Contacts of the strand formed by residues 217 - 223 (chain A) in PDB entry 5VAI
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ALA 5.6 0.7 - - - +
41A HIS* 4.0 17.9 - - + +
212A PHE 3.9 0.2 - - - +
213A GLN* 3.1 4.9 - - - +
214A VAL* 2.8 36.5 + - - +
215A ASP 3.4 11.4 - - - +
216A LYS* 1.3 84.2 - - - +
218A ASN* 1.3 61.7 + - - +
219A PHE* 3.4 36.2 + - + -
376A PHE* 3.4 27.8 - - + -
380A ARG* 5.8 0.9 - - - +
257R PHE* 6.1 4.7 - - + -
258R ALA* 5.9 8.3 - - + +
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Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 5.6 6.7 + - - +
39A ALA* 5.2 8.1 + - - +
40A THR* 3.5 24.9 + - + +
41A HIS* 3.0 24.8 + - - -
212A PHE 3.4 8.0 - - - +
213A GLN* 2.8 30.8 + - - +
216A LYS 5.9 0.2 - - - -
217A VAL* 1.3 71.9 - - - +
219A PHE* 1.3 66.9 + - - +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 3.9 3.3 - - - +
41A HIS* 3.4 32.5 - + + +
43A LEU* 4.6 9.2 - - + -
210A THR 3.3 4.0 - - - +
211A LYS* 3.5 3.1 - - - -
212A PHE* 2.9 41.9 + - + +
214A VAL* 4.8 19.3 - - + -
217A VAL* 3.4 29.4 - - + -
218A ASN* 1.3 82.7 - - - +
220A HIS* 1.3 62.5 + - - +
221A MET* 4.0 2.5 - - + +
372A ILE* 5.6 2.9 - - + -
375A VAL* 4.4 17.0 - - + -
376A PHE* 4.0 35.4 - + + -
379A CYS* 4.8 9.2 - - + -
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Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 4.0 10.3 - - + -
41A HIS 2.9 8.3 + - - +
42A ARG* 3.2 39.2 + - + +
43A LEU* 2.8 26.1 + - - +
209A GLU* 3.0 47.5 - - + +
210A THR 3.2 2.7 - - - -
211A LYS* 5.1 0.2 - - - +
219A PHE* 1.3 74.1 - - - +
221A MET* 1.3 64.9 + - - +
222A PHE* 5.2 0.3 - - - +
98B SER* 4.0 12.8 - - - -
99B TRP* 3.1 34.8 - + - -
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Residues in contact with MET 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.7 15.3 - - + +
45A LEU* 3.6 34.1 - - + -
53A LYS 4.1 13.0 - - - +
56A ILE* 6.0 6.7 - - + -
57A VAL* 3.8 31.9 - - + +
208A PHE 3.5 3.8 - - - +
209A GLU* 3.3 4.5 - - - -
210A THR* 2.9 51.5 + - + +
219A PHE* 4.0 2.5 - - + +
220A HIS* 1.3 79.5 - - - +
222A PHE* 1.3 65.5 + - - +
223A ASP* 6.5 1.1 - - + -
245A ILE* 5.3 7.4 - - + -
290A PHE* 6.4 0.9 - - - -
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU 3.0 14.5 + - - +
44A LEU* 3.8 8.7 - - + -
45A LEU* 2.9 33.8 + - - +
208A PHE* 3.5 29.2 - + + -
209A GLU* 4.3 4.5 - - + -
221A MET* 1.3 76.8 - - - +
223A ASP* 1.3 83.3 + - - +
224A VAL* 3.3 27.6 - - + -
227A GLN* 6.2 2.0 - - + -
238A PHE* 4.7 1.1 - + - -
99B TRP* 3.2 50.0 - + + -
117B LEU* 4.3 32.8 - - + -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.0 9.2 - - + +
46A LEU* 5.8 0.3 - - - -
53A LYS* 3.5 36.9 + - - +
207A ILE 5.3 0.2 - - - +
208A PHE* 3.0 49.7 + - + +
221A MET* 6.5 1.1 - - + -
222A PHE* 1.3 93.7 - - - +
224A VAL* 1.3 60.0 + - - +
225A GLY* 2.4 31.8 + - - -
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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