Contacts of the strand formed by residues 215 - 218 (chain H) in PDB entry 2VUT
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 ARG 215 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H TYR* 5.6 0.8 + - - -
132H PHE* 3.6 22.8 - - - -
135H GLU* 2.8 29.6 + - - +
136H ASN* 4.8 3.0 - - - +
139H ARG* 3.5 20.6 - - - +
147H PHE* 3.2 6.3 - - + +
149H TYR* 3.5 20.8 + - + -
213H GLY 4.2 0.2 + - - -
214H HIS* 1.3 76.4 + - - +
216H ILE* 1.3 61.5 + - - +
279H LEU* 3.9 19.1 - - - +
280H PRO* 6.0 0.4 - - - +
281H GLU* 2.8 44.0 + - + +
282H PHE* 3.5 24.1 - - + -
320H GLU* 3.6 10.2 - - - +
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Residues in contact with ILE 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H THR* 3.7 19.5 - - + -
147H PHE 2.7 11.1 + - - +
148H VAL* 3.4 8.7 - - + -
149H TYR* 2.9 26.5 + - - +
203H ILE* 3.4 33.7 - - + -
211H TRP* 3.7 34.5 - - + -
214H HIS* 4.7 1.6 - - + -
215H ARG* 1.3 76.7 - - - +
217H ALA* 1.3 71.2 + - - +
218H LEU* 3.4 5.4 + - + +
282H PHE* 3.8 2.7 - - - -
320H GLU* 4.1 16.8 - - + +
321H ALA* 4.8 2.0 - - - +
324H LEU* 3.7 22.9 - - + -
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Residues in contact with ALA 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H TYR* 3.7 5.6 - - - -
216H ILE* 1.3 77.2 - - - +
218H LEU* 1.3 59.1 + - - +
219H THR* 2.9 15.3 + - + +
277H PHE* 4.4 7.4 - - + -
282H PHE* 3.5 20.7 - - + -
317H VAL* 3.4 42.7 - - + +
320H GLU* 4.8 3.5 + - - +
321H ALA* 3.5 17.2 + - - +
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Residues in contact with LEU 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLN* 5.5 2.9 - - - +
78H PHE* 5.9 0.2 - - + -
148H VAL* 4.0 31.2 - - + -
149H TYR 2.8 20.4 + - - +
150H ALA* 4.1 11.0 - - + -
151H GLY 3.2 6.9 + - - -
190H LEU* 3.2 30.7 - - + +
196H VAL* 4.2 30.5 - - + -
199H ALA* 3.9 16.4 - - + -
200H LEU* 4.8 7.9 - - + -
216H ILE* 3.4 7.3 + - + +
217H ALA* 1.3 68.2 - - - +
219H THR* 1.3 59.0 + - - +
220H PHE* 3.6 32.8 - - + -
321H ALA* 4.8 2.5 - - + -
324H LEU* 6.4 1.1 - - + -
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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