Contacts of the helix formed by residues 198 - 207 (chain A) in PDB entry 3V4K
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A SER 3.6 2.6 + - - -
197A MET* 1.3 75.7 - - - +
199A PRO* 1.3 73.6 - - - +
200A PRO* 3.0 32.4 - - - +
201A THR* 3.0 30.3 + - - +
202A PHE* 3.0 18.0 + - - +
352A ASP* 5.1 1.3 - - - -
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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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197A MET 3.6 3.1 - - - +
198A ASP* 1.3 87.3 - - - +
200A PRO* 1.3 74.7 - - + +
202A PHE* 3.1 4.1 + - + +
203A THR* 2.9 27.5 + - - -
347A TRP* 3.8 22.8 - - + -
351A VAL* 3.8 15.3 - - + -
352A ASP* 3.3 31.2 - - + +
353A HIS* 4.6 2.0 - - - -
354A GLN* 6.2 0.2 - - + -
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Residues in contact with PRO 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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198A ASP* 3.0 27.4 - - - +
199A PRO* 1.3 94.1 - - + +
201A THR* 1.3 55.5 + - - +
203A THR* 4.0 5.9 - - - +
204A PHE* 2.9 31.9 + - - +
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Residues in contact with THR 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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197A MET* 4.4 8.1 - - + -
198A ASP* 3.0 29.3 + - - +
200A PRO* 1.3 76.4 - - - +
202A PHE* 1.3 65.5 + - - +
204A PHE* 4.6 1.8 - - - -
205A ASN* 2.9 43.7 + - - +
219A TYR* 3.5 34.8 - - + +
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Residues in contact with PHE 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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197A MET* 3.7 18.9 - - + -
198A ASP 3.0 8.4 + - - +
199A PRO* 3.1 7.6 + - + +
201A THR* 1.3 78.0 - - - +
203A THR* 1.3 63.7 + - - +
205A ASN 3.3 0.3 + - - -
206A PHE* 2.8 69.9 + + + +
221A CYS* 5.8 0.9 - - - -
343A PHE* 3.8 26.5 - + - -
346A CYS* 3.8 22.0 - - + -
347A TRP* 3.6 30.5 - + + -
350A PHE* 6.2 0.2 - - + -
351A VAL* 3.6 25.8 - - + -
358A PHE* 4.2 16.4 - + - -
361A TRP* 4.3 6.5 - + - -
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Residues in contact with THR 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* 2.9 17.2 + - - +
200A PRO* 4.0 5.6 - - - -
202A PHE* 1.3 85.6 - - - +
204A PHE* 1.3 63.2 + - - +
207A ASN* 3.2 27.8 + - + +
347A TRP* 4.1 9.7 - - - -
359A GLN 6.1 0.2 - - - +
361A TRP* 4.3 25.0 - - + -
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Residues in contact with PHE 204 (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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200A PRO 2.9 19.0 + - - +
201A THR* 3.9 4.0 - - - +
203A THR* 1.3 79.8 - - - +
205A ASN* 1.3 76.8 + - - +
207A ASN* 3.9 7.2 + - - +
213A ARG 4.8 5.2 - - - -
214A GLY* 3.6 33.7 - - - -
215A ARG* 3.5 34.3 - - + -
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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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201A THR* 2.9 34.1 + - - +
202A PHE* 4.1 1.1 - - - +
204A PHE* 1.3 97.2 - - - +
206A PHE* 1.3 64.7 + - + +
215A ARG* 4.8 7.2 - - - +
217A GLU* 4.0 23.8 + - - +
219A TYR* 3.5 40.9 - - + -
284A SER* 3.2 9.1 + - - -
313A ARG* 2.6 33.8 + - - -
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Residues in contact with PHE 206 (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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197A MET* 4.5 10.1 - - + -
202A PHE* 2.8 61.6 + + + +
205A ASN* 1.3 76.4 - - + +
207A ASN* 1.3 68.4 + - - +
208A ASN 3.2 2.1 + - - -
219A TYR* 3.8 39.3 - - + -
221A CYS* 4.3 10.5 - - - -
282A PHE* 3.9 13.0 - - + -
283A THR 3.8 19.7 - - - -
284A SER* 3.8 3.8 - - - -
312A ALA* 3.6 14.1 - - + +
313A ARG* 3.8 1.3 - - - +
338A MET* 4.0 31.2 - - + -
343A PHE* 3.3 22.8 - - + -
346A CYS* 5.3 0.7 - - - -
361A TRP* 3.9 4.0 - - + -
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Residues in contact with ASN 207 (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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203A THR* 3.2 22.0 + - + +
204A PHE* 3.9 9.9 + - - +
205A ASN 3.5 0.2 - - - -
206A PHE* 1.3 72.8 - - - +
208A ASN* 1.3 58.4 + - - +
209A GLU* 3.0 30.8 + - - +
212A VAL* 4.0 20.2 - - - +
215A ARG* 2.9 13.8 + - - +
313A ARG* 2.8 23.7 + - - -
361A TRP* 3.6 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