Contacts of the strand formed by residues 173 - 179 (chain A) in PDB entry 1ZN7
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 PHE 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.5 29.2 - - + -
136A MET* 3.9 15.0 - - - -
152A GLU* 4.3 2.2 - - - -
153A CYS* 3.2 20.9 - - + -
155A SER* 3.2 30.7 - - - -
158A GLU* 3.5 30.5 - - + -
165A ARG* 2.9 56.3 + - + +
168A LEU* 3.9 23.8 - - + -
171A VAL 3.7 2.4 + - - +
172A PRO* 1.3 76.1 - - - +
174A PHE* 1.3 73.2 + - - +
175A SER* 3.7 9.4 - - - -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 4.6 2.0 - - - -
46A LEU* 4.1 15.5 - - + -
49A HIS* 3.4 51.1 - + + +
152A GLU* 3.1 22.0 - - - +
153A CYS 3.1 6.1 + - - -
154A VAL* 3.1 9.9 - - + +
155A SER 3.0 23.0 + - - -
165A ARG* 4.6 2.2 - - - +
173A PHE* 1.3 80.0 - - - +
175A SER* 1.3 74.7 + - - +
176A LEU* 3.7 30.1 - - + -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 3.2 18.4 - - - -
157A VAL 4.3 0.2 - - - -
158A GLU* 2.6 46.2 + - - +
165A ARG* 5.2 1.4 + - - +
173A PHE* 3.7 3.0 - - - -
174A PHE* 1.3 91.5 - - - +
176A LEU* 1.3 60.8 + - - +
177A LEU 3.8 6.1 - - - -
178A GLN* 2.8 33.4 + - - -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.5 30.0 - - + +
9A VAL* 4.4 9.0 - - + -
42A ALA* 3.9 37.7 - - + +
45A LEU* 3.6 32.5 - - + -
46A LEU* 4.1 15.0 - - + -
155A SER 3.1 8.2 + - - +
156A LEU* 3.4 21.1 - - + +
174A PHE* 3.7 23.3 - - + -
175A SER* 1.3 74.6 - - - +
177A LEU* 1.3 65.7 + - + +
178A GLN* 3.5 7.0 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.6 21.8 - - + -
9A VAL* 3.9 11.7 - - + -
10A GLU* 3.7 42.0 - - + +
13A ILE* 3.7 31.9 - - + -
156A LEU* 2.8 14.2 + - + +
157A VAL* 3.4 3.0 - - + +
158A GLU 2.9 24.8 + - - -
175A SER* 3.6 5.0 + - - -
176A LEU* 1.3 90.4 - - + +
178A GLN* 1.3 65.7 + - - +
179A TYR* 4.1 18.6 - - + +
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 3.4 15.5 - - - +
160A THR* 3.9 19.5 - - + +
175A SER* 2.8 43.4 + - - +
176A LEU 3.5 4.8 + - - +
177A LEU* 1.3 86.6 - - - +
179A TYR* 1.3 69.6 + - - +
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.5 13.0 + - + +
13A ILE* 3.6 31.1 - - + +
15A SER* 5.2 1.3 - - - -
27A ARG* 3.5 49.4 - - + +
157A VAL* 3.6 33.9 - - + -
158A GLU 2.9 7.6 + - - +
159A LEU* 3.3 6.3 - - + -
160A THR* 2.8 35.6 + - - -
177A LEU* 4.1 23.7 - - + +
178A GLN* 1.3 77.0 - - - +
180A GLU* 1.3 58.6 + - - +
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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