Contacts of the helix formed by residues 338 - 347 (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 VAL 338 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with PHE 339 (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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157C PHE* 3.6 32.3 - - + -
158C THR* 3.7 5.6 - - - -
159C SER 4.1 2.5 - - - -
167C MET* 3.7 26.2 - - + -
175C PHE* 4.9 4.9 - + - -
232C PHE* 3.9 12.6 - + - -
236C LEU* 4.1 22.2 - - + -
334C TYR* 2.9 39.3 + + + +
335C ALA* 3.2 23.6 - - - +
338C VAL* 1.3 72.1 - - - +
340C PRO* 1.3 64.5 - - - +
342C GLU* 3.3 4.8 + - + +
343C GLU* 2.9 53.9 + - + +
350C TRP* 4.0 15.3 - + - -
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Residues in contact with PRO 340 (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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236C LEU* 3.7 19.7 - - + -
335C ALA 2.8 25.4 - - - +
336C ARG 3.1 23.3 - - - +
338C VAL 3.2 4.0 - - - +
339C PHE* 1.3 82.6 - - + +
341C ILE* 1.3 60.6 + - + +
343C GLU* 3.2 4.0 + - - +
344C GLU* 2.9 28.7 + - - +
350C TRP* 4.3 16.2 - - + -
351C MET* 4.0 17.4 - - + +
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Residues in contact with ILE 341 (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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337C GLU 3.5 21.5 - - - +
338C VAL* 2.8 13.3 + - + +
340C PRO* 1.3 74.9 - - + +
342C GLU* 1.3 60.1 + - + +
344C GLU* 3.7 14.4 - - - +
345C ALA* 2.8 31.7 + - + +
712K LEU* 5.7 8.7 - - + -
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Residues in contact with GLU 342 (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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155C ASN* 3.7 17.9 + - - +
157C PHE 4.6 2.6 - - - +
193C GLU* 3.9 14.4 - - - +
334C TYR* 2.5 33.4 + - - -
338C VAL* 2.9 35.6 + - + +
339C PHE* 3.6 5.8 - - + +
341C ILE* 1.3 76.7 - - + +
343C GLU* 1.3 66.8 + - + +
345C ALA* 3.2 9.5 + - - +
346C ASN* 3.0 28.8 + - - +
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Residues in contact with GLU 343 (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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157C PHE 4.6 0.5 - - - +
158C THR* 3.2 27.7 + - - -
159C SER* 2.4 39.7 + - - -
339C PHE* 2.9 36.7 + - + +
340C PRO 3.4 7.6 - - - +
341C ILE 3.2 0.2 - - - -
342C GLU* 1.3 75.4 - - + +
344C GLU* 1.3 61.4 + - - +
346C ASN* 2.8 29.4 + - - +
347C GLY 3.0 6.1 + - - -
348C LEU* 2.8 21.7 + - + +
350C TRP* 3.4 29.1 + - + +
351C MET* 3.9 4.5 - - + -
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Residues in contact with GLU 344 (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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340C PRO 2.9 11.6 + - - +
341C ILE* 3.7 18.0 - - - +
343C GLU* 1.3 76.3 - - - +
345C ALA* 1.3 64.5 + - - +
346C ASN 2.8 2.6 + - - +
347C GLY* 3.3 11.8 + - - -
348C LEU 3.7 5.0 - - - +
351C MET* 3.3 25.2 - - + +
352C LEU* 4.5 26.8 - - + +
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Residues in contact with ALA 345 (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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341C ILE* 2.8 21.1 + - + +
342C GLU* 3.3 12.6 - - - +
343C GLU 3.2 0.2 - - - -
344C GLU* 1.3 77.1 - - - +
346C ASN* 1.3 65.1 + - - +
712K LEU* 6.3 3.4 - - + -
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Residues in contact with ASN 346 (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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158C THR* 4.0 10.7 + - - -
160C LEU* 3.6 29.5 - - + +
342C GLU* 3.0 15.6 + - - +
343C GLU* 2.8 17.7 + - - +
344C GLU 3.4 1.4 - - - +
345C ALA* 1.3 86.6 + - - +
347C GLY* 1.3 60.7 + - - +
348C LEU* 4.2 7.4 - - + -
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Residues in contact with GLY 347 (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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160C LEU* 6.1 0.6 - - - +
343C GLU 3.0 3.0 + - - -
344C GLU 3.3 4.9 + - - -
346C ASN* 1.3 80.0 - - - +
348C LEU* 1.3 71.4 + - - +
349C ASP* 3.8 5.7 + - - +
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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