Contacts of the helix formed by residues 121 - 130 (chain D) in PDB entry 1KYO
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 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D VAL* 4.8 1.1 - - - -
117D GLY 5.1 1.1 - - - +
120D HIS* 1.3 79.3 - - - +
122D ASN* 1.3 65.7 + - - +
123D GLU* 3.7 13.0 + - - +
124D GLU* 3.0 40.7 + - - +
125D VAL* 2.9 25.7 + - - +
49I TRP* 4.0 14.8 - - + +
53I LYS* 5.1 15.5 - - + -
56I ILE* 5.8 5.8 - - + -
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Residues in contact with ASN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 3.9 30.0 - - + +
121D THR* 1.3 72.5 - - - +
123D GLU* 1.3 74.5 + - - +
125D VAL* 3.6 1.6 + - - +
126D ARG* 3.1 38.4 + - - +
151D LEU* 3.3 23.3 - - - +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D THR* 3.1 12.1 + - - +
122D ASN* 1.3 88.4 + - - +
124D GLU* 1.3 65.8 + - + +
126D ARG* 3.2 21.0 + - - +
127D ASN* 2.9 36.2 + - - +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG* 2.8 39.5 + - - -
120D HIS* 4.0 9.7 - - + -
121D THR* 3.0 48.1 + - - +
123D GLU* 1.3 77.2 - - + +
125D VAL* 1.3 57.6 + - - +
127D ASN* 3.4 7.8 + - - +
128D MET* 3.1 35.7 + - + +
237D GLU* 4.6 2.9 - - - +
49I TRP* 5.2 0.3 - - - -
56I ILE* 5.1 6.0 - - - +
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D TRP* 3.5 37.2 - - + +
115D LEU* 4.1 3.8 - - + -
116D VAL* 3.6 24.9 - - + +
120D HIS* 3.9 19.1 - - + -
121D THR 2.9 16.3 + - - +
122D ASN 4.0 0.4 - - - +
124D GLU* 1.3 72.0 - - - +
126D ARG* 1.3 66.7 + - - +
127D ASN 3.0 1.8 - - - -
128D MET* 3.0 12.5 + - + +
129D ALA* 2.9 23.0 + - - +
151D LEU* 3.3 25.4 - - + -
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Residues in contact with ARG 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ASN* 3.1 40.6 + - - +
123D GLU* 3.5 21.8 + - - +
125D VAL* 1.3 76.9 - - - +
127D ASN* 1.3 61.8 + - - +
129D ALA* 3.4 3.1 + - - +
130D GLU* 3.0 59.4 + - + +
150D LYS* 6.3 1.1 - - - +
151D LEU* 3.7 22.8 - - + +
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Residues in contact with ASN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 2.9 31.6 + - - +
124D GLU* 3.6 7.7 - - - +
126D ARG* 1.3 80.0 - - - +
128D MET* 1.3 64.8 + - + +
130D GLU* 3.7 17.7 + - - +
131D GLU* 3.5 22.8 + - - +
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Residues in contact with MET 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D TYR* 3.3 35.4 - - - +
112D TRP* 3.9 13.7 - - + -
115D LEU* 4.1 10.8 - - + -
120D HIS* 3.7 34.1 - - + +
124D GLU* 3.1 19.4 + - + +
125D VAL* 3.0 23.1 + - + +
127D ASN* 1.3 77.9 - - + +
129D ALA* 1.3 61.6 + - - +
131D GLU* 3.7 15.0 + - - +
132D PHE* 3.3 24.3 - - - -
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D TRP* 3.8 37.7 - - + -
125D VAL 2.9 15.3 + - - +
126D ARG* 3.6 7.2 - - - +
128D MET* 1.3 74.8 - - - +
130D GLU* 1.3 58.3 + - - +
131D GLU 3.0 10.7 + - - -
132D PHE* 3.1 16.5 + - - +
134D TYR* 4.3 0.9 - - - -
149D GLY* 3.3 26.7 - - - +
150D LYS* 4.1 8.3 - - - +
151D LEU* 4.7 0.7 - - + +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ARG* 3.0 40.2 + - + +
127D ASN* 4.3 14.5 + - - +
128D MET 3.5 0.6 - - - -
129D ALA* 1.3 73.5 - - - +
131D GLU* 1.3 60.0 + - - +
132D PHE 3.1 8.2 + - - +
148D PRO* 3.7 23.8 - - + +
149D GLY 3.2 24.0 - - - +
150D LYS* 5.5 0.2 - - - -
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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