Contacts of the strand formed by residues 159 - 167 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C THR* 5.8 0.9 - - - +
158C ARG* 1.3 74.9 - - - +
160C VAL* 1.3 65.1 + - - +
161C VAL* 4.0 23.3 - - + -
257C ILE 3.9 0.5 - - - +
258C GLU* 3.3 4.5 - - - +
259C TRP* 2.7 41.9 + - - +
260C GLU 4.2 0.4 + - - -
261C SER* 3.2 12.5 - - - -
262C PRO* 3.0 33.8 - - + +
265C ALA* 4.1 11.2 - - + -
298C PHE* 4.3 13.5 - - + -
299C PHE 3.8 11.7 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 5.8 1.3 - - - +
48C LEU* 4.0 33.4 - - + -
158C ARG* 4.1 5.1 + - - +
159C THR* 1.3 77.3 - - - +
161C VAL* 1.3 66.8 + - - +
162C ILE* 4.3 5.6 - - + -
256C HIS* 3.5 31.9 - - + +
257C ILE 3.6 4.0 - - - +
258C GLU* 4.1 21.5 - - + +
298C PHE* 3.7 0.7 - - - -
299C PHE* 2.7 45.1 + - + +
301C PRO* 4.3 16.8 - - + -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C THR* 4.0 3.1 - - + -
160C VAL* 1.3 76.9 - - - +
162C ILE* 1.3 63.2 + - - +
255C VAL 3.4 1.4 - - - +
256C HIS* 3.5 2.6 - - - -
257C ILE* 2.8 42.0 + - + +
259C TRP* 4.1 4.7 - - + +
265C ALA* 3.8 23.3 - - + -
269C LEU* 3.6 14.1 - - + -
296C TYR* 3.2 37.0 - - + -
297C MET 3.4 5.2 - - - +
298C PHE* 3.5 33.2 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.0 9.2 - - + -
77C PHE* 3.7 23.8 - - + -
79C TYR* 3.3 26.9 - - + +
160C VAL* 4.3 5.6 - - + -
161C VAL* 1.3 79.2 - - - +
163C GLY* 1.3 61.5 + - - +
164C ASP* 3.9 1.3 + - + +
199C MET* 5.3 0.2 - - + -
254C LEU* 3.9 40.2 - - + -
255C VAL 3.4 5.2 - - - +
256C HIS* 4.8 3.1 - - - +
295C TYR 3.3 2.8 - - - +
296C TYR* 3.3 3.4 - - - -
297C MET* 2.9 36.9 + - + +
299C PHE* 3.5 33.0 - - + -
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ILE* 1.3 71.4 - - - +
164C ASP* 1.3 60.0 + - - -
165C HIS* 2.9 18.8 + - - -
254C LEU* 3.4 5.8 - - - -
255C VAL 2.9 33.0 + - - -
295C TYR 3.2 7.0 - - - -
296C TYR* 3.3 28.8 - - - -
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Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ILE* 3.9 2.3 + - + +
163C GLY* 1.3 71.1 - - - -
165C HIS* 1.3 63.0 + - - +
166C TRP* 3.4 18.4 + - - -
252C GLN* 2.9 33.0 + - - +
254C LEU* 3.8 11.5 - - + +
292C LYS* 5.5 1.1 - - - -
293C GLY* 3.8 4.5 - - - -
294C PRO* 3.4 7.3 - - - +
295C TYR* 2.7 45.4 + - + +
297C MET* 6.3 2.9 - - - -
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Residues in contact with HIS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLY* 2.9 35.8 + - - -
164C ASP* 1.3 72.0 + - - +
166C TRP* 1.3 70.3 + - - +
167C VAL* 4.0 1.8 - - + -
175C PHE* 3.7 27.6 - + + -
251C THR 3.7 0.2 - - - +
252C GLN* 3.4 0.7 - - - +
253C TYR* 2.9 41.5 + - + +
255C VAL* 3.5 22.8 - - + +
282C HIS* 5.3 1.4 + - - -
286C VAL* 3.9 13.8 - - + +
290C LEU* 3.8 22.9 - - + -
292C LYS 3.6 4.9 - - - -
294C PRO* 3.5 25.9 - - + +
296C TYR* 3.9 16.2 + - - -
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Residues in contact with TRP 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ASP* 3.4 21.9 + - - -
165C HIS* 1.3 80.9 - - - +
167C VAL* 1.3 56.1 + - - +
248C GLN* 3.4 30.8 + - - -
249C THR 5.6 0.7 - - - -
250C PRO* 4.1 35.0 - - + -
251C THR 3.5 4.0 - - - -
252C GLN* 4.1 11.6 - - + +
290C LEU* 3.3 5.9 - - - +
291C ASP* 2.7 32.7 + - + -
292C LYS* 2.9 62.9 + - + +
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C HIS* 4.6 2.5 - - + -
166C TRP* 1.3 76.7 - - - +
168C MET* 1.3 77.0 + - - +
169C ASP* 3.5 0.7 + - - -
171C HIS 3.7 24.9 - - - +
172C GLU* 3.9 8.0 - - + +
175C PHE* 3.5 34.1 - - + -
250C PRO* 3.4 17.3 - - - +
251C THR* 2.9 19.1 + - - +
253C TYR* 3.5 30.5 - - + -
289C HIS 3.4 12.3 - - - +
290C LEU* 4.2 4.3 - - + -
291C ASP* 4.1 2.2 - - - -
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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