Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 1I6P
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLU 2.9 8.3 + - - -
92A HIS* 3.3 23.6 - - + -
93A ILE* 2.7 34.0 + - - +
173A LYS 5.5 0.3 - - - -
174A VAL* 1.3 77.0 + - - +
176A ILE* 1.3 59.7 + - - +
177A HIS* 3.4 14.3 - - + +
194A THR* 3.3 32.1 - - + -
195A ALA 3.4 8.1 - - - +
196A THR* 3.5 18.6 - - + +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 3.3 13.5 - - + +
95A ILE* 4.8 2.5 - - + -
155A VAL* 3.8 31.2 - - + +
158A LEU* 4.1 24.7 - - + -
159A GLY* 4.0 22.0 - - - +
164A MET* 4.0 20.6 - - + -
168A TRP* 3.8 28.0 - - + -
175A THR* 1.3 77.2 - - - +
177A HIS* 1.3 69.6 + - - +
193A VAL 4.4 0.9 - - - +
194A THR* 3.2 9.2 - - - +
195A ALA* 2.9 35.2 + - + +
201A LEU* 5.3 0.2 - - + -
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Residues in contact with HIS 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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92A HIS* 2.9 34.2 + + + -
93A ILE 2.8 18.5 + - - +
94A ILE* 4.2 17.5 - - + -
95A ILE* 3.0 26.1 + - - +
155A VAL* 3.9 10.4 - - - +
175A THR* 3.4 25.5 - - + +
176A ILE* 1.3 74.9 - - - +
178A GLY* 1.3 60.5 + - - +
179A TRP* 3.7 31.1 + + + +
190A ASP* 5.2 1.6 + - - -
194A THR* 3.6 24.3 + - + +
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Residues in contact with GLY 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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95A ILE 3.7 4.7 - - - -
151A VAL* 3.7 17.3 - - - -
155A VAL* 3.8 9.6 - - - -
177A HIS* 1.3 73.5 - - - +
179A TRP* 1.3 64.2 + - - -
190A ASP* 3.7 3.4 + - - +
191A LEU* 2.9 31.8 + - - +
193A VAL* 3.8 15.9 - - - +
194A THR 5.1 0.8 - - - +
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Residues in contact with TRP 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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39A TRP* 4.1 9.6 - + - -
53A THR* 4.5 5.6 - - + -
94A ILE* 3.6 41.5 - - + -
95A ILE 3.0 9.8 + - - +
96A CYS* 3.4 12.4 - - + -
97A GLY 3.0 20.9 + - - -
151A VAL* 3.7 7.4 - - - +
177A HIS* 3.7 23.5 - + + +
178A GLY* 1.3 86.9 - - - -
180A ALA* 1.3 64.7 + - - +
188A LEU* 3.8 40.6 - - + -
189A ARG 3.3 8.7 - - - +
190A ASP* 3.5 35.2 + - + -
191A LEU* 4.5 2.9 - - - -
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Residues in contact with ALA 180 (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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96A CYS* 4.2 1.8 - - - -
97A GLY* 3.2 17.7 - - - +
98A HIS* 4.8 0.9 - - - +
99A TYR* 3.9 27.1 - - + +
147A CYS* 5.1 2.9 - - - -
148A GLU* 5.0 2.9 - - + -
151A VAL* 5.0 2.7 - - + -
179A TRP* 1.3 79.7 - - - +
181A TYR* 1.3 59.2 + - - +
188A LEU* 3.7 1.2 - - - -
189A ARG* 2.7 38.9 + - - +
191A LEU* 4.6 14.6 - - + -
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Residues in contact with TYR 181 (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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39A TRP* 5.5 0.9 - + - -
45A SER* 4.3 2.1 - - - -
46A ARG* 3.4 14.9 + - - +
47A VAL* 3.2 36.3 + - + -
52A LEU* 3.7 28.9 - - + -
96A CYS* 3.6 17.7 - - - -
97A GLY 3.3 12.6 + - - -
98A HIS* 3.2 30.8 - + + +
99A TYR* 3.0 29.2 + - - -
180A ALA* 1.3 75.7 - - - +
182A GLY* 1.3 69.7 + - - +
183A ILE* 3.7 23.6 - - + -
186A GLY* 4.7 3.6 - - - -
187A LEU 3.5 18.8 - - - +
188A LEU* 4.0 11.0 - - + -
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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