Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 1CI1
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.1 2.2 - - + -
118A CYS* 3.8 12.1 - - - -
124A VAL* 3.8 3.8 - - + +
126A VAL* 4.6 13.7 - - + -
151A VAL* 5.6 2.0 - - + -
155A LEU* 3.8 23.3 - - + -
159A ALA 3.2 17.9 - - - +
160A TRP* 3.2 43.6 + - + +
161A SER 3.4 1.6 - - - +
162A ARG* 1.3 81.3 - - - +
164A VAL* 1.3 70.0 - - - +
165A ILE* 4.2 14.4 - - + -
207A LEU* 3.5 16.0 - - + +
208A ARG* 4.9 2.4 + - - -
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Residues in contact with VAL 164 (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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8A ILE* 3.8 26.2 - - + -
91A TRP* 4.5 11.7 - - + -
123A HIS* 5.2 2.2 - - + -
124A VAL 2.7 16.2 + - - +
125A ILE* 3.4 11.3 - - + -
126A VAL* 2.8 30.3 + - - +
162A ARG 5.0 4.3 - - - +
163A VAL* 1.3 78.1 - - - +
165A ILE* 1.3 66.1 + - - +
207A LEU* 4.7 0.4 - - - -
208A ARG* 3.7 28.3 - - + +
210A LEU* 3.7 33.0 - - + -
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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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126A VAL* 3.6 14.8 - - + +
128A VAL* 4.2 23.1 - - + -
148A LEU* 3.6 30.5 - - + -
151A VAL* 6.4 0.9 - - + -
160A TRP* 4.3 4.9 - - + -
163A VAL* 4.2 15.9 - - + -
164A VAL* 1.3 79.7 - - - +
166A ALA* 1.3 59.3 + - - +
167A TYR 4.1 0.2 - - - -
191A LEU* 4.5 11.0 - - + -
207A LEU* 4.0 13.0 - - + -
208A ARG 3.0 6.4 + - - +
209A ILE* 3.3 36.8 - - + -
210A LEU* 2.6 36.4 + - - +
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Residues in contact with ALA 166 (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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125A ILE* 3.6 25.6 - - + -
126A VAL 2.8 12.1 + - - +
127A CYS* 3.3 7.1 - - - +
128A VAL* 3.0 26.5 + - - +
164A VAL 4.1 0.2 + - - -
165A ILE* 1.3 76.3 - - - +
167A TYR* 1.3 59.7 + - - +
168A GLU* 3.6 2.0 + - + -
210A LEU* 3.5 9.4 - - + +
211A TYR 6.1 0.4 - - - -
212A GLY 5.7 0.2 - - - -
233A LEU* 3.9 26.9 - - + -
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Residues in contact with TYR 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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128A VAL* 3.6 16.4 - - + -
129A GLY* 4.2 7.4 - - - -
130A GLU* 3.1 36.1 + - - -
135A ARG* 3.5 13.2 + - - -
144A VAL* 4.3 4.0 - - + -
165A ILE* 4.1 1.0 - - - +
166A ALA* 1.3 71.2 - - - +
168A GLU* 1.3 60.3 + - - +
169A PRO* 3.5 30.6 - - + +
171A TRP* 4.6 0.9 - - - -
179A ALA* 5.6 1.8 - - + -
183A GLN 4.9 0.7 - - - -
184A ALA* 4.7 6.5 - - - -
187A VAL* 3.7 33.7 - - + +
188A HIS* 3.7 30.1 - + + +
191A LEU* 4.4 13.7 - - + -
209A ILE* 4.9 0.9 - - + -
210A LEU 2.7 16.4 + - - +
211A TYR* 3.6 10.2 - + - -
212A GLY 3.1 22.7 + - - +
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Residues in contact with GLU 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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96A HIS* 3.1 28.2 + - - -
97A SER* 3.0 33.4 + - - -
127A CYS* 3.5 19.1 - - + +
128A VAL 3.1 13.4 + - - +
129A GLY* 3.7 11.9 - - - -
166A ALA* 4.2 8.1 - - + +
167A TYR* 1.3 75.5 - - - +
169A PRO* 1.3 69.1 - - - +
170A VAL* 3.1 6.2 + - - +
173A ILE* 3.6 22.7 - - + +
212A GLY* 3.5 19.3 - - - +
213A GLY 4.8 0.2 - - - +
233A LEU* 4.6 7.7 - - + +
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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