Contacts of the strand formed by residues 311 - 317 (chain B) in PDB entry 2QCU
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 TRP 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.8 53.0 + - + -
261B TRP* 3.7 20.4 - + - -
309B ILE* 3.5 3.8 - - - +
310B VAL* 1.3 81.6 - - - +
312B THR* 1.3 86.0 + - - +
313B TYR* 3.4 24.2 - + + -
468B TRP* 3.4 31.4 - + - -
472B LYS* 4.5 4.9 - - - -
475B MET* 3.8 16.4 - - - -
801B SO4 3.7 24.9 - - - +
807B EDO 3.0 40.6 + - - -
809B EDO 5.7 1.6 - - - -
811B EDO 3.7 24.2 - - - -
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Residues in contact with THR 312 (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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233B HIS 3.3 15.7 - - - +
234B ILE* 4.0 11.2 - - + +
284B ILE* 3.5 28.4 + - + +
289B ILE* 5.4 0.4 - - + -
309B ILE* 3.7 18.6 - - + -
311B TRP* 1.3 100.3 + - - +
313B TYR* 1.3 70.4 + - - +
807B EDO 5.0 0.5 + - - -
809B EDO 4.2 19.7 - - - +
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Residues in contact with TYR 313 (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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44B ALA* 3.4 23.3 - - - -
45B SER 2.8 25.8 + - - -
46B SER* 4.2 0.7 - - - -
47B LYS* 3.5 23.9 + - - +
232B SER* 3.3 2.6 - - - -
233B HIS* 2.9 74.6 + + + +
235B VAL* 4.5 11.9 - - + -
267B ILE* 3.9 14.1 - - + +
284B ILE* 5.0 0.6 - - - +
311B TRP* 3.4 33.9 - + + -
312B THR* 1.3 78.8 - - - +
314B SER* 1.3 67.5 + - - +
807B EDO 5.4 0.2 - - - +
811B EDO 3.9 22.2 - - - -
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Residues in contact with SER 314 (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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44B ALA* 3.6 14.3 - - - +
230B LYS* 3.4 7.3 - - - +
231B GLY 3.4 7.2 + - - -
232B SER* 2.8 21.6 + - - +
282B VAL* 3.3 28.9 - - - +
283B LYS* 3.9 23.1 - - - -
284B ILE 3.9 2.5 - - - -
313B TYR* 1.3 81.7 - - - +
315B GLY* 1.3 60.8 + - - +
811B EDO 3.9 6.1 + - - -
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Residues in contact with GLY 315 (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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40B ALA 6.0 0.7 - - - -
41B THR* 5.4 2.7 - - - -
44B ALA* 3.7 18.1 + - - +
230B LYS* 3.3 5.4 - - - +
231B GLY 3.0 30.7 + - - +
282B VAL* 3.9 9.6 - - - -
314B SER* 1.3 76.8 + - - +
316B VAL* 1.3 65.6 + - - +
600B FAD 3.8 8.1 - - - +
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Residues in contact with VAL 316 (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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41B THR* 3.2 25.7 + - - +
208B PRO* 3.9 15.7 - - + +
228B LEU* 4.2 16.8 - - + -
229B ILE 3.7 3.6 - - - +
230B LYS* 3.9 7.2 - - - -
275B TYR* 3.6 36.3 - - + -
279B PRO* 3.7 32.3 - - + +
282B VAL* 3.8 15.0 - - + +
315B GLY* 1.3 77.4 - - - +
317B ARG* 1.3 64.5 + - - +
318B PRO* 3.3 2.8 - - - +
600B FAD 4.0 2.2 - - - +
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Residues in contact with ARG 317 (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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41B THR* 4.5 0.7 - - - -
227B ARG 3.0 12.0 - - - +
228B LEU* 3.5 2.6 - - - -
229B ILE* 2.9 37.6 + - + +
230B LYS 3.3 8.1 + - - -
231B GLY 3.6 5.9 - - - +
254B ARG* 4.3 3.4 - - - +
270B THR* 4.3 6.3 - - - -
271B THR 3.1 29.2 + - - -
272B ASP* 3.7 13.1 + - - -
316B VAL* 1.3 68.5 - - - +
318B PRO* 1.3 73.6 - - + +
319B LEU* 3.7 26.4 - - + +
332B ARG* 3.7 9.9 - - - +
600B FAD 3.5 47.9 - - + +
803B PO4 2.8 45.1 + - - -
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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