Contacts of the strand formed by residues 166 - 178 (chain A) in PDB entry 1QVJ
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 GLY 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 4.8 0.4 - - - -
147A PRO* 3.7 10.4 - - - +
164A ARG 3.5 0.8 + - - -
165A TRP* 1.3 73.4 - - - +
167A PRO* 1.3 63.7 - - - +
168A ASN* 2.7 25.1 + - - -
277A ASN 2.7 22.9 + - - -
279A TRP* 2.9 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU 4.5 4.0 - - - +
133A ARG* 3.5 23.5 - - - +
134A LYS 3.9 11.2 - - - +
135A SER* 4.4 0.2 - - - -
140A TYR* 3.7 27.6 - - + +
164A ARG* 4.1 10.7 - - - +
165A TRP 4.0 3.3 - - - +
166A GLY* 1.3 84.6 - - - +
168A ASN* 1.3 60.4 + - - +
169A HIS* 3.8 16.8 + - + +
279A TRP* 3.6 13.9 - - + +
281A GLU* 3.6 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.3 21.9 - - + +
163A GLY 3.5 3.6 + - - -
164A ARG* 2.9 48.5 + - + +
166A GLY 2.7 29.9 + - - -
167A PRO* 1.3 71.6 - - - +
169A HIS* 1.3 63.5 + - - +
216A MSE 3.9 15.7 - - + +
279A TRP 2.9 13.6 + - - +
280A MSE 3.5 17.4 - - - +
281A GLU 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.6 34.0 + - + +
134A LYS 2.9 25.9 + - - -
136A LYS* 3.8 28.8 + - + +
167A PRO* 3.8 12.4 + - + +
168A ASN* 1.3 72.4 - - - +
170A ALA* 1.3 61.1 + - - +
216A MSE 3.1 12.2 - - - +
217A VAL* 3.0 39.7 + - + +
223A ILE* 4.8 4.0 - - + -
281A GLU* 3.3 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 4.8 0.5 + - - -
169A HIS* 1.3 75.9 - - - +
171A ALA* 1.3 64.0 + - - +
215A GLY 3.2 15.5 - - - +
216A MSE 4.1 0.9 - - - +
217A VAL* 4.1 6.4 - - - +
223A ILE* 4.3 2.9 - - - +
280A MSE 3.8 19.1 - - + -
281A GLU 2.9 13.9 + - - +
282A THR* 3.4 5.7 - - - +
283A GLU* 3.4 19.4 + - - +
554A RP5 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 1.3 76.0 - - - +
172A ASP* 1.3 63.8 + - - +
173A PRO* 3.7 3.1 - - - +
214A GLY* 3.1 4.2 - - - -
215A GLY 2.9 29.5 + - - -
223A ILE* 4.2 13.2 - - + -
226A THR* 3.8 27.1 - - + +
227A LEU* 3.6 24.0 - - + +
230A GLU* 5.0 0.7 - - - +
282A THR* 3.9 0.4 - - - -
283A GLU 3.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 1.3 72.2 - - - +
173A PRO* 1.3 67.9 - - - +
174A ILE* 3.4 3.1 + - - +
212A ILE* 4.0 13.5 - - + +
214A GLY* 3.6 12.0 + - - -
227A LEU* 3.7 2.2 - - - -
282A THR* 2.6 26.9 + - - +
283A GLU 3.0 8.3 + - - -
284A ALA* 3.4 15.1 - - + -
285A VAL 3.0 25.3 + - - -
324A HIS* 3.5 15.2 + - - -
327A PHE* 3.9 3.0 - - + -
554A RP5 2.6 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 3.7 3.8 - - - +
172A ASP* 1.3 79.6 - - - +
174A ILE* 1.3 61.3 + - - +
175A ILE* 3.6 20.4 + - + +
212A ILE* 3.2 12.9 - - + +
213A PRO* 3.3 38.8 - - + +
214A GLY* 3.6 7.0 - - - -
227A LEU* 3.6 39.7 - - + +
230A GLU* 4.7 2.0 - - + -
231A PHE* 3.9 11.9 - - + +
257A PHE* 4.7 3.6 - - + -
285A VAL 3.7 4.7 - - - +
287A TYR* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP 3.9 6.7 - - - +
173A PRO* 1.3 71.6 - - - +
175A ILE* 1.3 60.7 + - - +
176A THR* 3.9 19.3 - - + -
199A PHE* 4.0 9.9 - - + -
212A ILE* 3.0 33.4 - - + -
264A ILE* 4.6 5.8 - - + -
284A ALA* 4.4 11.2 - - + -
285A VAL 2.9 13.8 + - - +
286A ASN* 2.9 22.7 + - - +
287A TYR 3.1 10.6 + - - -
327A PHE* 3.9 17.5 - - + -
328A ILE* 3.9 20.2 - - + -
331A VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO* 3.6 20.2 + - + -
174A ILE* 1.3 78.8 - - - +
176A THR* 1.3 62.0 + - - +
199A PHE* 2.9 23.9 - - - +
200A VAL* 3.0 12.2 + - + +
231A PHE* 3.6 47.3 - - + -
256A LEU* 3.9 21.5 - - + -
257A PHE* 4.0 10.8 - - + -
287A TYR* 3.3 12.1 - - + +
295A MSE 4.0 21.8 - - + -
311A TRP* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 3.9 8.7 - - + -
175A ILE* 1.3 81.8 - - - +
177A ARG* 1.3 64.6 + - - +
197A LEU* 4.0 14.0 - - + +
198A GLN 3.1 15.3 - - - +
199A PHE* 3.5 14.8 - - + +
286A ASN* 3.0 25.8 + - - +
287A TYR 3.1 5.3 + - - +
288A HIS* 2.9 21.5 + - - +
289A ASP* 2.9 27.4 + - - +
311A TRP* 4.1 2.6 - - - -
314A ILE* 4.4 2.0 - - + -
331A VAL* 4.1 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 1.3 77.2 - - - +
178A TRP* 1.3 68.7 + - - +
180A ARG* 5.9 2.2 - - - +
197A LEU* 3.5 7.7 - - - +
198A GLN* 2.9 52.4 + - - +
288A HIS* 4.4 2.7 - - - -
289A ASP* 3.8 23.8 - - + +
292A GLY* 5.2 8.5 - - - -
295A MSE 4.4 18.2 + - + +
296A ASP* 5.0 7.2 + - - +
311A TRP* 3.4 62.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 1.3 86.9 + - - +
179A LYS* 1.3 64.3 + - - +
180A ARG* 3.4 19.3 + - - +
186A LYS* 3.6 35.2 - - + -
195A HIS* 3.4 33.2 - - + -
196A ILE 3.4 17.3 - - - +
197A LEU* 3.6 15.3 - - + -
288A HIS* 3.4 16.3 + + - -
289A ASP 4.4 1.6 + - - -
290A GLU* 3.0 47.5 + - - -
335A ARG* 3.3 27.6 - - + -
337A ALA* 3.6 21.1 - - + -
553A TRS 3.5 26.6 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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