Contacts of the strand formed by residues 214 - 218 (chain G) 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 HIS 214 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ARG* 4.8 0.4 - - - -
145G SER 4.1 0.2 + - - -
146G THR* 3.5 6.9 - - + +
147G PHE* 2.8 26.5 + - - -
210G LYS 3.2 26.7 + - - -
211G TRP* 2.9 37.0 + + + +
212G ASN 3.0 23.2 + - - -
213G GLY* 1.3 78.2 - - - +
215G ARG* 1.3 64.6 + - - +
216G ILE* 4.0 1.8 - - + -
320G GLU* 4.4 14.1 + - - -
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Residues in contact with ARG 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G TYR* 5.9 0.2 - - - -
132G PHE* 3.5 20.8 - - - -
135G GLU* 2.8 29.1 + - - +
136G ASN* 4.9 3.6 - - - +
139G ARG* 4.2 18.9 - - - +
147G PHE* 3.2 8.7 - - + +
149G TYR* 3.7 17.7 + - + -
213G GLY 4.1 0.8 + - - -
214G HIS* 1.3 76.9 + - - +
216G ILE* 1.3 61.4 + - - +
279G LEU* 3.5 25.7 - - - +
280G PRO* 5.8 1.4 - - - +
281G GLU* 3.0 32.2 + - + +
282G PHE* 3.7 20.6 - - + -
320G GLU* 3.7 11.1 - - - +
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Residues in contact with ILE 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G THR* 3.7 21.5 - - + -
147G PHE 2.7 11.9 + - - +
148G VAL* 3.3 11.7 - - + -
149G TYR* 2.7 33.4 + - - +
203G ILE* 3.3 29.8 - - + -
211G TRP* 3.8 25.1 - - + -
214G HIS* 4.7 2.0 - - + -
215G ARG* 1.3 79.0 - - - +
217G ALA* 1.3 66.2 + - - +
218G LEU* 3.4 7.5 + - + +
282G PHE* 3.8 3.6 - - - -
320G GLU* 4.1 22.0 - - + +
321G ALA* 4.9 3.1 - - - +
324G LEU* 4.0 21.3 - - + -
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Residues in contact with ALA 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G TYR* 3.6 6.3 - - - -
216G ILE* 1.3 76.5 - - - +
218G LEU* 1.3 55.7 + - - +
219G THR* 2.8 17.5 + - + +
277G PHE* 4.3 8.1 - - + -
282G PHE* 3.6 27.0 - - + -
317G VAL* 3.1 37.5 + - + +
320G GLU* 4.8 2.7 + - - +
321G ALA* 3.4 17.3 + - - +
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Residues in contact with LEU 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G GLN* 6.0 2.9 - - - +
78G PHE* 5.9 0.4 - - + -
111G SER* 5.9 0.4 - - - +
148G VAL* 3.6 41.5 - - + -
149G TYR 2.6 17.9 + - - +
150G ALA* 4.0 11.7 - - + -
151G GLY 3.3 6.8 + - - -
190G LEU* 3.2 30.3 - - + +
196G VAL* 4.5 23.6 - - + -
199G ALA* 4.0 26.9 - - + -
200G LEU* 4.5 10.3 - - + -
203G ILE* 5.4 2.9 - - + -
216G ILE* 3.4 8.6 + - + +
217G ALA* 1.3 67.5 - - - +
219G THR* 1.3 57.8 + - - +
220G PHE* 4.8 11.0 - - + -
321G ALA* 4.7 4.5 - - + -
324G LEU* 5.9 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
------------------------------------------------------------
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