Contacts of the helix formed by residues 135 - 143 (chain A) 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 ASN 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ILE* 5.1 3.6 - - - +
78A SER* 3.0 28.0 + - - -
80A GLU* 3.7 30.9 + - - +
130A LEU* 2.6 40.2 + - - +
132A SER* 3.2 18.8 - - - +
133A SER 2.8 2.9 + - - +
134A SER* 1.3 77.1 - - - +
136A PHE* 1.3 61.6 + - - +
138A ALA* 3.8 6.2 - - - +
139A THR* 2.8 32.2 + - - -
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Residues in contact with PHE 136 (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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71A LEU* 4.5 13.7 - - + -
75A ILE* 4.7 14.1 - - + -
130A LEU 4.5 7.6 - - - +
131A LEU* 4.6 6.3 - - + +
132A SER 3.1 18.7 + - - +
133A SER* 4.5 3.1 - - - -
135A ASN* 1.3 76.9 - - - +
137A GLU* 1.3 79.9 + - + +
138A ALA 3.1 1.8 - - - -
139A THR* 3.7 4.4 - - - -
140A LYS* 2.8 43.7 + - + +
187A LEU* 4.2 8.7 - - + -
188A VAL* 3.7 14.8 - - + -
189A VAL* 3.6 45.1 - - + -
192A LEU* 3.7 31.6 - - + -
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Residues in contact with GLU 137 (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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133A SER* 4.6 10.3 + - - -
134A SER* 3.7 24.7 - - - +
135A ASN 3.9 0.4 - - - +
136A PHE* 1.3 101.6 - - + +
138A ALA* 1.3 60.2 + - - +
140A LYS* 3.7 17.1 - - - +
141A LYS* 3.4 28.3 + - - +
189A VAL* 5.6 0.3 - - - +
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Residues in contact with ALA 138 (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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134A SER 3.6 20.1 + - - +
135A ASN* 3.7 7.9 + - - +
136A PHE 3.1 0.4 - - - -
137A GLU* 1.3 78.1 - - - +
139A THR* 1.3 58.8 + - - +
140A LYS 3.2 0.4 - - - -
141A LYS* 3.3 8.4 + - - +
142A SER* 3.0 25.6 + - - -
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Residues in contact with THR 139 (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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71A LEU* 3.8 11.4 - - + -
74A ASN* 3.7 30.2 + - + +
75A ILE* 3.3 37.6 - - + +
78A SER* 4.5 8.7 + - - -
135A ASN* 2.8 22.5 + - - -
136A PHE 3.8 3.6 - - - -
138A ALA* 1.3 73.6 - - - +
140A LYS* 1.3 65.2 + - - +
142A SER* 3.4 7.0 - - - -
143A VAL* 3.0 24.4 + - - +
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Residues in contact with LYS 140 (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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71A LEU* 4.3 8.3 - - + -
136A PHE* 2.8 36.1 + - + +
137A GLU* 3.7 20.0 - - - +
139A THR* 1.3 78.5 - - - +
141A LYS* 1.3 59.9 - - - +
143A VAL* 3.5 10.7 - - + +
144A LEU* 3.3 31.0 + - + +
184A LEU 3.3 17.9 + - - +
185A GLU* 3.2 29.0 + - - +
187A LEU* 2.8 28.4 + - - +
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Residues in contact with LYS 141 (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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137A GLU* 3.4 13.9 + - - +
138A ALA* 3.3 10.6 + - - +
140A LYS* 1.3 78.1 - - - +
142A SER* 1.3 63.6 + - - +
144A LEU* 3.7 9.9 - - + +
145A LYS* 3.2 26.4 + - + +
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Residues in contact with SER 142 (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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74A ASN* 3.7 15.1 + - - -
138A ALA 3.0 13.6 + - - -
139A THR* 3.4 13.5 - - - -
141A LYS* 1.3 75.7 - - - +
143A VAL* 1.3 57.0 + - - +
144A LEU 3.0 7.4 + - - -
145A LYS* 3.4 3.6 + - - +
146A GLN* 3.0 31.7 + - - +
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Residues in contact with VAL 143 (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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70A ASN* 4.1 19.3 - - - +
71A LEU* 3.7 30.5 - - + -
74A ASN* 3.2 45.3 - - + +
139A THR 3.0 10.3 + - - +
140A LYS* 3.5 13.7 - - + +
142A SER* 1.3 73.7 - - - +
144A LEU* 1.3 57.9 + - + +
146A GLN* 3.7 12.3 - - - +
147A VAL* 3.1 29.8 + - - +
184A LEU* 3.5 11.7 - - + +
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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