Contacts of the strand formed by residues 181 - 184 (chain J) 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 GLN 181 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387E GLN* 6.2 0.2 - - - +
409E PRO* 4.0 23.9 - - + +
411E ILE* 4.4 1.6 - - - -
105I PHE* 3.4 33.9 - - + +
107I PRO* 3.3 28.7 - - - +
108I ARG* 4.4 18.6 - - - +
265I GLN* 4.3 7.7 + - - +
177J GLU* 3.4 3.2 - - - -
178J GLN* 2.7 47.0 + - - +
179J HIS 3.3 2.4 - - - +
180J GLY* 1.3 72.8 - - - +
182J LEU* 1.3 68.8 + - - +
183J MET* 3.7 4.5 + - + +
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Residues in contact with LEU 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E TYR* 5.0 0.7 - - - +
381E ALA* 6.6 0.2 - - - -
386E SER* 3.6 37.0 + - - +
409E PRO* 5.1 2.6 - - - +
410E VAL 4.6 6.0 + - - +
411E ILE* 4.2 9.9 - - + +
412E PRO* 3.9 22.7 - - + -
108I ARG* 5.0 2.9 + - - -
169I LEU* 4.5 5.8 - - + -
258I ILE* 3.6 30.3 - - + -
261I GLN* 3.7 22.0 - - - +
175J ALA* 3.6 26.2 - - + -
176J THR 3.5 17.9 - - - +
177J GLU* 4.6 1.3 - - - +
181J GLN* 1.3 77.7 + - - +
183J MET* 1.3 66.3 + - - +
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Residues in contact with MET 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I PHE* 4.4 11.7 - - - -
107I PRO* 3.8 25.8 - - + +
108I ARG* 6.2 0.4 - - + -
258I ILE* 3.6 9.6 - - - +
261I GLN* 4.2 7.6 - - + -
176J THR* 2.8 43.3 + - + +
178J GLN* 3.7 28.5 - - + -
181J GLN* 4.5 10.8 - - + +
182J LEU* 1.3 79.1 - - - +
184J THR* 1.3 66.4 + - - +
187J ASP* 4.1 24.0 - - + +
188J LEU* 4.0 23.6 - - + -
191J PHE* 4.2 7.6 - - + -
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Residues in contact with THR 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I ILE* 3.4 42.6 - - + +
259I PRO 3.4 17.3 - - - +
260I LEU* 3.6 7.5 - - + +
261I GLN* 4.4 0.2 - - - +
172J PHE 3.5 11.4 - - - -
173J HIS* 4.1 7.2 - - + +
174J GLN 3.4 6.1 - - - -
176J THR* 4.1 2.2 - - - -
183J MET* 1.3 75.8 - - - +
185J LEU* 1.3 65.2 + - - +
186J ALA* 4.4 1.1 - - - -
187J ASP* 2.5 39.8 + - - +
188J LEU* 3.1 21.3 + - - +
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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