Contacts of the helix formed by residues 161 - 168 (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 ASN 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D TYR* 3.2 10.6 - - - +
160D PRO* 1.3 93.5 - - - +
162D GLU* 1.3 63.6 + - - +
163D GLN* 3.0 37.0 + - - +
164D ALA* 3.2 10.1 + - - +
165D ALA* 3.2 16.3 + - - +
138O PRO* 3.6 13.8 - - + +
142O GLY* 3.0 26.9 + - - -
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Residues in contact with GLU 162 (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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161D ASN* 1.3 73.1 - - - +
163D GLN* 1.3 80.4 + - - +
165D ALA* 3.0 17.0 + - - +
166D ARG* 3.1 46.5 + - - +
173D LEU* 3.8 26.0 - - + +
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Residues in contact with GLN 163 (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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161D ASN* 3.0 16.4 + - - +
162D GLU* 1.3 93.1 + - - +
164D ALA* 1.3 61.9 + - - +
166D ARG* 3.5 8.1 + - - +
167D ALA* 3.2 17.7 + - - +
137O GLU* 5.1 7.5 - - - +
138O PRO* 3.3 23.8 - - - +
139O ASP 3.3 27.1 - - - +
140O GLU* 3.7 18.1 - - - +
142O GLY* 3.6 6.3 - - - +
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Residues in contact with ALA 164 (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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159D TYR* 4.1 7.0 - - + -
160D PRO* 4.2 18.6 - - + -
161D ASN* 3.2 20.1 + - - +
162D GLU 3.1 0.4 - - - -
163D GLN* 1.3 78.6 - - - +
165D ALA* 1.3 61.7 + - - +
167D ALA* 3.5 4.5 + - - +
168D ALA* 3.4 21.1 + - - +
141O GLN 3.9 19.1 - - - +
142O GLY* 3.7 8.2 - - - +
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Residues in contact with ALA 165 (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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159D TYR* 3.3 34.7 - - + -
161D ASN 3.2 11.3 + - - +
162D GLU* 3.0 10.2 + - - +
164D ALA* 1.3 75.7 - - - +
166D ARG* 1.3 62.0 + - - +
168D ALA* 3.3 7.1 + - - +
169D ASN* 3.1 25.3 + - - +
172D ALA 4.1 2.2 - - - -
173D LEU* 4.1 21.8 - - + -
174D PRO* 4.6 3.4 - - + -
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Residues in contact with ARG 166 (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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162D GLU* 3.1 38.6 + - - +
163D GLN* 3.9 9.6 - - - +
165D ALA* 1.3 73.4 - - - +
167D ALA* 1.3 64.8 + - - +
169D ASN 3.2 2.5 + - - -
171D GLY* 2.8 59.5 + - - +
172D ALA* 3.4 15.6 - - - +
173D LEU* 3.3 41.3 - - + +
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Residues in contact with ALA 167 (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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163D GLN 3.2 13.5 + - - +
164D ALA* 3.6 13.7 - - - +
165D ALA 3.3 0.4 - - - -
166D ARG* 1.3 77.0 - - - +
168D ALA* 1.3 58.6 + - - +
169D ASN 3.2 3.3 + - - -
170D GLN 4.2 4.5 + - - -
140O GLU 4.5 3.6 - - - +
141O GLN* 4.3 25.1 - - + +
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Residues in contact with ALA 168 (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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104D CYS* 5.9 0.3 - - - -
159D TYR* 3.8 33.2 + - + +
164D ALA 3.4 5.1 + - - +
165D ALA 3.3 3.7 + - - +
166D ARG 3.2 0.6 - - - -
167D ALA* 1.3 79.3 - - - +
169D ASN* 1.3 66.0 + - - +
170D GLN* 3.9 2.3 + - - -
503D HEC 5.6 0.7 - - - +
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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