Contacts of the helix formed by residues 200 - 204 (chain T) in PDB entry 3P71
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 200 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C AN6 3.4 22.6 - - + +
97T LEU* 3.4 24.0 - - + +
98T GLY* 3.4 17.3 - - - +
172T LEU* 3.7 30.3 - - + -
197T ALA* 4.5 11.3 + - + -
198T GLU 3.5 10.8 - - - +
199T CYS* 1.3 82.5 - - - +
201T LEU* 1.3 70.2 + - + +
202T VAL 3.1 3.2 - - - +
203T TYR* 3.0 26.3 + - - +
204T MET* 4.0 8.7 - - + +
212T LEU* 6.0 0.2 - - + -
228T TYR 4.5 1.2 + - - -
229T GLU* 5.1 0.8 + - - -
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Residues in contact with LEU 201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197T ALA* 3.9 13.9 - - + +
200T VAL* 1.3 78.6 - - + +
202T VAL* 1.3 62.1 + - - +
203T TYR 3.1 1.7 + - - -
204T MET* 3.3 30.1 + - + +
209T SER* 3.9 23.3 + - - +
212T LEU* 3.9 28.5 - - + -
213T LEU* 4.4 12.6 - - + -
225T PHE* 4.3 14.6 - - + -
227T ASN* 3.3 29.4 + - + +
229T GLU* 3.3 12.0 + - - +
254T GLY* 4.9 1.2 - - - -
267T ARG* 3.5 29.2 + - - +
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Residues in contact with VAL 202 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199T CYS* 4.7 7.2 - - - -
200T VAL 3.1 2.0 + - - +
201T LEU* 1.3 75.3 - - - +
203T TYR* 1.3 83.2 + - + +
204T MET 3.4 0.4 - - - -
229T GLU* 3.1 19.2 + - + +
230T GLN* 3.3 31.9 - - - +
252T LEU* 3.4 20.4 - - + -
253T ALA 3.3 7.3 + - - -
254T GLY 3.1 35.1 + - - +
255T VAL* 4.3 3.1 - - + +
258T CYS* 3.9 19.5 - - - -
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Residues in contact with TYR 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C LEU* 3.7 28.3 + - + +
310C AN6 3.8 20.4 + + + +
22T ASN* 4.8 2.3 + - - -
26T VAL* 3.7 44.0 - - + +
29T THR* 3.6 24.0 - - + +
173T ARG* 5.1 6.9 + - - -
199T CYS* 3.3 27.3 - - - -
200T VAL* 3.0 19.5 + - - +
202T VAL* 1.3 89.8 - - + +
204T MET* 1.3 59.0 + - - +
230T GLN* 5.3 0.3 + - - -
250T CYS* 3.6 24.2 - - - -
251T ASP 4.4 4.4 - - - +
252T LEU* 3.7 20.5 - - + +
253T ALA* 3.8 13.1 + - - +
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Residues in contact with MET 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C AN6 4.2 11.7 - - - +
172T LEU* 4.1 33.9 - - + +
173T ARG* 3.9 20.9 - - + +
200T VAL* 4.0 22.6 + - + +
201T LEU* 3.4 20.4 - - - +
203T TYR* 1.3 80.9 - - - +
205T THR* 1.3 66.8 + - - +
208T GLN* 3.7 19.7 - - - +
209T SER* 3.7 33.5 + - - +
212T LEU* 4.4 13.2 - - + -
253T ALA* 3.6 6.5 - - - -
254T GLY* 3.1 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