Contacts of the strand formed by residues 290 - 305 (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 LEU 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B HIS* 3.8 31.6 - - + -
166B TRP 3.3 12.6 - - - +
167B VAL* 4.0 11.0 - - + -
168B MET* 3.8 11.1 - - - +
175B PHE* 4.0 8.1 - - + -
286B VAL* 3.4 17.7 - - + +
287B LEU* 3.4 24.3 + - + +
288B ALA 3.6 1.4 - - - -
289B HIS* 1.3 79.8 - - - +
291B ASP* 1.3 60.5 + - - +
292B LYS 3.9 8.5 - - - +
293B GLY 3.6 24.7 - - - +
294B PRO* 3.7 17.5 - - + -
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Residues in contact with ASP 291 (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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166B TRP* 2.8 13.9 + - + +
168B MET* 3.4 31.8 - - - +
169B ASP 4.4 1.4 + - - -
250B PRO* 3.3 35.0 - - + +
290B LEU* 1.3 73.0 - - - +
292B LYS* 1.3 60.3 + - + +
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Residues in contact with LYS 292 (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* 4.8 0.9 - - - -
165B HIS* 3.7 3.7 - - - -
166B TRP* 3.0 84.9 + - + +
290B LEU* 3.5 6.8 - - - +
291B ASP* 1.3 80.5 - - - +
293B GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 293 (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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60B TYR* 5.2 4.5 - - - -
164B ASP 3.8 6.3 - - - -
287B LEU* 4.9 0.5 - - - +
290B LEU* 3.6 9.5 - - - +
292B LYS* 1.3 85.2 - - - +
294B PRO* 1.3 76.8 - - - +
295B TYR* 3.9 3.8 - - - -
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Residues in contact with PRO 294 (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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56B MET* 3.5 33.0 - - + +
60B TYR* 3.8 8.3 + - - -
164B ASP 3.4 5.2 - - - +
165B HIS* 3.4 29.4 - - + +
282B HIS* 4.6 10.5 - - + +
287B LEU* 3.4 31.0 - - + -
290B LEU* 3.7 2.7 - - + -
293B GLY* 1.3 86.2 - - - +
295B TYR* 1.3 60.4 + - - +
296B TYR* 3.8 18.2 - - + -
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Residues in contact with TYR 295 (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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50B GLN* 5.3 0.6 + - - -
53B ILE* 3.3 33.5 - - + +
54B HIS 5.6 0.2 - - - -
60B TYR* 3.5 51.1 - + - +
162B ILE 3.4 2.4 - - - +
163B GLY* 3.3 0.7 - - - -
164B ASP* 2.7 48.6 + - + +
293B GLY* 5.0 2.7 - - - -
294B PRO* 1.3 74.2 - - - +
296B TYR* 1.3 62.8 + - - +
297B MET* 3.7 32.4 - - + +
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Residues in contact with TYR 296 (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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53B ILE* 3.3 7.1 - - - +
54B HIS* 3.0 48.7 + - + +
56B MET* 4.7 14.0 - - + -
161B VAL* 3.2 28.0 - - + -
162B ILE 3.4 0.4 - - - -
163B GLY* 3.3 28.0 - - - -
165B HIS* 3.7 16.8 + + - -
183B LEU* 5.9 0.2 - - - +
255B VAL* 4.1 11.7 - - - +
257B ILE* 4.2 11.4 - - + +
269B LEU* 3.9 30.0 - - + +
282B HIS* 5.1 7.9 + + - -
294B PRO* 3.8 26.0 - - + -
295B TYR* 1.3 78.5 - - - +
297B MET* 1.3 62.1 + - - +
298B PHE* 4.9 0.4 - - + -
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Residues in contact with MET 297 (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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14B LYS* 4.5 15.5 - - - +
50B GLN* 3.4 37.5 - - - +
52B GLY 3.7 4.0 - - - -
53B ILE* 4.4 0.7 - - + +
75B GLY* 4.6 2.5 - - - -
77B PHE* 4.3 24.9 - - + -
161B VAL* 3.3 5.0 - - - -
162B ILE* 2.9 37.2 + - + +
164B ASP* 6.4 2.0 - - - -
295B TYR* 3.7 29.8 - - + +
296B TYR* 1.3 71.9 - - - +
298B PHE* 1.3 63.3 + - - +
299B PHE* 3.5 30.7 - - + -
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Residues in contact with PHE 298 (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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50B GLN* 3.3 8.8 - - - +
51B THR* 2.8 34.9 + - - +
52B GLY* 2.9 20.2 + - - +
53B ILE 3.7 10.3 - - - -
54B HIS* 3.7 29.8 - + + -
65B VAL* 3.8 28.0 - - + -
159B THR* 4.2 11.0 - - + -
160B VAL 3.7 3.4 - - - -
161B VAL* 3.5 19.3 - - + -
262B PRO* 3.5 27.4 - - + -
265B ALA* 3.7 20.6 - - + -
266B HIS* 3.8 16.8 - - + -
269B LEU* 4.2 4.7 - - + -
296B TYR 4.2 1.3 - - - -
297B MET* 1.3 75.9 - - - +
299B PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 299 (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* 3.6 28.5 - - + -
49B LEU 3.2 7.9 - - - +
50B GLN* 3.4 33.0 - - + -
51B THR* 4.1 6.0 + - - -
75B GLY 4.3 2.5 - - - -
77B PHE* 3.8 37.5 - + - -
159B THR* 3.7 9.2 + - - +
160B VAL* 2.6 46.1 + - + +
162B ILE* 3.5 27.4 - - + -
297B MET* 3.5 45.3 - - + -
298B PHE* 1.3 76.5 - - - +
300B SER* 1.3 60.8 + - - +
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Residues in contact with SER 300 (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* 3.6 2.4 - - - -
49B LEU* 2.8 33.3 + - - -
51B THR* 3.9 18.8 - - - +
156B SER 5.4 1.6 + - - -
158B ARG 4.3 4.1 + - - -
299B PHE* 1.3 76.6 - - - +
301B PRO* 1.3 75.2 + - - +
302B MET* 3.2 18.4 + - - +
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Residues in contact with PRO 301 (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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46B GLU* 4.7 0.4 - - - +
47B GLN 3.4 7.0 - - - +
48B LEU* 3.8 15.7 - - + -
156B SER* 3.4 26.0 - - - +
158B ARG* 3.0 46.0 - - + +
160B VAL* 4.2 14.8 - - + -
299B PHE 4.0 3.1 - - - +
300B SER* 1.3 85.6 + - - +
302B MET* 1.3 65.1 + - - +
303B MET 3.6 0.7 - - - -
304B GLU* 3.9 24.5 - - + +
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Residues in contact with MET 302 (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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22B TYR* 5.3 9.2 - - + -
25B MET* 5.8 5.4 - - + -
47B GLN* 2.8 34.5 + - + +
49B LEU* 4.0 40.4 - - + +
156B SER* 3.1 15.1 + - - -
300B SER* 4.0 21.8 - - - +
301B PRO* 1.3 74.1 - - - +
303B MET* 1.3 62.9 + - + +
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Residues in contact with MET 303 (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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25B MET 5.2 1.6 - - - +
29B GLY* 4.2 22.9 - - - -
30B PRO* 4.3 18.4 - - + -
33B CSS 4.4 15.3 - - - -
45B PHE* 3.7 17.3 - - + -
47B GLN* 2.9 65.8 + - + +
156B SER* 4.0 2.5 - - - -
302B MET* 1.3 82.5 - - + +
304B GLU* 1.3 67.9 + - - +
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Residues in contact with GLU 304 (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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45B PHE* 3.6 11.8 - - - +
46B GLU* 2.7 30.9 - - - +
129B ILE* 3.8 23.2 - - + +
155B SER* 3.5 8.5 + - - +
156B SER* 2.7 36.9 + - - +
158B ARG* 2.8 34.8 + - - -
301B PRO* 3.9 14.1 - - + +
303B MET* 1.3 80.2 - - - +
305B GLN* 1.3 60.5 + - - +
306B GLY 3.8 1.4 + - - +
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Residues in contact with GLN 305 (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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42B PHE* 4.2 12.3 + - + -
43B LEU 3.7 6.9 + - - +
44B GLY* 3.2 23.0 - - - +
45B PHE* 3.0 55.7 + - + +
304B GLU* 1.3 72.8 - - - +
306B GLY* 1.3 55.6 + - - +
307B LEU* 2.9 52.2 + - + +
308B TRP* 3.3 3.6 - - - -
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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