Contacts of the strand formed by residues 169 - 177 (chain C) in PDB entry 4QY2
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 HIS 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C ILE* 4.2 18.6 - - + +
161C TYR* 2.5 33.7 + - + +
163C ASN* 3.1 25.3 + - - +
164C THR 5.3 0.4 - - - -
165C ASP* 3.2 31.1 + - + +
167C ALA 3.2 12.3 - - - -
168C GLU* 1.3 79.8 - - - +
170C LEU* 1.3 61.2 + - - +
171C ILE 3.6 0.5 + - - -
229C LEU* 3.2 7.2 - - - -
230C VAL* 2.7 40.6 + - + +
250C VAL* 3.6 16.4 - - + +
251C SER 3.4 9.0 - - - +
252C LYS* 4.1 19.2 - - + +
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Residues in contact with LEU 170 (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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60C LEU* 4.0 13.9 - - + -
98C LEU* 3.8 20.6 - - + -
101C LYS* 4.2 12.6 - - + -
168C GLU 4.4 0.4 + - - -
169C HIS* 1.3 70.8 - - - +
171C ILE* 1.3 62.8 + - - +
172C MET* 4.0 12.4 + - + +
227C TRP* 3.7 38.8 - - + -
228C THR 3.6 4.0 - - - +
229C LEU* 3.7 21.7 - - + +
250C VAL* 3.8 1.8 - - - +
251C SER* 2.7 50.0 + - - +
252C LYS* 4.8 1.0 - - - +
253C LEU* 4.4 19.9 - - + +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C THR* 5.0 0.4 - - + -
161C TYR* 4.5 9.6 - - + -
169C HIS 3.6 1.2 + - - -
170C LEU* 1.3 73.2 - - - +
172C MET* 1.3 70.9 + - - +
173C TRP* 3.8 8.9 - - + -
227C TRP* 3.2 6.2 - - - +
228C THR* 3.0 39.0 + - - +
230C VAL* 3.5 25.4 - - + -
236C ILE* 4.1 25.4 - - + -
238C PHE* 3.6 33.7 - - + -
247C PRO* 3.9 10.3 - - + -
250C VAL* 3.5 28.5 - - + +
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Residues in contact with MET 172 (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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57C ILE* 4.7 6.1 - - + -
60C LEU* 3.8 23.8 - - + +
61C ILE* 3.8 30.7 - - + -
92C THR* 4.2 9.4 - - + +
98C LEU* 3.8 27.6 - - + -
142C LEU* 3.9 6.1 - - + +
170C LEU* 4.0 9.7 + - + +
171C ILE* 1.3 75.3 - - - +
173C TRP* 1.3 64.1 + - - +
225C PHE* 3.7 29.8 - - + -
226C HIS 3.3 9.4 - - - +
227C TRP* 3.6 16.6 - - + -
247C PRO* 3.3 25.3 - - - +
249C ARG 5.3 1.6 + - - +
250C VAL* 5.3 0.6 - - - +
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Residues in contact with TRP 173 (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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142C LEU* 4.1 5.8 - - - -
171C ILE* 3.8 22.9 - - + -
172C MET* 1.3 81.4 - - - +
174C GLY* 1.3 70.1 + - - +
175C ILE* 4.0 10.7 - - + +
197C VAL* 4.1 13.0 - - + +
202C TYR* 3.4 43.1 - + - -
206C PHE* 3.6 25.5 - + - -
225C PHE* 3.3 10.5 - - - +
226C HIS* 2.9 52.0 + - + +
227C TRP* 3.8 12.8 - - - -
228C THR* 3.9 12.3 - - - -
236C ILE* 4.8 0.7 - - + -
238C PHE* 3.7 30.1 - + + -
244C LEU* 4.0 7.9 - - + -
245C ILE 3.6 12.3 - - - +
247C PRO* 4.0 6.5 - - + -
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Residues in contact with GLY 174 (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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142C LEU* 4.7 0.2 - - - +
173C TRP* 1.3 75.0 - - - +
175C ILE* 1.3 70.4 + - - +
223C ILE* 3.8 9.4 - - - -
224C ASP 3.1 9.6 - - - -
225C PHE* 3.9 6.1 - - - -
244C LEU* 3.6 2.8 - - - +
245C ILE* 2.7 46.8 + - - +
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Residues in contact with ILE 175 (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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173C TRP* 4.0 7.4 - - + -
174C GLY* 1.3 82.9 - - - +
176C HIS* 1.3 68.7 + - - +
177C HIS* 3.4 24.7 - - + +
195C ILE* 3.9 23.6 - - + -
206C PHE* 3.6 47.8 - - + -
207C VAL 4.8 0.4 - - - -
208C PRO* 4.3 13.7 - - + -
223C ILE* 3.3 5.5 - - - +
224C ASP* 2.7 34.4 + - + +
226C HIS* 3.9 18.6 - - + +
243C GLY 3.3 5.6 - - - +
244C LEU* 4.6 0.9 - - + -
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Residues in contact with HIS 176 (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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88C TYR* 3.1 23.5 + - - -
144C TRP* 3.3 24.3 - + - -
175C ILE* 1.3 73.1 - - - +
177C HIS* 1.3 62.2 + - - +
178C PRO* 3.5 29.0 - - + +
183C GLU* 3.5 18.7 + - - -
187C LEU* 4.0 5.6 - - + -
188C TYR* 2.8 27.8 + - + +
208C PRO* 3.2 29.1 - - - +
222C ARG 3.1 25.1 - - - -
223C ILE* 4.0 12.1 - - + -
243C GLY* 2.7 18.9 + - - +
245C ILE* 4.2 11.7 - - + +
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Residues in contact with HIS 177 (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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175C ILE* 3.4 35.7 - - + +
176C HIS* 1.3 72.1 - - - +
178C PRO* 1.3 64.4 - - - +
207C VAL 3.4 24.7 - - - -
208C PRO* 3.8 3.6 - - + +
209C VAL* 3.0 30.8 + - + +
213C ARG* 2.9 17.5 + - - +
222C ARG* 2.8 37.0 + - + +
224C ASP* 3.5 14.6 + - - +
226C HIS* 5.9 0.4 - - - -
203E ARG* 3.0 47.1 + - - +
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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