Contacts of the strand formed by residues 245 - 251 (chain D) in PDB entry 6QCG
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 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D THR* 3.0 15.5 - - - -
53D ARG* 3.4 18.4 + - - +
240D LYS* 3.8 10.0 + - - +
241D ILE* 3.1 24.2 + - - +
243D ASP 5.5 0.5 + - - -
244D MET* 1.3 81.4 - - - +
246D HIS* 1.3 68.0 + - - +
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Residues in contact with HIS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN* 3.7 15.8 + - - -
50D LEU* 3.7 3.1 - - - +
51D THR* 2.9 61.6 + - + +
53D ARG* 5.9 2.2 + - - -
238D GLU* 4.6 6.3 - - + -
239D TYR 3.5 8.7 - - - +
240D LYS* 3.5 31.9 + - + +
241D ILE* 4.0 8.8 - - - +
245D GLY* 1.3 76.7 - - - +
247D LEU* 1.3 61.8 - - - +
248D LYS* 3.8 35.3 + - + +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 5.2 3.1 - - - +
18D ALA* 3.9 11.4 - - + -
19D LEU* 4.1 8.1 - - + -
48D VAL* 3.6 30.7 - - + -
49D GLN 3.9 0.9 - - - -
50D LEU* 4.1 22.0 - - + -
218D ALA* 3.9 7.4 - - + -
221D LEU* 3.8 22.7 - - + -
237D VAL 3.7 2.1 - - - +
238D GLU* 3.7 0.9 - - - -
239D TYR* 2.9 40.4 + - + +
241D ILE* 4.1 11.0 - - + -
246D HIS* 1.3 73.4 - - - +
248D LYS* 1.3 62.7 + - - +
249D TYR* 3.7 27.7 + - + +
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Residues in contact with LYS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU 3.9 0.5 - - - +
48D VAL* 3.5 4.5 - - - +
49D GLN* 2.8 44.2 + - + +
236D VAL* 4.2 12.8 - - + -
237D VAL 3.7 3.4 - - - -
238D GLU* 3.3 43.4 + - + -
240D LYS* 5.7 0.6 - - - +
246D HIS* 3.8 30.9 + - + +
247D LEU* 1.3 71.5 - - - +
249D TYR* 1.3 59.9 + - - +
250D TYR* 3.8 33.7 - - + +
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Residues in contact with TYR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 3.1 39.8 + - - +
19D LEU* 3.9 2.0 - - + +
22D LEU* 3.8 19.7 - - + -
47D LEU 3.4 2.5 - - - -
48D VAL* 3.9 26.5 - - + -
214D PHE 4.3 0.2 + - - -
215D PHE* 3.3 70.0 + + + -
218D ALA* 3.8 13.6 - - + +
235D LEU 3.5 1.0 - - - +
236D VAL* 3.3 4.3 - - - -
237D VAL* 2.8 48.5 + - + +
239D TYR* 4.1 7.9 - + - -
247D LEU* 3.7 16.5 - - + +
248D LYS* 1.3 73.4 - - - +
250D TYR* 1.3 63.0 + - - +
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Residues in contact with TYR 250 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D VAL 3.9 0.5 - - - +
46D SER* 3.1 8.8 - - - -
47D LEU* 2.8 66.8 + - + +
49D GLN* 4.1 13.6 - - + +
128D ILE* 3.4 38.6 - - + +
133D TYR* 4.4 5.6 - - - -
215D PHE* 4.6 0.7 - - - -
234D PRO* 4.6 15.3 - - + -
235D LEU 3.2 5.4 - - - +
236D VAL* 3.5 33.3 - - + +
248D LYS* 3.8 38.3 - - + +
249D TYR* 1.3 74.7 - - - +
251D LEU* 1.3 59.4 + - - +
252D ALA 4.3 0.2 - - - -
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 3.8 26.2 - - + +
207D PHE* 3.7 32.0 - - + -
208D ALA* 3.8 18.6 - - + +
211D TYR* 4.0 24.7 - - + -
212D LEU* 4.0 18.4 - - + -
215D PHE* 3.8 16.4 - - + -
234D PRO* 3.3 6.5 - - - +
235D LEU* 2.9 39.4 + - + +
249D TYR 4.2 0.2 - - - -
250D TYR* 1.3 73.7 - - - +
252D ALA* 1.3 78.3 + - - +
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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