Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 1Y67
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 THR 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A VAL* 3.2 1.7 - - - -
139A VAL 2.9 40.0 + - - -
156A LEU* 4.1 14.0 - - + +
166A GLY* 1.3 72.0 - - - -
168A PRO* 1.3 78.7 - - + +
169A ILE* 3.5 5.6 + - + +
206A ARG 5.8 0.4 - - - +
210A ALA* 4.3 24.0 - - + +
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Residues in contact with PRO 168 (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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83A MET* 3.5 16.4 - - + +
136A TRP* 3.5 30.5 - - + -
137A LEU 3.5 7.6 - - - +
138A VAL* 3.8 4.9 - - + -
154A ASN* 3.5 24.2 - - - +
155A PRO* 3.9 14.8 - - + -
156A LEU* 3.6 22.0 - - + -
166A GLY 3.6 7.1 - - - +
167A THR* 1.3 92.4 - - + +
169A ILE* 1.3 62.6 + - - +
206A ARG* 4.8 5.2 + - - +
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Residues in contact with ILE 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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83A MET* 3.2 13.8 - - - +
87A ILE* 3.8 5.9 - - - +
104A LEU* 4.2 3.6 - - + -
137A LEU* 2.9 37.6 + - + +
139A VAL* 4.1 11.4 - - + -
144A LEU* 3.9 19.7 - - + -
167A THR* 3.8 9.4 - - + +
168A PRO* 1.3 78.8 - - - +
170A LEU* 1.3 62.5 + - - +
203A VAL* 3.5 35.3 - - + +
206A ARG* 3.8 41.3 - - + +
207A TYR* 3.9 18.2 - - + +
210A ALA* 4.4 4.3 - - + -
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Residues in contact with LEU 170 (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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83A MET* 3.5 4.7 - - - +
87A ILE* 3.7 24.5 - - + -
118A PHE* 4.3 15.9 - - + -
122A PHE* 4.4 13.9 - - + -
136A TRP* 3.3 10.2 - - - -
137A LEU* 2.8 38.5 + - + +
169A ILE* 1.3 80.5 - - - +
171A GLY* 1.3 64.6 + - - +
194A PHE* 4.0 10.8 - - + -
195A TRP* 4.3 11.0 - - + -
198A VAL* 3.9 19.5 - - + -
200A TRP* 3.7 30.7 - - + -
203A VAL* 4.1 13.2 - - + -
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Residues in contact with GLY 171 (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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83A MET* 4.6 2.2 - - - +
84A PHE* 3.6 16.6 - - - -
87A ILE* 3.6 16.3 - - - +
122A PHE* 4.4 2.9 - - - -
134A TRP* 4.2 6.1 - - - -
135A ALA 3.1 11.4 - - - -
136A TRP* 3.7 18.3 - - - -
170A LEU* 1.3 78.9 - - - +
172A VAL* 1.3 60.0 + - - -
194A PHE* 3.6 5.3 - - - -
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Residues in contact with VAL 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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84A PHE* 4.0 2.9 - - + -
122A PHE* 3.4 24.2 - - + -
126A ALA* 4.2 2.7 - - + -
134A TRP* 3.3 10.4 - - - -
135A ALA* 3.0 37.3 + - + +
171A GLY* 1.3 72.1 - - - +
173A ASP* 1.3 66.5 + - - +
174A VAL* 3.5 2.3 + - + -
190A TYR* 3.6 25.4 - - + +
191A LEU* 4.1 18.4 - - + -
194A PHE* 3.9 36.1 - - + -
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Residues in contact with ASP 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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27A HIS* 2.8 10.4 + - - -
81A HIS* 3.4 2.4 + - - -
84A PHE* 3.7 14.7 - - + -
133A GLY 3.8 0.3 - - - +
134A TRP* 3.4 29.1 - - + -
172A VAL* 1.3 72.9 - - - +
174A VAL* 1.3 58.9 + - - +
175A TRP* 3.1 31.3 + - - +
177A HIS* 3.5 0.2 + - - -
178A ALA* 3.6 17.0 - - + +
190A TYR* 2.7 31.2 + - - -
229A FE 1.9 32.4 - - - -
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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