Contacts of the strand formed by residues 173 - 179 (chain B) in PDB entry 4MZF
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 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A M3L 3.1 23.9 - - - -
151B TRP* 4.0 9.2 - - + -
169B THR* 3.6 0.3 + - - -
170B TYR* 3.0 22.6 + - + +
172B LYS* 1.3 82.7 - - - +
174B PRO* 1.3 60.7 - - - +
175B VAL* 2.9 25.4 + - - +
177B TYR* 2.5 31.3 + - - -
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B THR* 3.3 15.5 - - + +
170B TYR 3.5 7.9 - - - +
171B GLU 4.5 6.5 - - - +
172B LYS 3.9 4.5 - - - +
173B ASP* 1.3 84.4 - - - +
175B VAL* 1.3 58.8 + - + +
254B TYR* 3.5 10.9 - - + -
255B VAL 2.8 37.5 + - - +
256B TYR* 3.8 31.0 - - + +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B CYS* 4.3 13.2 - - - -
169B THR* 2.8 16.7 + - - -
173B ASP* 2.9 19.1 + - - +
174B PRO* 1.3 77.8 - - + +
176B LEU* 1.3 63.5 + - - +
177B TYR* 3.3 43.5 - - + +
252B HIS* 4.1 20.0 - - + -
253B ILE 3.3 9.6 - - - +
254B TYR* 3.6 36.3 - - + -
255B VAL* 4.3 1.6 - - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 5.0 2.0 - - + -
96B CYS* 3.5 8.3 - - - +
97B VAL* 3.0 56.3 + - + +
156B LEU* 3.6 30.3 - - + -
167B TYR* 3.7 28.5 - - + -
168B ILE 4.1 1.1 - - - +
175B VAL* 1.3 73.0 - - - +
177B TYR* 1.3 62.1 + - - +
244B PHE* 3.7 30.3 - - + -
253B ILE* 2.8 33.3 + - + +
255B VAL* 4.0 6.7 - - + +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A M3L 3.5 27.6 - - - -
95B ASP* 3.5 23.1 - - + -
96B CYS* 3.5 21.5 - - - +
97B VAL* 4.3 1.3 - - - -
167B TYR* 3.4 5.9 - - - -
168B ILE* 2.9 38.0 + - + +
170B TYR* 3.6 16.8 - + + -
173B ASP* 2.5 32.3 + - - -
175B VAL* 3.3 42.3 - - + +
176B LEU* 1.3 75.2 - - - +
178B MET* 1.3 63.8 + - - +
179B TYR* 3.8 26.2 - - + -
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.6 28.0 - - + -
90B LYS* 3.6 39.5 - - + -
95B ASP* 3.1 9.1 + - - +
97B VAL* 3.8 11.0 - - + -
159B ALA* 3.8 17.3 - - + -
162B MET* 3.8 31.9 - - + -
165B TRP* 3.7 34.4 - - + -
166B PHE 3.2 14.8 - - - +
167B TYR* 4.0 6.3 - - + -
177B TYR* 1.3 80.7 - - - +
179B TYR* 1.3 73.1 + - - +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.7 38.8 - - - +
4A M3L 3.2 22.4 - - - -
95B ASP* 3.0 46.3 + - + +
139B HIS* 3.9 5.6 - + - -
141B PHE* 3.7 14.8 - + - -
165B TRP* 3.8 11.7 - + - -
166B PHE* 2.9 30.3 + - - +
168B ILE* 3.8 11.9 - - + -
170B TYR* 3.4 26.0 - - - -
177B TYR* 3.8 16.8 - + + -
178B MET* 1.3 76.5 - - - +
180B GLN* 1.3 59.3 + - - +
181B LEU* 3.1 23.9 + - + +
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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