Contacts of the strand formed by residues 168 - 173 (chain A) in PDB entry 2Z98
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 VAL 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ALA* 3.3 13.0 - - + +
136A VAL* 3.9 20.0 - - + -
157A SER* 5.2 7.9 - - - +
160A LEU* 4.0 21.3 - - + -
165A ILE 3.6 21.5 - - - +
166A THR* 3.4 8.0 + - - +
167A ASP* 1.4 80.1 + - - +
169A LYS* 1.3 67.6 + - - +
170A PHE* 3.7 37.0 + - + -
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Residues in contact with LYS 169 (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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133A LYS* 6.3 4.0 - - - -
134A ALA 2.9 12.2 + - - +
135A ILE* 3.3 8.0 - - + +
136A VAL* 2.9 25.6 + - - +
167A ASP* 4.4 15.5 + - - +
168A VAL* 1.3 76.7 - - - +
170A PHE* 1.3 61.0 + - - +
197A ILE* 3.9 41.5 - - + +
200A ALA* 6.2 3.6 - - - -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 3.6 33.2 - - + -
138A THR* 4.7 3.6 - - + -
153A THR* 3.6 45.1 - - + -
156A LEU* 4.2 6.7 - - + -
157A SER* 3.4 31.6 - - - -
168A VAL* 3.7 28.9 - - + -
169A LYS* 1.3 75.8 - - - +
171A VAL* 1.3 63.1 + - - +
172A PHE* 3.6 22.6 - + + -
193A ALA* 5.4 0.7 - - - +
197A ILE* 5.6 0.3 - - - +
203A EDO 3.6 12.3 + - - -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.9 13.9 - - + -
136A VAL 2.8 11.8 + - - +
137A ILE* 3.5 12.2 - - + +
138A THR* 2.8 29.2 + - - +
170A PHE* 1.3 75.0 - - - +
172A PHE* 1.3 61.7 + - - +
190A ALA* 3.7 40.2 - - + +
193A ALA* 4.2 11.9 - - + -
194A ILE* 4.1 17.3 - - + -
197A ILE* 3.5 31.6 - - + -
203A EDO 3.6 3.6 - - - -
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Residues in contact with PHE 172 (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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138A THR* 3.5 16.2 - - + -
140A ARG* 3.8 22.2 - - - -
145A LYS* 3.7 44.2 - - + -
150A ASP* 3.8 3.8 - - - -
153A THR* 3.6 32.1 - - + -
170A PHE* 3.6 29.6 - + + -
171A VAL* 1.3 76.2 - - - +
173A ALA* 1.3 60.3 + - - +
174A GLU* 3.9 12.0 + - + -
186A ALA* 4.3 1.2 - - - +
189A ASP* 4.9 1.2 - - - +
190A ALA* 3.7 12.2 + - - +
203A EDO 2.9 43.7 + - - +
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Residues in contact with ALA 173 (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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16A GLN* 5.6 0.7 - - + -
20A LEU* 3.8 28.5 - - + -
137A ILE* 5.8 0.4 - - + -
138A THR 2.9 11.8 + - - +
139A SER* 3.2 10.6 - - - -
140A ARG 2.9 25.6 + - - +
172A PHE* 1.3 71.9 - - - +
174A GLU* 1.3 60.8 + - - +
176A ILE* 3.7 9.9 - - + +
186A ALA* 4.1 24.2 - - + +
187A GLN* 5.6 0.7 - - + -
190A ALA* 4.2 0.7 - - + -
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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