Contacts of the strand formed by residues 122 - 129 (chain A) in PDB entry 2KOY
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MET* 3.3 29.3 - - - +
10A ARG* 6.2 0.6 - - - +
117A HIS* 4.3 32.6 + - + +
118A GLU* 3.2 30.3 + - + +
120A LYS* 3.4 5.6 - - + -
121A GLY* 1.3 80.3 - - - +
123A THR* 1.3 62.0 + - - +
138A ALA* 3.0 37.6 - - - +
139A ILE 2.7 20.9 - - - +
140A ALA* 4.0 5.8 - - + +
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Residues in contact with THR 123 (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 ASN* 6.1 1.1 - - + -
118A GLU* 5.0 4.5 - - - +
121A GLY 4.0 6.6 + - - -
122A GLN* 1.3 77.3 + - - +
124A ALA* 1.3 67.2 + - - +
125A ILE* 3.7 11.4 + - + -
138A ALA* 3.5 5.8 - - - +
139A ILE* 2.7 58.4 + - + +
141A ASP* 4.6 6.2 - - - +
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Residues in contact with ALA 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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95A ASN* 2.9 32.4 - - + +
96A ARG* 4.3 20.9 - - + +
114A MET* 5.1 14.6 - - + -
118A GLU* 5.2 11.8 + - + +
122A GLN 4.3 0.6 + - - -
123A THR* 1.3 74.1 - - - +
125A ILE* 1.3 65.6 + - - +
126A LEU* 4.2 3.8 - - + -
137A ILE 4.1 2.9 - - - -
138A ALA* 5.1 1.8 - - - +
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Residues in contact with ILE 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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8A VAL* 6.0 0.7 - - + -
93A ILE* 5.2 13.5 - - + -
94A GLY* 3.5 10.3 - - - +
95A ASN* 5.1 2.0 - - + -
123A THR* 4.2 10.5 - - + +
124A ALA* 1.3 80.6 - - - +
126A LEU* 1.3 55.5 + - - +
137A ILE* 2.8 74.7 + - + +
139A ILE* 3.4 41.5 - - + -
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Residues in contact with LEU 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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93A ILE* 3.3 3.8 - - - +
94A GLY 2.9 57.6 + - - +
95A ASN 4.0 3.6 - - - +
96A ARG 5.5 0.2 - - - +
98A TRP* 5.7 1.6 - - + -
99A LEU* 3.2 53.4 - - + +
124A ALA* 5.4 3.4 - - + -
125A ILE* 1.3 76.5 - - - +
127A VAL* 1.3 64.9 + - - +
128A ALA 5.9 0.2 - - - +
133A LEU* 3.7 26.2 - - + -
135A GLY 3.5 12.8 - - - +
136A MET* 3.6 18.6 - - + +
137A ILE* 4.0 0.7 - - - +
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Residues in contact with VAL 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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91A VAL* 3.9 22.0 - - + -
92A LEU 2.9 21.5 - - - +
93A ILE* 3.2 34.1 - - + -
126A LEU* 1.3 75.6 - - - +
128A ALA* 1.3 62.0 + - - +
129A ILE* 4.3 6.7 - - + -
133A LEU* 4.0 2.9 - - - -
134A CYS* 3.1 16.3 + - + +
135A GLY* 2.8 26.8 + - - +
137A ILE* 4.0 15.3 - - + -
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Residues in contact with ALA 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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90A SER 3.8 0.2 - - - +
91A VAL* 3.4 0.9 - - - -
92A LEU* 2.7 64.7 + - + +
126A LEU* 5.9 0.8 - - + +
127A VAL* 1.3 73.5 - - - +
129A ILE* 1.3 68.4 + - - +
130A ASP 4.3 0.2 - - - -
131A GLY 5.0 1.1 - - - -
132A VAL 3.6 15.7 - - - +
133A LEU* 3.8 19.7 - - + +
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Residues in contact with ILE 129 (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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20A LEU* 5.4 3.8 - - + -
28A VAL* 4.5 22.0 - - + -
32A ALA* 6.0 4.0 - - + -
89A PHE* 5.5 2.0 - - + -
90A SER 3.2 4.5 - - - +
91A VAL* 3.6 31.9 - - + -
127A VAL* 4.3 7.2 - - + +
128A ALA* 1.3 82.9 - - - +
130A ASP* 1.3 96.3 + - - +
131A GLY 3.2 1.1 - - - -
132A VAL* 2.7 27.0 + - - +
134A CYS* 3.2 33.4 - - + -
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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