Contacts of the helix formed by residues 190 - 193 (chain K) in PDB entry 4PHZ
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 PRO 190 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K TYR* 5.2 0.4 - - - +
157K TYR* 3.9 34.5 - - + +
158K SER* 3.3 27.4 - - - +
161K ALA* 4.6 6.3 - - + -
186K VAL 3.1 26.7 - - - +
187K ALA* 3.7 13.9 - - - +
188K ILE 3.6 0.2 - - - -
189K GLY* 1.4 82.0 - - - +
191K PHE* 1.3 59.2 + - + +
193K ILE* 3.0 32.7 + - + +
194K ILE* 4.1 1.0 + - - +
228K ALA* 4.8 8.5 - - + -
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Residues in contact with PHE 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.1 34.8 - - + -
230B MET* 3.7 22.6 - - + +
158K SER* 3.5 24.7 - - - -
162K VAL* 4.9 15.9 - - + -
187K ALA 3.6 20.0 - - - -
188K ILE* 2.9 32.0 + - + +
190K PRO* 1.3 70.2 - - - +
192K MET* 1.3 59.6 + - + +
193K ILE 3.6 0.4 - - - -
194K ILE* 3.7 14.0 - - - +
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Residues in contact with MET 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA* 6.3 0.2 - - - -
151B VAL* 5.5 5.8 - - - -
230B MET* 4.1 26.9 - - - +
231B MET* 3.7 36.2 - - + +
234B PHE* 4.3 29.4 - - + -
188K ILE* 4.1 12.6 - - + +
189K GLY* 2.7 20.3 + - - +
191K PHE* 1.3 77.1 - - + +
193K ILE* 1.3 59.2 + - - +
194K ILE 3.3 1.1 - - - -
195K PRO* 3.4 26.5 - - + +
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Residues in contact with ILE 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J VAL* 4.7 18.2 - - + -
122K ALA* 5.7 1.8 - - + -
154K TYR* 4.0 42.0 - - + +
157K TYR* 3.9 20.6 - - + +
189K GLY 3.5 2.7 + - - +
190K PRO* 3.0 26.3 + - + +
192K MET* 1.3 78.3 - - - +
194K ILE* 1.3 64.6 + - + +
195K PRO 2.9 15.8 - - - +
196K ASN 3.8 7.1 - - - +
197K VAL* 4.2 8.4 - - + +
227K MET* 5.9 7.0 - - - -
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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