Contacts of the helix formed by residues 306 - 315 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.2 38.8 - + + -
52A LEU* 3.9 2.5 - - - -
53A GLU* 3.1 42.8 + - + -
110A MET* 4.1 16.4 - - + -
277A ASP* 3.7 21.1 - - - -
278A PHE* 3.8 21.5 - - + -
279A MET* 3.2 33.1 - - + +
304A HIS 3.5 6.5 - - - -
305A LEU* 1.3 94.9 - - + +
307A PRO* 1.3 68.6 - - - +
308A GLU* 3.1 5.0 + - - -
309A VAL* 3.2 11.2 + - + -
310A GLY* 2.9 23.9 + - - -
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Residues in contact with PRO 307 (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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51A TYR* 3.8 12.1 - - - +
303A THR* 6.1 0.2 - - - +
305A LEU 3.3 4.5 - - - +
306A TYR* 1.3 89.0 - - - +
308A GLU* 1.3 65.5 + - + +
310A GLY* 4.5 0.7 - - - +
311A ALA* 3.0 29.6 + - - +
323A LEU* 3.8 7.1 - - + +
324A GLU 4.1 13.9 - - - +
325A TRP* 4.3 9.0 - - + -
326A GLN* 3.7 44.2 - - - +
329A ALA* 6.1 0.2 - - + -
344A LEU* 3.5 20.6 - - + +
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Residues in contact with GLU 308 (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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51A TYR* 2.6 36.0 + - - -
306A TYR 4.2 1.0 - - - -
307A PRO* 1.3 85.8 - - + +
309A VAL* 1.3 68.0 + - + +
311A ALA 3.5 0.2 + - - -
312A HIS* 3.2 29.1 + - - -
329A ALA* 5.6 1.6 - - - +
330A ASP* 4.5 8.0 - - - +
333A LEU* 3.5 23.6 - - + +
336A PRO* 5.1 2.8 - - - +
337A TYR* 3.5 48.4 + - + +
344A LEU* 6.0 0.4 - - + -
352A LEU* 4.3 3.8 - - + +
354A LEU* 3.9 19.1 - - + -
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Residues in contact with VAL 309 (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 ALA* 5.5 1.3 - - + -
51A TYR* 6.5 1.6 - - + -
110A MET* 4.0 22.7 - - + -
124A LEU* 4.9 0.4 - - + -
278A PHE* 3.9 22.9 - - + -
284A VAL* 3.8 27.8 - - + -
306A TYR* 3.2 16.3 + - + +
308A GLU* 1.3 78.1 - - + +
310A GLY* 1.3 63.8 + - - +
312A HIS* 3.2 4.2 + - - +
313A VAL* 3.1 21.7 + - + +
352A LEU* 3.6 38.1 - - + -
354A LEU* 6.1 0.4 - - + -
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Residues in contact with GLY 310 (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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278A PHE* 3.6 25.1 - - - -
303A THR* 4.0 9.2 - - - -
306A TYR 2.9 13.7 + - - -
307A PRO* 4.0 1.3 - - - -
309A VAL* 1.3 77.7 - - - +
311A ALA* 1.3 57.2 + - - +
312A HIS 3.2 0.2 + - - -
313A VAL* 3.3 1.4 + - - +
314A MET* 2.9 34.6 + - - +
323A LEU* 3.6 8.3 - - - -
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Residues in contact with ALA 311 (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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135A VAL* 3.6 11.7 - - + +
307A PRO 3.0 19.3 + - - +
308A GLU 4.0 4.0 - - - +
309A VAL 3.3 0.4 - - - -
310A GLY* 1.3 75.3 - - - +
312A HIS* 1.3 63.3 + - - +
314A MET 3.6 0.2 + - - -
315A ARG* 3.1 28.1 + - - +
323A LEU* 3.2 16.9 - - + +
337A TYR* 4.5 4.9 - - + -
344A LEU* 4.0 15.3 - - + -
346A VAL* 3.7 19.7 - - + -
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Residues in contact with HIS 312 (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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123A PRO* 4.0 9.2 - - + -
124A LEU* 3.4 28.5 - - + +
125A CYS* 2.9 47.8 + - - +
128A LEU* 5.2 0.4 - - - -
308A GLU 3.2 20.5 + - - -
309A VAL* 3.2 9.3 + - - +
310A GLY 3.1 0.6 - - - -
311A ALA* 1.3 81.4 - - - +
313A VAL* 1.3 62.6 + - - +
315A ARG* 3.4 7.1 + - - +
316A VAL* 4.0 2.8 + - - +
337A TYR* 3.1 22.4 + + - -
346A VAL* 3.4 29.2 - - + +
347A PRO* 4.8 3.5 + - - +
349A LYS 4.9 0.6 + - - -
351A GLY 3.3 23.8 + - - -
352A LEU* 4.0 8.6 + - + -
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Residues in contact with VAL 313 (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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124A LEU* 4.9 0.7 - - + -
128A LEU* 4.0 20.0 - - + -
278A PHE* 3.5 19.3 - - + -
284A VAL* 4.4 23.3 - - + -
287A TRP* 3.4 42.0 - - + +
288A MET* 4.4 2.9 - - - -
309A VAL* 3.1 11.1 + - + +
310A GLY 3.4 9.4 - - - +
312A HIS* 1.3 74.9 - - + +
314A MET* 1.3 59.5 + - - +
315A ARG 3.1 1.8 - - - -
316A VAL* 2.8 25.3 + - - +
317A THR* 2.7 20.5 + - - -
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Residues in contact with MET 314 (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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135A VAL* 3.9 25.4 - - + -
287A TRP* 4.0 12.8 - - + -
301A MET 3.9 10.8 - - - +
303A THR* 3.6 23.6 - - + -
310A GLY 2.9 26.4 + - - +
311A ALA 3.9 4.5 - - - +
313A VAL* 1.3 76.6 - - - +
315A ARG* 1.3 61.6 + - - +
316A VAL 3.2 1.0 + - - -
317A THR* 3.3 12.9 + - - +
320A ALA* 3.6 38.8 - - + +
321A HIS 3.7 11.2 - - - +
322A TRP 3.5 33.2 - - - +
323A LEU* 4.0 3.8 - - + +
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Residues in contact with ARG 315 (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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125A CYS* 4.1 7.9 - - + -
130A GLY* 4.8 3.8 - - - -
131A THR* 2.9 47.6 + - - +
132A PRO 3.8 4.4 + - - -
133A GLY* 3.6 16.7 - - - +
134A SER* 3.2 25.5 + - - +
135A VAL* 3.6 19.5 - - + -
311A ALA 3.1 17.5 - - - +
312A HIS 3.4 9.2 - - - +
313A VAL 3.1 0.8 - - - -
314A MET* 1.3 76.7 - - - +
316A VAL* 1.3 63.4 + - + +
346A VAL* 3.9 10.3 - - + -
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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