Contacts of the helix formed by residues 167 - 174 (chain D) in PDB entry 3KHU
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 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D ALA* 3.1 17.0 + - - +
165D GLU 3.4 2.4 - - - +
166D GLY* 1.3 82.2 - - - +
168D ALA* 1.3 68.0 + - - +
169D ILE 3.2 3.0 + - - -
170D LYS* 3.2 19.6 + - + +
171D ASP* 2.6 48.7 + - - +
339D LYS* 6.2 0.2 - - - +
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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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14D TYR 5.8 0.4 - - - +
18D PRO* 4.8 11.2 - - + -
54D GLU* 3.0 34.7 + - + +
163D LEU* 4.4 24.2 - - + -
164D ALA 3.5 5.1 + - - +
167D THR* 1.3 77.5 - - - +
169D ILE* 1.3 58.3 + - + +
171D ASP* 3.2 8.8 + - - +
172D LEU* 2.9 35.1 + - - +
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Residues in contact with ILE 169 (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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18D PRO* 4.9 3.6 - - + -
22D VAL* 3.9 21.8 - - + -
54D GLU* 4.5 3.5 + - + -
55D PRO 3.2 25.9 + - - +
56D GLY* 4.7 6.1 - - - +
57D LEU* 3.7 38.4 - - + +
60D VAL* 4.3 9.9 - - + -
167D THR 3.3 0.6 - - - -
168D ALA* 1.3 75.3 - - + +
170D LYS* 1.3 63.3 + - + +
172D LEU* 3.1 9.0 + - + +
173D LYS* 2.8 57.2 + - + +
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Residues in contact with LYS 170 (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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167D THR* 3.2 21.5 + - + +
169D ILE* 1.3 79.2 - - + +
171D ASP* 1.3 59.2 + - - +
173D LYS* 4.5 4.7 - - - +
174D ASN* 2.8 38.6 + - + +
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Residues in contact with ASP 171 (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 PHE 3.7 21.9 - - - +
163D LEU* 3.8 8.0 - - + +
164D ALA* 3.0 21.0 + - - +
167D THR* 2.6 48.2 + - - +
168D ALA 3.5 4.9 - - - +
170D LYS* 1.3 78.5 - - - +
172D LEU* 1.3 57.0 + - - +
174D ASN 4.7 3.1 - - - -
175D PRO* 3.2 28.6 - - - +
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Residues in contact with LEU 172 (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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18D PRO* 3.7 41.5 - - + +
19D THR* 3.8 27.4 - - + +
22D VAL* 3.9 21.1 - - + -
161D GLN* 6.1 1.3 - - + -
163D LEU* 3.4 25.4 - - + -
168D ALA 2.9 22.5 + - - +
169D ILE* 3.1 4.5 + - + +
171D ASP* 1.3 78.6 - - - +
173D LYS* 1.3 61.7 + - - +
174D ASN 3.4 0.4 - - - -
175D PRO* 3.5 9.1 - - - +
199D TYR* 6.1 3.4 - - + -
202D TRP* 3.0 26.9 + - + -
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Residues in contact with LYS 173 (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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22D VAL* 4.5 9.4 - - + -
25D HIS* 4.3 15.0 + - - -
26D MET* 3.6 29.8 - - + +
60D VAL* 4.2 21.1 - - - +
169D ILE* 2.8 41.6 + - + +
170D LYS* 4.3 3.6 - - - +
172D LEU* 1.3 74.6 - - - +
174D ASN* 1.3 61.0 + - + +
175D PRO* 3.5 3.5 - - - +
202D TRP* 3.4 27.3 - - - +
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Residues in contact with ASN 174 (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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170D LYS* 2.8 21.1 + - + +
171D ASP* 4.4 1.4 - - - +
173D LYS* 1.3 80.5 - - + +
175D PRO* 1.3 64.0 - - - +
176D ASP* 3.7 4.5 + - - +
207D LYS* 3.4 19.1 + - - -
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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