Contacts of the helix formed by residues 306 - 315 (chain B) in PDB entry 3UGV
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 TYR 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.2 40.8 - + + -
52B LEU* 3.9 1.9 - - - -
53B GLU* 2.9 43.9 + - + -
110B MET* 4.1 16.2 - - + -
277B ASP* 3.5 21.1 - - - -
278B PHE* 3.8 20.9 - - + -
279B MET* 3.4 30.1 - - + +
304B HIS 3.5 6.3 - - - -
305B LEU* 1.3 92.9 - - + +
307B PRO* 1.3 64.0 - - - +
308B GLU* 2.9 4.7 + - - -
309B VAL* 3.1 13.6 + - + -
310B GLY* 2.7 32.6 + - - -
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Residues in contact with PRO 307 (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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51B TYR* 3.9 11.4 - - - +
53B GLU* 4.8 0.4 - - - +
303B THR* 6.1 0.2 - - - +
305B LEU 3.2 4.2 - - - +
306B TYR* 1.3 88.5 - - - +
308B GLU* 1.3 67.4 + - - +
310B GLY* 4.5 2.0 - - - +
311B ALA* 2.8 32.7 + - - +
323B LEU* 3.9 5.9 - - + +
324B GLU 4.1 16.4 - - - +
325B TRP* 4.3 9.9 - - + +
326B GLN* 3.4 38.8 - - - +
329B ALA* 6.3 0.7 - - + -
344B LEU* 3.6 19.9 - - + +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 2.5 36.8 + - + -
306B TYR 3.1 1.9 - - - -
307B PRO* 1.3 87.5 - - + +
309B VAL* 1.3 67.5 + - + +
311B ALA 3.6 0.2 + - - -
312B HIS* 3.1 31.0 + - - -
326B GLN 5.7 0.2 - - - +
329B ALA* 5.7 1.4 - - - +
330B ASP* 4.4 8.8 - - - +
333B LEU* 3.5 23.8 - - + +
337B TYR* 3.7 43.3 + - + +
352B LEU* 4.5 4.9 - - + +
354B LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 309 (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 ALA* 5.5 0.9 - - + -
51B TYR* 6.3 3.1 - - + -
110B MET* 3.8 24.5 - - + -
124B LEU* 5.2 0.2 - - + -
278B PHE* 3.5 31.9 - - + -
284B VAL* 3.9 21.5 - - + -
306B TYR* 3.1 16.8 + - + +
308B GLU* 1.3 76.5 - - + +
310B GLY* 1.3 63.6 + - - +
312B HIS* 3.2 5.4 + - - +
313B VAL* 3.1 22.0 + - + +
352B LEU* 3.8 35.0 - - + -
354B LEU* 6.2 0.2 - - + -
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Residues in contact with GLY 310 (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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278B PHE* 3.6 22.6 - - - -
303B THR* 3.9 9.6 - - - -
306B TYR 2.7 20.7 + - - -
307B PRO* 3.8 2.0 - - - -
309B VAL* 1.3 73.4 - - - +
311B ALA* 1.3 61.7 + - - +
313B VAL* 3.4 0.5 - - - +
314B MET* 2.9 30.4 + - - +
323B LEU* 3.7 7.0 - - - -
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Residues in contact with ALA 311 (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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135B VAL* 3.6 12.1 - - + +
307B PRO 2.8 21.0 + - - +
308B GLU 4.0 4.0 - - - +
309B VAL 3.4 0.2 - - - -
310B GLY* 1.3 72.0 - - - +
312B HIS* 1.3 62.8 + - - +
314B MET 3.6 0.2 + - - -
315B ARG* 3.2 27.0 + - - +
323B LEU* 3.3 18.2 - - + +
337B TYR* 4.3 4.5 - - + -
344B LEU* 3.8 16.6 - - + -
346B VAL* 3.6 21.3 - - + -
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Residues in contact with HIS 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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123B PRO* 4.0 5.2 - - + -
124B LEU* 3.4 26.8 - - + +
125B CYS* 3.1 49.2 + - - +
128B LEU* 5.2 0.4 - - - -
308B GLU 3.1 21.2 + - - -
309B VAL 3.2 9.5 + - - +
311B ALA* 1.3 80.0 - - - +
313B VAL* 1.3 60.6 + - - +
315B ARG* 3.3 10.7 + - - +
316B VAL* 4.0 2.4 + - - +
337B TYR* 3.0 25.3 + + - -
346B VAL* 3.5 23.3 - - + +
347B PRO* 4.9 3.6 + - - +
349B LYS 5.0 0.4 + - - -
351B GLY 3.4 25.1 + - - -
352B LEU* 3.7 11.5 + - + -
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.0 0.4 - - + -
128B LEU* 4.0 20.4 - - + -
278B PHE* 3.4 34.3 - - + -
284B VAL* 4.3 25.1 - - + -
287B TRP* 3.4 31.9 - - + +
288B MET* 4.4 2.7 - - - -
309B VAL* 3.1 7.1 + - + +
310B GLY 3.4 6.7 - - - +
312B HIS* 1.3 74.8 - - + +
314B MET* 1.3 59.8 + - - +
316B VAL* 3.0 25.6 + - - +
317B THR* 2.8 20.7 + - - -
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Residues in contact with MET 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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135B VAL* 3.9 24.0 - - + -
287B TRP* 4.0 11.9 - - + -
301B MET 3.8 10.5 - - - +
303B THR* 3.5 22.0 - - + -
310B GLY 2.9 25.4 + - - +
311B ALA 3.7 5.4 - - - +
313B VAL* 1.3 75.7 - - - +
315B ARG* 1.3 63.1 + - - +
316B VAL 3.1 0.5 + - - -
317B THR* 3.2 13.2 + - - +
320B ALA* 3.7 30.0 - - + +
321B HIS 3.6 25.1 - - - +
322B TRP 3.3 33.7 - - - +
323B LEU* 4.0 4.3 - - + +
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Residues in contact with ARG 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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125B CYS* 4.0 10.3 - - + -
130B GLY* 5.0 2.9 - - - -
131B THR* 2.8 46.9 + - - +
132B PRO 4.0 0.4 + - - -
133B GLY* 3.5 22.0 - - - +
134B SER* 3.3 26.7 + - - +
135B VAL* 3.7 18.2 - - - -
311B ALA 3.2 15.9 - - - +
312B HIS 3.4 10.3 - - - +
313B VAL 3.2 1.0 - - - -
314B MET* 1.3 77.2 - - - +
316B VAL* 1.3 62.3 + - + +
317B THR 4.1 0.4 + - - -
346B VAL* 4.0 11.0 - - + -
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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