Contacts of the strand formed by residues 290 - 305 (chain A) 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 LEU 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A HIS* 3.8 39.7 - - + -
166A TRP 3.3 12.1 - - - +
167A VAL* 4.0 5.8 - - + -
168A MET* 3.7 11.7 - - - +
175A PHE* 3.9 17.7 - - + -
286A VAL* 3.3 20.4 - - + +
287A LEU* 3.5 21.5 + - + +
288A ALA 3.6 1.2 + - - +
289A HIS* 1.3 77.1 - - - +
291A ASP* 1.3 61.3 - - - +
292A LYS 4.0 8.5 - - - +
293A GLY 3.7 26.0 - - - +
294A PRO* 3.8 8.1 - - + -
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TRP* 2.7 16.3 + - + +
168A MET* 3.5 35.1 - - - +
169A ASP 4.5 1.6 + - - -
250A PRO* 3.4 31.0 - - + +
290A LEU* 1.3 73.3 - - - +
292A LYS* 1.3 58.7 + - + +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 4.7 1.1 - - - +
165A HIS* 3.6 3.6 - - - -
166A TRP* 3.0 87.3 + - + +
290A LEU* 3.5 6.5 - - - +
291A ASP* 1.3 80.6 - - - +
293A GLY* 1.3 67.4 + - - +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 5.4 3.4 - - - -
164A ASP 3.8 5.4 - - - -
287A LEU* 4.9 0.9 - - - +
290A LEU* 3.7 10.2 - - - +
292A LYS* 1.3 84.1 - - - +
294A PRO* 1.3 77.4 - - - +
295A TYR* 3.9 3.4 - - - -
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Residues in contact with PRO 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET* 3.6 33.0 - - + +
60A TYR* 3.9 8.7 + - - -
164A ASP 3.5 5.8 - - - +
165A HIS* 3.3 28.7 - - + +
282A HIS* 4.5 9.6 - - + -
287A LEU* 3.5 30.3 - - + -
290A LEU* 3.8 3.1 - - + -
293A GLY* 1.3 84.6 - - - +
295A TYR* 1.3 59.5 + - - +
296A TYR* 3.7 21.3 - - + -
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 5.4 0.2 + - - -
53A ILE* 3.3 31.6 - - + +
54A HIS 5.4 0.4 - - - -
56A MET* 5.1 0.4 - - - -
60A TYR* 3.4 53.6 - + - +
162A ILE 3.3 2.6 - - - +
163A GLY* 3.2 0.5 - - - -
164A ASP* 2.7 48.5 + - + +
293A GLY* 5.0 3.1 - - - -
294A PRO* 1.3 74.3 - - - +
296A TYR* 1.3 63.4 + - - +
297A MET* 3.7 30.9 - - + +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.4 7.4 - - - +
54A HIS* 3.0 44.2 + + + +
56A MET* 4.6 14.3 - - + -
60A TYR* 5.7 0.2 - - - -
161A VAL* 3.2 26.7 - - + -
162A ILE 3.3 0.7 - - - -
163A GLY* 3.3 24.5 - - - -
165A HIS* 3.8 15.3 + + - -
255A VAL* 4.3 10.5 - - - +
257A ILE* 4.1 10.5 - - + +
269A LEU* 3.7 34.1 - - + +
282A HIS* 5.0 8.9 + + - -
294A PRO* 3.7 25.1 - - + -
295A TYR* 1.3 80.4 - - - +
297A MET* 1.3 60.8 + - - +
298A PHE* 4.7 0.9 - - + -
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Residues in contact with MET 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 4.2 16.6 - - - +
50A GLN* 3.3 36.6 - - - +
52A GLY 3.7 3.6 - - - -
53A ILE* 4.3 0.9 - - + +
75A GLY* 4.6 2.9 - - - -
77A PHE* 4.4 17.9 - - + -
161A VAL* 3.3 4.7 - - - -
162A ILE* 3.0 36.1 + - + +
164A ASP* 6.3 2.5 - - - -
295A TYR* 3.7 30.5 - - + -
296A TYR* 1.3 73.7 - - - +
298A PHE* 1.3 63.3 + - - +
299A PHE* 3.6 32.3 - - + -
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.3 11.8 - - - +
51A THR* 2.8 39.6 + - - +
52A GLY* 2.8 21.2 + - - +
53A ILE 3.8 11.7 - - - -
54A HIS* 3.6 36.6 - + + -
65A VAL* 3.6 26.9 - - + +
159A THR* 4.3 11.0 - - + -
160A VAL 3.8 3.4 - - - -
161A VAL* 3.5 19.3 - - + -
262A PRO* 3.6 26.2 - - + -
265A ALA* 3.7 17.0 - - + -
266A HIS* 4.0 11.2 - - + -
269A LEU* 4.2 5.4 - - + -
296A TYR 4.3 1.3 - - - -
297A MET* 1.3 76.6 - - - +
299A PHE* 1.3 56.1 + - - +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.6 27.8 - - + -
49A LEU 3.2 9.0 - - - +
50A GLN* 3.4 32.5 - - + -
51A THR* 4.1 5.8 - - - -
75A GLY 4.3 3.8 - - - -
77A PHE* 3.8 35.9 - + - -
159A THR* 3.7 8.5 + - - +
160A VAL* 2.7 45.8 + - + +
162A ILE* 3.6 26.5 - - + -
297A MET* 3.6 47.1 - - + -
298A PHE* 1.3 75.6 - - - +
300A SER* 1.3 59.8 + - - +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.5 0.2 - - - -
49A LEU* 2.8 31.4 + - - -
51A THR* 4.0 18.3 - - - +
156A SER 5.4 2.6 + - - -
158A ARG 4.3 4.5 + - - -
159A THR* 5.3 0.2 - - - +
299A PHE* 1.3 76.0 - - - +
301A PRO* 1.3 73.1 + - - +
302A MET* 3.2 21.3 + - - +
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Residues in contact with PRO 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 4.6 0.7 - - - +
47A GLN 3.3 7.9 - - - +
48A LEU* 3.8 16.4 - - + -
156A SER* 3.5 22.6 - - - +
158A ARG* 3.0 45.3 - - + +
160A VAL* 4.3 14.8 - - + -
299A PHE 4.0 3.8 - - - +
300A SER* 1.3 86.8 + - - +
302A MET* 1.3 63.8 + - - +
303A MET 3.6 0.4 - - - -
304A GLU* 3.8 25.4 - - + +
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 6.1 3.6 - - + -
25A MET* 5.8 5.4 - - + -
47A GLN* 2.7 35.5 + - + +
49A LEU* 4.0 34.1 - - + -
156A SER* 3.2 15.2 + - - -
300A SER* 3.2 24.4 + - - +
301A PRO* 1.3 72.7 - - - +
303A MET* 1.3 64.9 + - + +
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Residues in contact with MET 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET* 3.9 20.6 - - + +
26A MET* 4.5 9.2 - - + -
29A GLY 5.2 0.9 - - - -
30A PRO* 4.0 28.3 - - + -
33A CSS 6.2 1.3 - - - -
45A PHE* 3.9 21.9 - - + -
47A GLN* 3.0 53.9 + - + +
156A SER* 4.0 2.2 - - - -
302A MET* 1.3 83.6 - - + +
304A GLU* 1.3 68.4 + - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.7 12.1 - - - +
46A GLU* 2.6 32.0 - - - +
129A ILE* 3.9 22.0 - - + +
155A SER* 3.6 7.8 + - - +
156A SER* 2.8 35.6 + - - +
158A ARG* 2.8 35.5 + - - -
301A PRO* 3.8 15.6 - - + +
303A MET* 1.3 81.5 - - - +
305A GLN* 1.3 60.8 + - - +
306A GLY 3.8 1.7 + - - +
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Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.6 10.4 + - + -
43A LEU 3.8 13.4 + - - -
44A GLY* 3.5 18.4 - - - -
45A PHE* 3.1 49.8 + - + +
304A GLU* 1.3 72.3 - - - +
306A GLY* 1.3 58.3 + - - +
307A LEU* 3.0 34.2 + - - +
308A TRP* 3.3 8.7 - - - -
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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