Contacts of the helix formed by residues 157 - 161 (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 VAL 157 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116K ASN* 5.8 2.2 - - + +
122K MET* 4.0 11.7 - - + -
142K ARG* 3.5 39.3 - - - +
144K TYR* 3.5 15.3 - - + +
155K CYS* 3.0 4.4 - - - -
156K PRO* 1.4 79.5 - - + +
158K LEU* 1.4 68.3 + - - +
160K LEU* 3.1 25.0 + - + +
161K ILE* 4.1 6.2 + - - +
198K PHE* 4.0 28.7 - - + -
339L ILE* 4.2 21.7 - - + +
340L PRO* 5.3 7.0 - - + +
342L SER* 5.8 1.6 - - - +
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Residues in contact with LEU 158 (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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144K TYR* 3.7 40.1 + - + -
152K ASN* 3.6 43.1 - - + +
155K CYS* 3.4 15.9 + - + +
157K VAL* 1.4 81.3 - - + +
159K ASN* 1.4 58.1 + - - +
161K ILE* 3.3 17.6 + - + +
167K ARG* 3.1 46.1 + - + +
170K LEU* 3.8 27.4 - - + -
171K ILE* 5.2 7.4 - - + -
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Residues in contact with ASN 159 (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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152K ASN 4.9 1.7 - - - +
153K ALA* 3.4 16.7 + - - +
154K LYS* 3.3 21.0 + - - +
155K CYS 2.8 25.1 + - - +
156K PRO* 4.1 8.0 - - + +
157K VAL 3.1 0.2 - - - -
158K LEU* 1.4 72.5 - - - +
160K LEU* 1.3 66.6 + - - +
161K ILE 3.1 8.8 + - - +
162K GLU* 5.4 0.3 - - - -
167K ARG* 3.9 23.7 + - - +
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Residues in contact with LEU 160 (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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450J ARG* 3.6 41.0 - - - +
156K PRO 3.5 16.8 + - - +
157K VAL* 3.1 13.3 + - + +
159K ASN* 1.3 79.5 - - - +
161K ILE* 1.4 60.1 + - - +
162K GLU* 3.4 5.9 + - - +
337L VAL* 4.3 16.4 - - + +
338L SER 4.2 4.0 - - - +
339L ILE* 4.1 16.4 - - + -
340L PRO* 3.6 31.9 - - + -
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Residues in contact with ILE 161 (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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157K VAL 4.4 3.4 - - - +
158K LEU* 3.3 21.7 + - + +
159K ASN 3.1 1.6 - - - +
160K LEU* 1.4 76.5 - - - +
162K GLU* 1.4 59.1 + - - +
163K GLN 3.5 9.8 + - - +
166K ARG* 3.9 29.8 - - + -
167K ARG* 3.0 41.3 + - + -
170K LEU* 4.0 27.6 - - + -
196K VAL* 4.1 17.3 - - + -
198K PHE* 4.5 5.8 - - + -
337L VAL* 4.3 23.6 - - + -
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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