Contacts of the helix formed by residues 198 - 205 (chain A) in PDB entry 3VAS
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 ALA 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.7 16.4 - - + -
169A PHE* 3.7 6.5 - - + -
196A LEU 2.7 12.2 + - - +
197A SER* 1.3 77.5 - - - +
199A PRO* 1.3 77.8 - - + +
200A PHE* 3.7 30.5 - - + -
201A LEU* 3.2 20.4 + - + +
202A SER* 3.9 4.0 + - - -
225A GLU* 3.4 9.1 + - - +
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Residues in contact with PRO 199 (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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37A ASN* 4.1 20.9 - - - +
38A ILE* 5.7 0.2 - - + -
198A ALA* 1.3 88.0 - - + +
200A PHE* 1.3 62.1 + - + +
201A LEU 3.1 1.0 + - - -
202A SER* 3.2 14.2 + - - -
203A GLN* 3.2 24.2 + - - +
222A ASN* 6.2 0.2 - - - +
224A SER* 3.9 31.9 - - - +
225A GLU* 3.8 10.7 - - + +
228A ALA* 3.8 21.7 - - + +
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Residues in contact with PHE 200 (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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37A ASN* 5.6 0.6 + - - -
38A ILE* 3.6 35.9 - - + -
39A VAL* 4.9 2.9 - - + -
40A LEU* 4.0 28.0 - - + -
169A PHE* 4.2 10.8 - + - -
172A ASN* 3.4 28.3 - - - -
198A ALA* 3.7 21.8 - - + -
199A PRO* 1.3 78.2 - - + +
201A LEU* 1.3 74.2 + - + +
203A GLN* 3.6 11.6 + - - +
204A PHE* 2.8 51.4 + + + +
205A ASN* 4.0 3.9 + - - +
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Residues in contact with LEU 201 (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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168A GLY* 3.4 38.1 - - - +
169A PHE* 3.6 12.1 - - + +
171A ILE* 4.4 8.1 - - + -
172A ASN* 3.7 15.7 - - - +
196A LEU 3.4 22.7 - - - +
197A SER* 3.7 7.9 - - - -
198A ALA* 3.2 10.5 + - + +
199A PRO 3.1 1.0 - - - -
200A PHE* 1.3 101.6 - - + +
202A SER* 1.3 57.7 + - - +
205A ASN* 2.8 50.5 + - + +
209A VAL* 3.8 12.1 - - + -
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Residues in contact with SER 202 (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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196A LEU* 4.6 10.0 + - - +
198A ALA 3.9 3.9 + - - -
199A PRO* 3.2 10.2 + - - +
201A LEU* 1.3 78.5 - - - +
203A GLN* 1.3 54.7 + - - +
206A THR* 2.6 34.2 + - - +
209A VAL* 4.2 14.1 - - - +
225A GLU* 4.3 5.0 + - - +
228A ALA* 4.4 0.9 - - - -
229A TYR* 3.5 50.8 - - - +
232A VAL* 3.7 7.5 - - - +
233A HIS* 5.3 0.2 - - - -
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Residues in contact with GLN 203 (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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199A PRO* 3.2 20.0 + - - +
200A PHE* 3.6 17.5 + - - +
201A LEU 3.2 0.4 - - - -
202A SER* 1.3 80.2 - - - +
204A PHE* 1.3 84.6 + - + +
205A ASN 3.6 0.2 - - - -
206A THR* 3.3 10.3 + - - -
228A ALA* 3.8 23.1 - - + +
231A GLU* 5.0 7.7 + - - -
232A VAL* 3.8 20.5 - - + +
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Residues in contact with PHE 204 (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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200A PHE* 2.8 41.0 + + + +
203A GLN* 1.3 100.8 - - + +
205A ASN* 1.3 74.0 + - - +
206A THR 3.6 1.8 - - - -
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Residues in contact with ASN 205 (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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171A ILE* 3.9 24.6 - - + +
172A ASN* 3.7 19.2 + - - +
200A PHE* 4.2 4.0 - - - +
201A LEU* 2.8 30.9 + - + +
204A PHE* 1.3 91.6 + - - +
206A THR* 1.3 63.7 + - - +
207A LYS 3.3 3.1 - - - -
208A GLU* 3.2 29.4 + - - +
209A VAL* 3.0 19.6 + - - +
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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