Contacts of the strand formed by residues 165 - 169 (chain A) in PDB entry 2PU1
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 GLU 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASN* 3.5 29.8 + - + +
151A ILE 4.0 0.2 - - - -
163A PHE 3.7 1.0 - - - -
164A GLN* 1.3 104.5 - - + +
166A PHE* 1.3 62.9 + - - +
167A MET* 3.4 19.0 - - + +
208A GLU* 3.9 14.6 - - - +
242A MET* 3.1 13.2 - - - +
243A ASP* 2.8 45.2 + - + +
371A HIS* 5.2 0.2 + - - -
394A LYS* 2.8 34.5 + - - +
600A FSG 3.4 8.7 + - - +
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Residues in contact with PHE 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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149A ASN* 3.5 0.6 + - - -
150A VAL* 3.1 25.1 + - - +
151A ILE* 2.8 39.3 + - + +
152A ASN* 4.4 0.9 - - - -
161A LEU* 3.6 22.7 - - + -
163A PHE* 3.9 16.2 - - + -
165A GLU* 1.3 75.9 - - - +
167A MET* 1.3 61.9 + - - +
218A ILE* 3.1 39.5 - - + -
221A PRO* 3.6 26.2 - - + -
222A LEU* 3.8 16.2 - - + -
225A LEU* 4.1 11.7 - - + -
242A MET* 3.3 36.3 - - + -
281A TRP* 4.6 2.7 - + - -
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Residues in contact with MET 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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147A CYS* 3.9 25.4 - - - +
148A PHE 3.1 11.2 - - - +
149A ASN* 3.6 25.1 - - + +
165A GLU* 3.4 21.8 - - + +
166A PHE* 1.3 75.2 - - - +
168A ILE* 1.3 67.1 + - - +
225A LEU* 4.1 1.1 - - - +
240A ILE* 3.2 13.9 - - - +
241A CYS* 2.8 47.5 + - + +
242A MET 3.8 29.2 - - - +
243A ASP* 3.8 4.3 - - + +
291A GLU* 4.5 2.7 - - + +
368A MET* 5.3 3.1 - - - +
394A LYS* 3.8 24.7 - - + -
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Residues in contact with ILE 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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147A CYS* 4.6 0.7 - - - -
148A PHE* 2.8 50.4 + - + +
150A VAL* 4.0 18.8 - - + -
167A MET* 1.3 77.3 - - - +
169A ALA* 1.3 60.6 + - - +
170A PRO* 4.4 0.2 - - - -
183A GLY* 4.3 10.1 - - - +
186A VAL* 3.5 35.4 - - + -
187A TYR* 4.6 1.8 - - - +
190A LEU* 6.0 0.4 - - + -
225A LEU* 4.0 34.5 - - + -
229A ILE* 4.3 16.2 - - + -
238A PHE* 3.8 18.2 - - + -
239A ALA 3.5 4.0 - - - +
240A ILE* 5.0 1.1 - - + -
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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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145A VAL* 4.1 2.5 - - + -
146A PRO 3.6 11.2 - - - +
147A CYS* 3.9 19.7 - - - -
168A ILE* 1.3 75.5 - - - +
170A PRO* 1.4 56.9 - - + +
171A VAL* 2.9 29.0 + - + +
238A PHE* 3.3 4.3 - - - -
239A ALA* 2.8 41.9 + - + +
241A CYS* 4.2 11.9 - - - -
428A TRP* 5.0 0.9 - - + -
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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