Contacts of the helix formed by residues 279 - 283 (chain E) 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 LEU 279 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E PRO* 4.2 17.7 - - + -
119E TYR* 4.2 19.7 - - + +
132E PHE* 6.1 0.9 - - + -
149E TYR* 4.1 10.5 - - + +
215E ARG* 3.7 30.1 - - - +
277E PHE 2.9 4.2 + - - -
278E PRO* 1.3 99.7 - - + +
280E PRO* 1.3 61.3 - - + +
281E GLU* 3.2 16.4 - - - +
282E PHE* 2.8 58.9 + - + -
283E SER* 2.9 15.7 + - - -
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Residues in contact with PRO 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E TYR* 4.7 9.6 - - + -
278E PRO 4.0 4.9 - - - +
279E LEU* 1.3 85.1 - - + +
281E GLU* 1.3 71.4 + - - +
282E PHE 3.5 0.2 + - - -
283E SER* 3.6 18.4 + - - -
144F PRO* 4.2 18.2 - - + -
208F PRO* 3.8 27.4 - - + -
209F GLN* 4.1 13.2 - - - +
212F ASN* 4.1 11.4 - - - +
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Residues in contact with GLU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E ARG* 3.0 31.5 + - + +
279E LEU* 3.2 19.5 - - - +
280E PRO* 1.3 78.5 - - - +
282E PHE* 1.3 85.3 + - + +
283E SER 3.3 5.0 + - - +
317E VAL* 5.4 2.3 - - - +
208F PRO 4.0 4.3 - - - +
209F GLN* 3.7 28.6 - - - +
210F LYS 6.1 0.2 - - - -
212F ASN* 3.0 40.0 + - - +
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Residues in contact with PHE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E TYR* 3.9 21.8 - + + -
215E ARG* 3.8 29.2 - - + -
216E ILE* 4.0 2.7 - - - -
217E ALA* 3.6 38.4 - - + -
277E PHE* 3.5 37.7 - + + +
279E LEU* 2.8 48.0 + - + +
281E GLU* 1.3 92.4 - - + +
283E SER* 1.3 58.4 + - - +
317E VAL* 3.9 24.4 - - + +
320E GLU* 5.3 3.1 - - - -
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Residues in contact with SER 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PRO* 5.3 5.4 - - - +
277E PHE 3.8 6.9 + - - -
278E PRO* 4.5 3.1 - - - +
279E LEU 2.9 21.3 + - - -
280E PRO* 4.0 13.6 - - - +
281E GLU 3.3 5.9 - - - +
282E PHE* 1.3 80.3 + - - +
316E ARG* 5.7 3.5 - - - -
317E VAL 5.7 3.1 + - - -
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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