Contacts of the strand formed by residues 159 - 167 (chain B) in PDB entry 6QPA
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 THR 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 5.8 0.7 - - - +
158B ARG* 1.3 79.0 + - - +
160B VAL* 1.3 72.2 + - - +
161B VAL* 4.2 4.3 - - + -
257B ILE 4.0 0.2 - - - +
258B GLU* 3.3 5.5 - - - +
259B TRP* 2.8 32.9 + - - +
260B GLU 4.2 0.4 + - - -
261B SER* 3.1 13.7 - - - -
262B PRO* 3.0 38.8 - - + +
265B ALA* 4.1 21.5 - - + -
298B PHE* 4.2 9.6 - - + -
299B PHE 3.7 10.4 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 6.0 0.9 - - - +
48B LEU* 3.9 37.2 - - + -
158B ARG* 4.2 4.7 + - - +
159B THR* 1.3 77.4 - - - +
161B VAL* 1.3 68.7 + - - +
162B ILE* 4.4 2.9 - - + -
256B HIS* 3.6 30.1 - - + +
257B ILE 3.7 3.6 - - - +
258B GLU* 4.2 21.8 - - + +
298B PHE* 3.5 1.4 - - - -
299B PHE* 2.6 45.9 + - + +
301B PRO* 4.2 15.9 - - + -
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Residues in contact with VAL 161 (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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159B THR* 4.2 1.6 - - + -
160B VAL* 1.3 80.1 - - - +
162B ILE* 1.3 63.2 + - - +
255B VAL 3.6 0.2 - - - +
256B HIS* 3.5 3.3 - - - -
257B ILE* 2.8 41.9 + - + +
259B TRP* 4.2 5.2 - - + -
265B ALA* 3.8 22.4 - - + -
269B LEU* 3.7 15.3 - - + -
296B TYR* 3.2 35.9 - - + -
297B MET 3.3 4.7 - - - +
298B PHE* 3.5 34.8 - - + -
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Residues in contact with ILE 162 (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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48B LEU* 4.0 8.7 - - + -
77B PHE* 3.6 26.7 - - + -
79B TYR* 3.4 26.5 - - + +
160B VAL* 4.4 5.4 - - + -
161B VAL* 1.3 77.9 - - - +
163B GLY* 1.3 59.6 + - - +
164B ASP* 3.8 1.3 + - + +
199B MET* 5.2 0.7 - - + -
254B LEU* 4.0 39.3 - - + -
255B VAL 3.4 4.5 - - - +
256B HIS* 4.8 2.2 - - - +
295B TYR 3.4 2.6 - - - +
296B TYR* 3.4 4.6 - - - -
297B MET* 2.9 39.0 + - + +
299B PHE* 3.5 31.6 - - + -
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Residues in contact with GLY 163 (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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162B ILE* 1.3 72.5 - - - +
164B ASP* 1.3 60.8 + - - -
165B HIS* 2.9 14.4 + - - -
254B LEU* 3.4 4.2 - - - -
255B VAL 2.8 38.7 + - - -
295B TYR 3.3 7.0 - - - -
296B TYR* 3.3 29.2 - - - -
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Residues in contact with ASP 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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162B ILE* 3.8 2.3 + - + +
163B GLY* 1.3 70.8 - - - -
165B HIS* 1.3 62.5 + - - +
166B TRP* 3.5 18.3 + - - -
252B GLN* 3.1 33.9 + - - +
254B LEU* 3.9 11.6 - - + +
292B LYS* 4.3 0.8 - - - +
293B GLY* 3.8 5.0 - - - -
294B PRO* 3.4 7.3 - - - +
295B TYR* 2.7 44.3 + - + +
297B MET* 6.4 2.0 - - - -
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Residues in contact with HIS 165 (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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163B GLY* 2.9 35.2 + - - -
164B ASP* 1.3 72.3 + - - +
166B TRP* 1.3 64.0 + - - +
167B VAL* 4.0 1.1 - - + -
175B PHE* 3.9 15.9 - + + -
251B THR 3.6 0.3 - - - +
252B GLN* 3.4 4.2 - - - -
253B TYR* 2.8 42.7 + - + +
255B VAL* 3.5 23.5 - - + +
282B HIS* 5.1 1.6 + - - -
286B VAL* 3.9 28.2 - - + +
290B LEU* 3.8 19.1 - - + -
292B LYS 3.7 4.3 - - - -
294B PRO* 3.4 27.4 - - + +
296B TYR* 3.7 16.6 + - - -
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Residues in contact with TRP 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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164B ASP* 3.5 22.2 + - - -
165B HIS* 1.3 81.7 - - - +
167B VAL* 1.3 57.1 + - - +
248B GLN* 3.4 29.9 + - - -
249B THR 5.6 0.2 - - - -
250B PRO* 4.0 35.2 - - + -
251B THR 3.4 3.8 - - - +
252B GLN* 4.2 12.3 - - + +
290B LEU* 3.3 6.1 - - - -
291B ASP* 2.8 31.7 + - + -
292B LYS* 3.0 65.4 + - + +
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Residues in contact with VAL 167 (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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165B HIS* 4.6 2.2 - - + -
166B TRP* 1.3 76.9 - - - +
168B MET* 1.3 76.8 + - - +
169B ASP* 3.5 1.0 + - - -
171B HIS* 3.7 26.5 - - + +
172B GLU* 3.9 8.3 - - + +
175B PHE* 3.5 33.0 - - + -
250B PRO* 3.3 16.8 - - - +
251B THR* 2.9 20.1 + - - +
253B TYR* 3.5 28.3 - - + -
289B HIS 3.4 10.3 - - - +
290B LEU* 4.0 6.7 - - + -
291B ASP* 4.2 2.0 - - - -
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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