Contacts of the helix formed by residues 199 - 203 (chain F) 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 199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E PHE* 3.7 21.1 - - + -
139E ASN* 3.8 19.5 - - + +
197F SER* 3.5 7.9 - - - +
198F MET* 1.3 90.9 - - - +
200F GLU* 1.3 67.6 + - - +
201F TYR* 2.7 50.6 + - + +
202F ILE* 2.9 35.6 + - + +
203F ARG 4.2 0.2 + - - -
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E PHE* 3.6 31.1 - - + -
107E PRO 3.9 4.7 - - - +
108E ARG* 3.4 22.2 - - + +
109E SER* 3.0 26.9 + - - -
262E ALA* 3.5 1.4 - - - -
263E GLY 3.2 22.4 + - - +
198F MET* 3.4 4.7 + - - -
199F PRO* 1.3 69.8 - - - +
201F TYR* 1.3 62.5 + - - +
202F ILE 3.2 1.0 + - - -
203F ARG* 2.9 54.5 + - - +
207F ARG* 3.2 10.1 + - - -
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Residues in contact with TYR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 5.7 3.6 + - - +
82E VAL* 3.5 30.7 - - + -
83E SER* 4.0 15.3 - - - -
84E PHE* 4.2 0.9 - - + -
109E SER* 3.6 12.0 - - - +
139E ASN* 3.5 24.5 - - - +
140E VAL 3.0 21.5 + - - -
141E GLU* 3.3 43.1 + - + +
144E GLY* 5.0 1.7 + - - -
199F PRO* 2.7 39.7 + - + +
200F GLU* 1.3 79.2 + - - +
202F ILE* 1.3 79.1 - - + +
203F ARG 3.3 0.7 - - - -
204F MET 4.8 0.2 + - - -
207F ARG* 3.5 17.9 + - - +
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Residues in contact with ILE 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 5.2 0.7 - - - +
59F TRP* 3.6 16.0 - - + -
197F SER 4.8 5.6 - - - +
198F MET* 3.4 33.0 - - + -
199F PRO* 2.9 28.8 + - + +
201F TYR* 1.3 95.2 - - + +
203F ARG* 1.3 67.5 + - - +
204F MET* 3.3 11.6 + - - +
211J ARG* 5.8 6.5 - - - +
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Residues in contact with ARG 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ARG* 4.8 0.2 - - - +
260E LEU* 3.5 17.0 - - - +
261E GLN 3.1 17.4 + - - -
262E ALA* 3.4 8.9 - - - +
58F ASP* 3.1 38.5 + - - +
59F TRP* 2.8 54.5 - - + +
187F ASP* 2.6 28.0 + - - +
198F MET* 5.4 2.2 - - - -
199F PRO 5.0 0.9 - - - +
200F GLU* 2.9 56.5 + - - +
201F TYR 3.3 1.0 - - - -
202F ILE* 1.3 78.2 - - + +
204F MET* 1.3 64.6 + - - +
205F VAL* 4.0 14.4 - - + +
207F ARG* 3.8 6.7 - - - +
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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