A GLN* 5.6 1.0 - - - -
306A THR* 2.9 43.8 + - + +
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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