Contacts of the helix formed by residues 330 - 338 (chain A) in PDB entry 2VUU
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 ASP 330 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN* 3.8 2.0 - - - -
221A GLU* 3.3 24.9 - - - +
328A TRP* 3.9 22.0 + - + -
329A ARG* 1.3 78.6 - - - +
331A MET* 1.3 64.0 + - - +
332A GLU* 3.2 16.4 + - - +
333A GLU* 2.9 27.7 + - - +
334A TYR* 3.0 17.3 + - - +
680I THR* 5.2 1.4 - - - +
682I PRO* 6.1 1.4 - - - +
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Residues in contact with MET 331 (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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154A ASN* 3.7 30.5 - - + +
157A PHE* 4.1 3.8 - - + -
189A TRP* 3.7 43.1 - - + -
221A GLU* 2.8 19.9 + - - +
223A LEU* 4.0 13.7 - - + -
228A VAL* 4.0 21.5 - - + -
231A ALA* 3.9 15.7 - - + -
232A PHE* 3.7 29.6 - - + -
330A ASP* 1.3 71.5 - - - +
332A GLU* 1.3 54.9 + - - +
334A TYR* 3.0 2.5 + - - +
335A ALA* 2.6 37.6 + - - +
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 4.3 13.0 - - + +
234A ARG* 3.5 38.1 + - + +
235A ALA* 3.6 3.9 - - - +
330A ASP* 3.2 15.4 + - - +
331A MET* 1.3 77.8 - - - +
333A GLU* 1.3 57.3 + - - +
335A ALA* 4.5 4.3 - - - -
336A ARG* 2.9 54.5 + - - +
237B ASN* 4.9 15.4 - - - +
680I THR* 3.9 19.7 - - - +
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Residues in contact with GLU 333 (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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194A HIS* 4.7 5.1 + - - -
328A TRP 4.8 1.7 - - - +
329A ARG* 3.1 42.2 + - + +
330A ASP* 2.9 18.8 + - - +
332A GLU* 1.3 71.8 - - - +
334A TYR* 1.3 59.1 + - - +
336A ARG* 4.6 0.2 - - - -
337A GLU* 2.7 44.8 + - + +
676I CYS* 5.4 0.9 - - - -
678I THR* 2.6 31.0 + - - +
680I THR* 2.8 34.8 - - + +
681I THR* 5.3 1.2 - - - -
682I PRO* 5.6 2.9 - - - +
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Residues in contact with TYR 334 (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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154A ASN* 3.3 44.7 + - + +
155A ASN* 3.3 23.8 - - + -
157A PHE* 3.9 9.5 + - + -
191A ASP* 4.0 13.7 - - - +
232A PHE* 3.9 16.2 - + - -
329A ARG* 4.0 2.9 - - - +
330A ASP 3.0 14.6 + - - +
331A MET* 3.0 8.7 + - - +
333A GLU* 1.3 76.9 - - - +
335A ALA* 1.3 63.0 + - - +
338A VAL* 2.7 55.9 + - + -
339A PHE* 2.8 34.6 + + + -
342A GLU* 2.3 32.3 + - - -
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Residues in contact with ALA 335 (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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231A ALA 4.3 1.3 - - - +
232A PHE* 3.6 44.4 - - + +
235A ALA* 3.8 7.9 - - + -
236A LEU* 3.6 6.0 - - + +
331A MET 2.6 21.0 + - - +
332A GLU 3.8 3.8 - - - +
334A TYR* 1.3 75.4 - - - +
336A ARG* 1.3 58.7 + - - +
339A PHE* 3.0 14.8 - - - +
340A PRO* 2.8 27.0 - - - +
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Residues in contact with ARG 336 (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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234A ARG* 3.7 11.9 + - - +
235A ALA* 3.3 44.3 + - + +
236A LEU* 4.6 3.4 - - - -
237A ASN* 5.7 2.2 + - - +
332A GLU* 2.9 40.8 + - - +
333A GLU 4.2 0.9 - - - +
335A ALA* 1.3 77.3 - - - +
337A GLU* 1.3 68.9 + - - +
340A PRO* 3.1 24.7 - - - +
341A ILE* 5.9 0.2 - - - +
234B ARG 5.9 0.6 + - - -
237B ASN* 4.7 13.9 + - - -
679I GLN* 6.1 1.6 - - - -
680I THR* 3.5 26.1 + - - +
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Residues in contact with GLU 337 (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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329A ARG* 5.4 2.0 - - - +
333A GLU* 2.7 33.1 + - + +
336A ARG* 1.3 83.0 - - - +
338A VAL* 1.3 61.7 + - + +
341A ILE* 3.2 21.9 - - - +
677I PHE 4.7 2.4 - - - +
678I THR* 3.2 29.8 - - - +
679I GLN* 2.8 36.1 + - - +
680I THR* 3.4 15.8 + - - +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 5.5 4.5 - - - +
329A ARG* 3.2 46.0 - - - +
333A GLU 4.3 0.9 - - - +
334A TYR* 2.7 33.2 + - + +
337A GLU* 1.3 78.1 - - + +
339A PHE* 1.3 68.1 + - - +
340A PRO* 3.2 3.4 - - - -
341A ILE* 2.9 18.6 + - + +
342A GLU* 2.9 39.5 + - + +
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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