Contacts of the helix formed by residues 330 - 338 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ASN* 4.4 1.8 - - - -
221C GLU* 3.3 17.8 - - - +
328C TRP* 3.4 28.0 + - + -
329C ARG* 1.3 76.9 - - - +
331C MET* 1.3 64.9 - - - +
332C GLU* 3.0 14.5 + - - +
333C GLU* 2.9 25.2 + - - +
334C TYR* 3.0 18.4 + - - +
680K THR* 5.4 1.0 - - - +
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Residues in contact with MET 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ASN* 3.1 41.0 - - + +
157C PHE* 4.3 1.6 - - + -
189C TRP* 3.5 36.3 - - + -
221C GLU* 2.7 16.0 + - - +
223C LEU* 3.8 13.7 - - + -
228C VAL* 3.8 20.0 - - + -
231C ALA* 3.9 14.1 - - + -
232C PHE* 3.7 33.4 - - + -
330C ASP* 1.3 72.7 - - - +
332C GLU* 1.3 53.0 + - - +
334C TYR* 3.1 6.0 + - - +
335C ALA* 2.7 37.9 + - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ALA* 4.3 16.5 - - + +
234C ARG* 3.7 31.6 + - - +
235C ALA* 3.5 8.2 - - + +
330C ASP* 3.0 14.1 + - - +
331C MET* 1.3 76.9 - - - +
333C GLU* 1.3 58.5 + - - +
335C ALA* 4.4 4.5 - - - -
336C ARG* 2.8 67.1 + - - +
680K THR* 4.8 7.8 - - + +
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C HIS* 4.9 5.3 + - - -
328C TRP 4.4 3.5 - - - +
329C ARG* 3.2 39.3 - - + +
330C ASP* 2.9 18.4 + - - +
332C GLU* 1.3 78.0 - - - +
334C TYR* 1.3 55.6 + - - +
337C GLU* 2.7 51.5 + - + +
676K CYS* 5.7 0.5 - - - -
678K THR* 2.9 17.2 + - - +
680K THR* 2.7 44.8 - - + +
681K THR* 4.5 5.5 + - - -
682K PRO* 5.3 3.8 - - - +
694K CYS* 5.4 0.5 - - - +
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Residues in contact with TYR 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN* 3.3 33.7 - - + -
155C ASN* 3.2 25.1 - - + -
157C PHE* 3.7 5.4 + - + -
191C ASP* 3.9 21.1 - - - +
232C PHE* 4.2 7.0 - + - -
329C ARG* 4.0 5.1 - - - +
330C ASP 3.0 12.6 + - - +
331C MET* 3.1 17.0 + - - +
333C GLU* 1.3 74.4 - - - +
335C ALA* 1.3 74.9 + - - +
338C VAL* 2.6 56.3 + - + -
339C PHE* 2.9 41.6 + + + -
342C GLU* 2.5 29.9 + - - -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.8 36.3 - - + -
235C ALA* 3.6 19.5 - - + -
236C LEU* 3.8 8.0 - - + +
331C MET 2.7 21.3 + - - +
332C GLU* 3.7 0.7 - - - +
334C TYR* 1.3 74.9 - - - +
336C ARG* 1.3 58.0 + - - +
339C PHE* 3.2 14.1 - - - +
340C PRO* 2.8 27.7 - - - +
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Residues in contact with ARG 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ARG* 3.5 13.7 + - - +
235C ALA* 3.4 37.8 + - + +
236C LEU* 5.0 0.9 - - - -
332C GLU* 2.8 50.6 + - - +
333C GLU 4.1 0.9 - - - +
335C ALA* 1.3 78.1 - - - +
337C GLU* 1.3 70.7 + - - +
340C PRO* 3.1 25.2 - - - +
341C ILE* 5.9 0.2 - - - +
679K GLN* 5.6 2.5 - - - -
680K THR* 3.1 30.8 + - - +
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ARG* 5.6 0.9 - - - +
333C GLU* 2.7 34.8 + - + +
336C ARG* 1.3 85.6 - - - +
338C VAL* 1.3 63.5 + - + +
340C PRO* 4.3 0.4 - - - -
341C ILE* 3.5 24.7 - - - +
677K PHE 4.1 3.6 - - - +
678K THR* 3.3 37.6 - - - +
679K GLN* 3.3 21.4 + - - +
680K THR* 2.8 22.9 + - - +
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLU* 6.5 0.2 - - - -
329C ARG* 3.4 43.7 - - - +
334C TYR* 2.6 29.9 + - + +
337C GLU* 1.3 81.9 - - + +
339C PHE* 1.3 67.0 + - - +
340C PRO* 3.2 3.1 - - - -
341C ILE* 2.8 18.6 + - + +
342C GLU* 2.9 41.9 + - + +
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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