Contacts of the helix formed by residues 148 - 155 (chain K) in PDB entry 1YKN
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 GLU 148 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110K LYS* 2.7 40.9 + - - +
124K PRO* 3.9 30.6 - - + +
145K PHE* 3.1 16.4 + - + +
147K ASP* 1.3 85.7 - - - +
149K ALA* 1.3 51.7 + - - +
150K GLN 3.3 3.4 - - - -
151K ALA* 3.2 13.6 + - + +
152K ASN* 2.8 42.7 + - - +
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Residues in contact with ALA 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ASP 3.8 11.8 + - - +
147K ASP 3.4 3.2 + - - -
148K GLU* 1.3 72.4 - - - +
150K GLN* 1.4 60.1 + - - +
152K ASN* 3.8 10.7 - - - +
153K ALA* 2.9 31.7 + - - +
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Residues in contact with GLN 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K GLU 3.3 1.2 - - - -
149K ALA* 1.4 80.8 - - - +
151K ALA* 1.4 64.3 + - - +
153K ALA* 3.3 12.4 + - - +
154K LYS* 3.4 19.3 - - + +
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Residues in contact with ALA 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K VAL* 5.6 3.8 - - + -
122K MET 5.7 0.4 - - - -
123K ALA* 3.6 22.0 - - + +
124K PRO* 4.1 15.0 - - + -
148K GLU* 3.2 15.7 + - - +
150K GLN* 1.4 74.3 - - - +
152K ASN* 1.4 65.1 + - - +
154K LYS* 3.0 9.7 + - - +
155K CYS* 2.8 20.8 + - - -
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Residues in contact with ASN 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K ALA* 3.2 22.9 - - - +
124K PRO 5.0 0.5 - - - +
144K TYR* 3.6 11.8 - - - +
145K PHE 2.8 32.2 + - - +
146K ASP* 4.7 1.6 - - - +
148K GLU* 2.8 30.8 + - - +
149K ALA* 3.8 9.1 - - - +
150K GLN 3.3 0.4 - - - -
151K ALA* 1.4 73.9 - - - +
153K ALA* 1.3 64.4 + - - +
154K LYS 3.2 0.2 + - - -
155K CYS* 3.5 6.8 + - - +
158K LEU* 3.6 33.6 - - + +
159K ASN* 4.9 1.7 - - - +
171K ILE* 4.3 14.6 - - + +
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Residues in contact with ALA 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K ALA 2.9 17.6 + - - +
150K GLN* 3.5 9.0 - - - +
151K ALA 3.2 0.4 - - - -
152K ASN* 1.3 77.3 - - - +
154K LYS* 1.3 67.0 + - + +
159K ASN* 3.4 21.7 + - - +
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Residues in contact with LYS 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K VAL* 5.1 3.6 - - - +
121K PRO 4.8 3.4 - - - +
150K GLN* 3.4 17.7 - - + +
151K ALA* 3.0 8.0 + - - +
153K ALA* 1.3 89.0 - - + +
155K CYS* 1.3 66.3 + - - +
156K PRO* 3.2 6.9 - - - +
159K ASN* 3.3 8.1 + - - +
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Residues in contact with CYS 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K PRO 4.4 1.6 - - - -
122K MET* 3.8 8.3 - - - -
123K ALA* 3.6 32.8 - - + +
144K TYR* 3.2 25.8 - - + -
151K ALA 2.8 15.7 + - - +
152K ASN 3.5 3.0 + - - +
154K LYS* 1.3 68.6 - - - +
156K PRO* 1.3 76.1 - - - +
157K VAL* 3.2 17.5 - - - -
158K LEU* 3.5 15.9 - - + +
159K ASN* 2.8 27.0 + - - -
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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