Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 3QN3
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 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASN* 3.5 31.0 + - - +
154B HIS* 3.7 9.5 - - - +
161B PHE* 3.7 1.5 - - - +
162B GLN* 1.3 108.0 + - + +
164B PHE* 1.3 64.0 + - - +
165B MET* 4.0 10.0 - - + +
204B GLU* 4.2 9.0 - - - +
237B ALA 4.0 0.3 - - - +
238B LEU* 3.4 7.4 - - - +
239B ASP* 2.9 50.7 + - + +
383B LYS* 2.8 36.2 + - - +
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASN* 3.3 0.8 + - - -
148B ILE* 3.1 25.8 + - - +
149B ILE* 2.8 34.7 + - + +
150B ASN 4.7 0.9 - - - -
151B GLY 4.8 0.9 - - - -
159B VAL* 3.5 31.4 - - + -
161B PHE* 3.6 34.8 - + + -
163B GLU* 1.3 75.9 - - - +
165B MET* 1.3 59.8 + - - +
214B ASN* 3.4 25.6 - - - -
217B PRO* 3.7 23.3 - - + -
218B ILE* 3.8 15.0 - - + -
221B LEU* 3.9 16.3 - - + +
237B ALA 3.9 2.5 - - - -
238B LEU* 3.6 22.2 - - + -
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 3.8 33.4 - - + +
146B CYS 3.1 12.6 - - - +
147B ASN* 3.5 23.8 - - + +
163B GLU* 4.0 16.6 - - + +
164B PHE* 1.3 74.7 - - - +
166B ILE* 1.3 67.1 + - - +
221B LEU* 4.2 1.1 - - - +
236B ILE* 3.3 10.4 - - - +
237B ALA* 2.8 45.5 + - + +
238B LEU 3.8 30.5 - - - +
239B ASP* 3.8 7.2 - - + +
280B GLU* 4.7 3.1 - - + +
383B LYS* 3.7 25.4 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PRO 3.6 2.1 - - - +
145B MET* 3.5 2.6 - - - -
146B CYS* 3.0 39.4 + - + +
148B ILE* 3.9 13.2 - - + -
165B MET* 1.3 78.2 - - - +
167B MET* 1.3 60.9 + - - +
168B PRO* 4.1 1.2 - - - +
181B VAL* 3.7 34.5 - - + +
184B ILE* 3.7 32.5 - - + -
221B LEU* 4.0 28.3 - - + -
225B ILE* 4.4 14.1 - - + -
234B VAL* 3.7 14.6 - - + -
235B LYS 3.4 2.5 - - - -
236B ILE* 4.4 1.6 - - + -
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Residues in contact with MET 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.8 26.2 - - + +
144B PRO 3.6 1.1 - - - +
145B MET* 3.4 44.9 - - + -
166B ILE* 1.3 72.6 - - - +
168B PRO* 1.3 64.0 - - - +
169B PHE* 3.3 35.7 + - + -
234B VAL* 3.9 2.7 - - - +
235B LYS 2.8 40.5 + - - +
237B ALA* 4.0 10.3 - - + -
277B CYS* 3.6 23.1 - - - -
278B SER* 4.9 1.8 - - - -
303B GLN* 5.5 0.2 - - - -
381B GLN* 3.6 23.1 - - + +
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Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 3.9 4.3 - - + -
144B PRO* 3.1 36.6 - - + +
167B MET* 1.3 79.5 - - - +
169B PHE* 1.3 60.7 + - - +
170B GLY 3.6 1.6 - - - -
171B PHE* 3.6 12.6 - - + -
177B ALA* 3.8 13.7 - - + +
180B SER* 3.6 22.9 - - - +
181B VAL* 3.7 22.7 - - + -
233B ARG 3.9 6.5 - - - +
234B VAL* 4.2 4.0 - - + -
409B TYR* 2.6 29.3 + - - -
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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