Contacts of the strand formed by residues 164 - 169 (chain A) in PDB entry 3I89
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.1 14.7 - - - +
118A THR* 4.0 0.2 + - - -
134A ARG* 2.9 37.1 + - + +
137A ASP* 4.7 0.4 + - - -
159A LEU* 4.4 14.1 - - + -
161A GLU* 3.8 17.9 - - + +
162A LEU 4.2 0.2 - - - -
163A HIS* 1.3 76.9 + - - +
165A ILE* 1.3 66.2 + - - +
166A ASP 3.8 3.4 - - - +
167A VAL* 3.7 30.1 - - + -
180A PHE* 3.7 30.7 - - + -
181A VAL 3.5 11.7 - - - +
182A TYR* 4.0 2.2 - - + -
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Residues in contact with ILE 165 (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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117A GLU* 5.5 1.8 - - + +
118A THR* 3.2 38.9 + - + +
121A ILE* 4.2 3.4 - - - +
163A HIS* 3.5 30.5 - - + +
164A VAL* 1.3 75.3 - - - +
166A ASP* 1.3 60.0 + - - +
181A VAL* 2.7 26.4 + - + +
182A TYR* 4.2 9.9 - - - -
183A GLN* 4.3 1.3 - - + +
188A ARG* 3.4 35.9 - - - +
216A ALA 3.7 4.7 - - - +
217A SER* 3.6 37.1 - - - +
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 5.8 1.1 - - + -
121A ILE* 4.4 13.8 - - - +
164A VAL* 3.8 0.7 - - - +
165A ILE* 1.3 80.8 - - - +
167A VAL* 1.3 91.1 + - - +
168A LYS* 2.9 23.8 + - - -
180A PHE* 3.2 6.8 - - - +
181A VAL* 3.1 25.7 + - - +
217A SER 3.6 18.6 - - - +
218A MET* 3.8 3.8 - - - +
219A VAL* 2.8 36.0 + - + +
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Residues in contact with VAL 167 (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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121A ILE* 4.0 20.1 - - + +
123A ILE* 3.4 30.7 - - + +
134A ARG* 5.2 8.5 - - + -
140A PHE* 5.1 7.6 - - + -
164A VAL* 3.7 19.1 - - + -
166A ASP* 1.3 94.3 + - - +
168A LYS* 1.3 81.4 + - - +
178A ILE* 4.3 15.7 - - + -
179A CYS 3.1 18.4 - - - +
180A PHE* 3.6 10.1 - - + -
219A VAL* 4.8 1.6 - - - -
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Residues in contact with LYS 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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121A ILE* 5.8 1.1 - - - -
123A ILE* 4.0 22.2 - - + -
166A ASP* 2.9 18.7 + - - -
167A VAL* 1.3 85.7 - - - +
169A PHE* 1.3 69.3 + - - +
178A ILE* 3.6 1.7 - - - +
179A CYS* 2.8 31.9 + - + +
218A MET* 6.2 0.8 - - - +
219A VAL* 2.5 45.9 + - + +
220A ILE* 5.4 0.4 - - - -
221A ALA* 3.9 17.3 - - + +
261A HIS* 3.9 18.9 + - + -
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Residues in contact with PHE 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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123A ILE* 3.5 28.5 - - + +
124A ILE 3.4 8.5 - - - +
125A ASP* 3.3 34.8 - - + -
126A PRO* 4.0 20.0 - - + +
130A MET* 3.6 36.8 - - + -
132A GLY* 4.0 15.0 - - - -
140A PHE* 4.7 2.5 - + - -
168A LYS* 1.3 75.2 - - - +
170A LEU* 1.3 60.7 + - - +
171A TYR* 4.7 4.3 - - - -
176A PRO* 4.4 6.3 - - + -
177A THR 3.3 25.1 - - - +
178A ILE* 3.4 21.5 - - + -
195A VAL* 4.8 0.9 - - + -
221A ALA* 3.4 18.6 - - - +
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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