Contacts of the strand formed by residues 170 - 175 (chain A) in PDB entry 1H5Y
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 GLU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 2.6 39.5 + - - -
102A LYS* 2.8 34.4 + - + +
126A GLN 5.9 1.1 - - - +
128A THR 3.6 1.4 + - - +
129A VAL* 3.4 17.4 - - + +
130A VAL 3.1 23.4 + - - -
168A ALA* 3.5 3.9 - - - +
169A GLY* 1.3 80.7 - - - +
171A ILE* 1.3 65.8 + - - +
172A LEU 4.2 0.2 - - - -
199A ILE* 3.8 3.5 - - - +
200A PRO* 3.4 19.8 - - + +
202A ILE* 3.5 30.5 - - + +
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Residues in contact with ILE 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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130A VAL* 3.2 9.9 - - + +
132A ILE* 3.7 24.0 - - + -
160A ALA* 3.7 35.0 - - + +
163A VAL* 4.1 16.2 - - + -
170A GLU* 1.3 78.6 - - - +
172A LEU* 1.3 67.6 + - - +
173A LEU* 3.7 12.6 + - + -
193A VAL* 4.6 9.0 - - + -
197A VAL* 4.3 12.8 - - + -
199A ILE* 3.7 21.3 - - + -
200A PRO 3.1 8.5 + - - +
201A VAL* 3.5 5.9 - - + -
202A ILE* 2.8 29.6 + - - +
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Residues in contact with LEU 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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51A ALA* 5.7 0.7 - - + -
53A LEU* 4.8 16.4 - - + -
81A LEU* 4.6 21.1 - - + -
104A SER* 4.5 6.7 - - - +
129A VAL* 4.0 15.3 - - + +
130A VAL 2.9 7.5 + - - -
131A ALA* 3.2 19.3 - - + +
132A ILE 2.9 28.2 + - - +
133A ASP* 5.1 0.2 - - - +
171A ILE* 1.3 71.6 - - - +
173A LEU* 1.3 57.7 + - - +
174A THR* 3.9 7.4 + - - +
202A ILE* 3.6 27.1 - - + -
204A SER* 4.0 8.7 - - - -
225A LEU* 3.3 36.6 - - + -
401A GOL 5.0 5.4 - - - -
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Residues in contact with LEU 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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132A ILE* 3.5 30.7 - - + +
134A ALA* 5.0 0.7 - - + -
156A ALA* 5.1 0.2 - - + -
171A ILE* 3.6 5.8 - - + -
172A LEU* 1.3 73.0 - - - +
174A THR* 1.3 60.5 + - - +
175A SER 4.3 0.2 + - - -
189A LEU* 3.8 37.2 - - + +
190A ILE* 3.9 18.0 - - + +
193A VAL* 3.7 42.6 - - + -
201A VAL* 3.8 17.5 - - + -
202A ILE 2.9 13.5 + - - +
203A ALA* 3.8 1.7 - - - -
204A SER* 2.9 26.5 + - - +
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Residues in contact with THR 174 (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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132A ILE 3.0 7.3 + - - +
133A ASP* 3.3 17.4 + - - +
134A ALA* 2.9 26.5 + - - -
172A LEU* 4.6 5.4 + - - +
173A LEU* 1.3 72.4 - - - +
175A SER* 1.3 72.5 + - - +
176A ILE 3.5 0.2 + - - -
179A ASP* 3.8 26.7 - - + +
189A LEU* 4.0 5.5 - - - +
204A SER* 3.2 31.2 + - - +
401A GOL 3.4 21.6 + - - +
501A GOL 3.9 7.2 - - - +
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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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134A ALA 3.5 6.2 + - - -
173A LEU 4.3 0.2 - - - -
174A THR* 1.3 74.8 - - - +
176A ILE* 1.3 60.9 + - - +
177A ASP* 3.2 14.9 + - - +
178A ARG* 2.9 29.6 + - - +
179A ASP* 3.0 23.7 + - - +
186A ASP* 3.8 29.4 + - - +
189A LEU* 3.8 11.2 - - - +
204A SER 3.4 6.0 + - - -
205A GLY* 4.7 2.6 - - - -
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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