Contacts of the helix formed by residues 173 - 180 (chain C) in PDB entry 1XKH
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 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C THR* 3.0 33.2 + - - +
144C SER 4.9 0.2 + - - -
146C SER 3.7 9.6 + - - +
147C TYR* 3.1 42.6 - - + +
148C THR 4.8 2.0 - - - -
149C PRO 5.4 0.4 - - - -
171C VAL* 3.7 7.2 + - - +
172C VAL* 1.3 89.5 - - - +
174C ARG* 1.3 70.3 + - - +
175C GLN* 3.5 5.1 + - - +
176C ASN* 3.3 24.6 - - + +
177C MSE 3.4 11.1 + - - +
244C ASP 4.2 1.6 - - - -
245C ARG* 4.5 2.0 - - - -
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Residues in contact with ARG 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C THR* 3.5 16.9 + - - +
142C GLU* 4.3 18.2 - - + -
173C THR* 1.3 79.7 + - - +
175C GLN* 1.3 61.9 + - - +
176C ASN 2.8 6.8 + - - -
177C MSE 3.1 30.9 + - - +
178C ASP* 2.8 61.4 + - - +
182C LEU 4.9 3.2 + - - -
240C MSE 3.3 26.3 + - - +
241C ALA* 4.5 4.6 - - - +
243C TYR 3.2 26.4 + - - -
244C ASP* 3.2 20.8 + - - +
271C LYS* 3.7 21.6 - - - +
294C GLU* 5.3 6.0 + - - -
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Residues in contact with GLN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C THR 4.3 5.8 + - - +
143C ASP 4.5 4.9 - - - +
144C SER 4.5 2.5 - - - +
145C GLY* 3.2 44.2 - - - +
146C SER 4.2 2.7 - - - +
147C TYR* 3.8 7.0 - - + -
173C THR* 3.5 6.0 + - + +
174C ARG* 1.3 79.8 - - - +
176C ASN* 1.3 54.5 + - - +
178C ASP* 4.1 11.4 - - - +
179C ASP* 2.5 58.5 + - - +
686C GLN* 5.8 0.2 - - + -
768C ARG* 3.5 18.5 + - - +
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Residues in contact with ASN 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TYR* 3.4 30.0 - - + -
172C VAL* 4.0 12.2 - - + +
173C THR* 3.3 27.8 - - + +
174C ARG 2.8 1.0 - - - -
175C GLN* 1.3 77.1 - - - +
177C MSE 1.3 68.9 + - - +
178C ASP 3.0 1.4 + - - -
179C ASP 3.2 9.5 + - - -
180C PHE* 3.3 21.0 + - - -
182C LEU* 3.8 13.2 - - - +
191C HIS* 5.6 2.5 + - - +
688C GLN* 3.0 32.3 + - - +
716C TYR* 5.5 6.0 - - - +
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Residues in contact with MSE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C VAL* 3.7 14.8 - - + +
173C THR 3.4 13.4 + - - +
174C ARG* 3.1 29.7 + - - +
176C ASN* 1.3 79.6 + - - +
178C ASP* 1.3 64.8 + - - +
181C GLY* 3.1 2.8 + - - -
182C LEU* 3.0 47.3 + - + +
188C VAL* 4.4 6.1 - - + -
240C MSE 3.6 42.4 - - - +
243C TYR* 4.2 4.9 - - + +
244C ASP 3.7 8.7 - - - +
245C ARG* 3.4 41.5 - - - +
246C VAL* 4.2 2.7 - - - +
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ARG* 2.8 57.5 + - - +
175C GLN* 3.9 15.3 - - - +
177C MSE 1.3 76.7 - - - +
179C ASP* 1.3 67.0 + - - +
181C GLY* 3.0 15.0 + - - -
282C GLU* 5.2 5.7 - - - +
768C ARG* 4.6 5.8 + - - +
812C ARG* 5.0 13.5 + - - -
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Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TYR* 2.9 32.1 + - - +
175C GLN* 2.5 30.7 + - - +
176C ASN 3.2 4.5 + - - +
178C ASP* 1.3 81.5 - - - +
180C PHE* 1.3 62.3 + - + +
181C GLY 3.4 1.4 + - - -
718C SER* 4.1 7.8 + - - -
729C THR* 5.1 2.9 - - - +
766C MSE 3.5 30.8 - - + +
768C ARG* 2.5 33.4 + - - +
778C SER* 5.9 1.4 - - - -
780C ASN* 3.1 17.7 + - - +
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Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TYR* 3.2 30.1 - + - -
176C ASN* 3.3 22.5 + - - -
178C ASP 3.3 0.6 - - - -
179C ASP* 1.3 79.0 - - + +
181C GLY* 1.3 66.4 + - - +
182C LEU* 3.3 25.6 - - + +
191C HIS* 4.2 19.3 - + + +
716C TYR* 4.0 23.3 - + + -
717C THR 4.0 7.0 - - - -
718C SER* 5.1 0.9 - - - -
731C GLY* 4.8 3.8 - - - -
732C GLY* 3.8 42.8 - - - -
733C GLY 4.3 0.4 - - - -
764C ASP* 4.8 6.1 - - + -
766C MSE 4.9 6.1 - - + -
780C ASN* 3.2 25.8 + - - +
782C ASN* 4.7 12.3 + - - +
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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