Contacts of the helix formed by residues 169 - 178 (chain C) in PDB entry 4HYY
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 ARG 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C GLN* 2.9 37.1 + - - +
137C HIS* 3.7 21.8 + - + +
166C ARG* 3.1 27.1 + - + +
168C ASP* 1.3 77.2 - - - +
170C LEU* 1.3 58.9 + - - +
171C ARG 3.0 4.1 + - - -
172C ASP* 3.9 11.2 + - - +
173C ILE* 3.6 31.4 - - - +
331C THR 3.6 13.7 + - - -
332C ALA* 2.9 30.9 + - - +
334C GLY 3.9 0.6 - - - +
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Residues in contact with LEU 170 (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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137C HIS* 3.2 51.8 - - + +
140C CYS* 3.7 21.8 - - + -
141C VAL* 4.2 6.3 - - + +
165C PHE* 4.0 17.7 - - + -
166C ARG 4.3 6.7 - - - +
167C PRO 3.0 12.7 + - - +
168C ASP 2.9 1.8 - - - -
169C ARG* 1.3 77.0 - - - +
171C ARG* 1.3 60.7 + - + +
172C ASP 3.5 0.4 - - - -
173C ILE* 3.4 9.4 + - + +
174C ALA* 3.0 26.2 + - - +
184C VAL* 4.2 13.2 - - + +
185C LEU* 3.8 25.6 - - + -
188C VAL* 4.8 3.6 - - + -
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Residues in contact with ARG 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PRO 3.8 12.6 - - - +
168C ASP* 2.8 34.7 + - - +
170C LEU* 1.3 87.1 - - + +
172C ASP* 1.3 61.8 + - - +
174C ALA* 3.4 4.9 + - - +
175C ASP* 3.1 31.1 + - - +
181C HIS* 3.0 57.6 + - + +
182C ASP* 4.5 5.4 + - - -
184C VAL* 5.9 0.2 - - + -
185C LEU* 3.5 29.7 - - + +
92D SER* 5.6 3.8 + - - -
96D LYS* 5.7 5.6 - - - +
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Residues in contact with ASP 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ASP 4.1 9.5 - - - +
169C ARG* 3.9 10.2 + - - +
171C ARG* 1.3 73.6 - - - +
173C ILE* 1.3 64.1 + - - +
174C ALA 3.2 0.4 - - - -
175C ASP* 3.7 14.0 - - + +
176C ARG* 3.1 23.0 + - - +
332C ALA* 3.2 37.7 - - + +
333C GLY* 3.6 3.5 - - - +
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Residues in contact with ILE 173 (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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134C GLN 5.1 0.7 - - - +
137C HIS* 4.2 14.1 - - + -
138C THR* 4.1 24.9 - - + +
141C VAL* 3.9 21.5 - - + -
169C ARG* 3.6 33.0 - - - +
170C LEU* 3.4 10.6 + - + +
171C ARG 3.2 0.6 - - - -
172C ASP* 1.3 81.5 - - - +
174C ALA* 1.3 60.7 + - - +
176C ARG* 3.4 2.1 + - - +
177C PHE* 3.0 40.1 + - + -
332C ALA 3.8 2.9 - - - +
333C GLY* 3.5 14.4 - - - +
334C GLY* 3.4 27.8 - - - +
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Residues in contact with ALA 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 VAL* 4.5 10.2 - - - +
170C LEU 3.0 15.8 + - - +
171C ARG 3.4 10.5 - - - +
172C ASP 3.2 0.2 - - - -
173C ILE* 1.3 73.8 - - - +
175C ASP* 1.3 60.7 + - - +
177C PHE* 3.2 2.0 + - - -
178C ASN 2.8 23.7 + - - -
179C VAL* 3.1 27.8 + - - +
181C HIS* 4.1 20.6 - - + +
184C VAL* 4.6 11.7 - - + -
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Residues in contact with ASP 175 (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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171C ARG 3.1 16.0 + - - +
172C ASP* 3.5 13.2 + - - +
173C ILE 3.3 0.4 - - - -
174C ALA* 1.3 72.1 - - - +
176C ARG* 1.3 68.2 + - - +
178C ASN* 2.8 19.7 + - - +
179C VAL 5.2 2.4 - - - +
181C HIS* 4.5 13.2 + - - -
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLY* 2.7 29.9 + - - -
138C THR* 4.9 1.2 - - - +
172C ASP 3.1 15.7 + - - +
173C ILE 3.5 2.7 - - - +
175C ASP* 1.3 78.9 - - - +
177C PHE* 1.3 92.2 + - + +
178C ASN* 3.6 1.0 + - - +
331C THR* 5.4 2.4 + - - -
333C GLY* 2.7 46.2 + - - -
334C GLY 3.9 1.4 + - - -
335C ILE 2.6 26.0 + - - +
336C GLY* 3.8 7.3 - - - +
337C ASP* 5.0 2.0 + - - +
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Residues in contact with PHE 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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102C THR* 5.7 3.1 - - + -
104C GLY* 4.3 7.4 - - - -
138C THR* 4.9 1.1 - - + -
141C VAL* 4.2 14.6 - - + -
142C THR* 3.7 27.6 - - + -
145C LEU* 3.5 32.9 - - + +
173C ILE* 3.0 38.6 + - + +
174C ALA 3.5 2.2 - - - +
175C ASP 3.0 1.0 - - - -
176C ARG* 1.3 120.1 - - + +
178C ASN* 1.3 70.7 + - - +
179C VAL* 3.5 9.1 + - + +
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Residues in contact with ASN 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 ALA 2.8 7.2 + - - -
175C ASP* 2.8 14.1 + - - +
176C ARG 4.9 1.3 - - - +
177C PHE* 1.3 80.4 - - - +
179C VAL* 1.3 60.2 + - - +
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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