Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 1CK7
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 GLN 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS* 3.5 25.0 + - - +
122A ASN* 1.3 77.2 - - - +
124A ILE* 1.3 60.9 + - - +
125A THR* 5.3 3.6 - - + +
158A ARG* 3.4 16.6 - - + +
160A SER* 4.3 16.5 + - - +
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Residues in contact with ILE 124 (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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119A TRP* 3.2 51.8 - - + -
121A LYS* 4.3 11.7 - - + +
122A ASN 4.5 0.2 - - - -
123A GLN* 1.3 79.7 - - - +
125A THR* 1.3 63.2 + - - +
157A LEU* 4.2 17.3 - - + -
158A ARG 3.0 6.5 + - - +
159A PHE* 3.0 37.5 - - + -
160A SER* 2.7 32.6 + - - -
168A ASP* 3.4 21.8 - - + -
169A ILE* 4.3 9.2 - - + -
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Residues in contact with THR 125 (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 LYS* 5.7 2.5 - - - +
123A GLN* 5.3 5.2 - - + +
124A ILE* 1.3 83.2 - - - +
126A TYR* 1.3 64.2 + - - +
160A SER* 3.0 20.0 - - - +
162A ILE* 3.9 26.7 - - + +
166A GLU 5.0 0.3 + - - -
167A ALA* 3.8 5.0 - - - -
168A ASP* 2.8 38.6 + - - +
169A ILE* 3.1 22.5 + - - +
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Residues in contact with TYR 126 (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 THR* 1.3 77.5 - - - +
127A ARG* 1.3 57.8 + - - +
128A ILE* 4.6 9.4 - - + -
141A ASP 5.5 1.0 + - - -
144A PHE* 5.0 5.6 - - + -
145A ALA* 4.3 17.4 + - - +
148A PHE* 3.2 48.8 - + + -
159A PHE* 4.0 12.6 - + + -
160A SER 2.7 35.6 + - - -
161A ARG* 3.2 36.0 + - + +
162A ILE 2.7 31.5 + - - -
167A ALA* 3.6 4.3 - - - -
169A ILE* 2.9 19.7 - - + +
171A ILE* 3.6 18.8 - - + -
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Residues in contact with ARG 127 (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 TYR* 1.3 76.2 - - - +
128A ILE* 1.3 73.8 + - - +
129A ILE* 3.4 15.2 + - + +
161A ARG* 5.0 0.2 - - - -
162A ILE* 3.3 20.6 - - - +
163A HIS* 2.8 25.7 + - - -
164A ASP* 3.7 7.7 + - - +
165A GLY* 2.7 41.4 + - - +
167A ALA* 3.5 5.1 - - + +
169A ILE 3.0 6.1 + - - -
170A MET* 3.5 32.7 - - - +
171A ILE* 3.0 26.5 + - - +
311A THR* 3.0 42.8 + - - +
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Residues in contact with ILE 128 (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 TYR* 4.6 8.0 - - + -
127A ARG* 1.3 80.0 + - - +
129A ILE* 1.3 61.7 - - - +
130A GLY 3.0 28.0 - - - +
131A TYR* 4.0 16.5 - - + -
141A ASP* 3.4 30.5 - - + +
144A PHE* 3.6 37.9 - - + -
161A ARG* 3.6 30.9 + - - +
162A ILE 4.7 0.4 + - - -
163A HIS* 6.3 0.2 - - - -
171A ILE* 3.9 15.7 - - + +
311A THR 5.0 1.9 - - - +
312A ASP* 4.5 12.5 - - - +
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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