Contacts of the helix formed by residues 166 - 177 (chain D) 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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D HIS* 2.9 20.5 + - + +
163D ASN* 2.6 41.2 + - - +
164D THR* 3.6 15.1 - - - +
165D PHE* 1.3 87.7 + - - +
167D PRO* 1.3 56.6 - - - +
168D ASP* 2.8 21.5 + - + +
169D ARG* 2.8 33.0 + - + +
170D LEU 3.8 0.5 + - - -
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Residues in contact with PRO 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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165D PHE* 3.6 30.4 - - + +
166D ARG* 1.3 82.9 - - - +
168D ASP* 1.3 62.1 + - - +
170D LEU* 3.2 27.6 + - + +
171D ARG* 3.7 11.6 + - - +
185D LEU* 3.7 24.9 - - + +
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Residues in contact with ASP 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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166D ARG* 2.8 12.2 + - + +
167D PRO* 1.3 74.2 - - - +
169D ARG* 1.3 65.5 + - + +
171D ARG* 2.9 43.0 + - - +
172D ASP* 3.3 14.1 - - - +
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Residues in contact with ARG 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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134D GLN* 2.8 38.5 + - - +
137D HIS* 3.8 24.8 - - + +
166D ARG* 2.8 29.8 + - + +
168D ASP* 1.3 74.1 - - - +
170D LEU* 1.3 64.5 + - - +
171D ARG 3.1 1.0 + - - -
172D ASP* 3.2 14.7 + - - +
173D ILE* 3.2 33.9 + - - +
331D THR 3.4 15.0 + - - -
332D ALA* 2.8 32.7 + - - +
334D GLY* 3.5 10.3 - - - +
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Residues in contact with LEU 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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137D HIS* 3.3 51.4 - - + +
140D CYS* 3.6 21.3 - - + -
141D VAL* 4.0 11.8 - - + +
165D PHE* 3.8 23.8 - - + -
167D PRO* 3.2 17.2 + - + +
168D ASP 3.1 1.4 - - - -
169D ARG* 1.3 77.3 - - - +
171D ARG* 1.3 57.1 + - - +
173D ILE* 4.0 2.7 - - + +
174D ALA* 2.9 28.4 + - - +
181D HIS* 6.3 0.2 - - - -
184D VAL* 4.4 7.8 - - + +
185D LEU* 3.9 20.2 - - + -
188D VAL* 4.3 12.3 - - + -
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Residues in contact with ARG 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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167D PRO* 4.1 13.6 + - - +
168D ASP* 2.9 34.7 + - - +
170D LEU* 1.3 76.0 - - - +
172D ASP* 1.3 62.5 + - - +
174D ALA* 3.4 5.9 + - - +
175D ASP* 2.9 36.8 + - - +
181D HIS* 3.6 46.4 + - + +
182D ASP* 5.0 6.1 + - - -
185D LEU* 3.7 25.6 - - + +
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Residues in contact with ASP 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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168D ASP* 3.3 19.2 - - - +
169D ARG* 3.2 18.5 + - - +
171D ARG* 1.3 77.7 - - - +
173D ILE* 1.3 65.6 + - - +
175D ASP* 3.3 12.8 + - - +
176D ARG* 3.2 19.4 + - - +
332D ALA* 3.3 33.0 - - - +
333D GLY* 4.1 3.3 - - - -
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Residues in contact with ILE 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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137D HIS* 3.9 38.4 - - + +
138D THR* 3.9 13.5 - - + +
141D VAL* 3.8 26.2 - - + -
169D ARG* 3.2 29.2 + - - +
170D LEU* 4.0 1.6 - - + +
172D ASP* 1.3 76.3 - - - +
174D ALA* 1.3 57.0 + - - +
176D ARG* 3.0 5.2 + - - +
177D PHE* 3.0 42.9 + - + -
333D GLY 3.8 14.4 - - - +
334D GLY* 3.6 25.6 - - - +
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Residues in contact with ALA 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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141D VAL* 4.4 9.8 - - + +
170D LEU 2.9 20.2 + - - +
171D ARG* 3.6 7.9 - - - +
172D ASP 3.3 0.2 - - - -
173D ILE* 1.3 74.9 - - - +
175D ASP* 1.3 61.8 + - - +
177D PHE* 3.5 1.9 + - - +
178D ASN 2.9 6.9 + - - -
179D VAL* 2.9 43.3 + - - +
181D HIS* 4.4 11.2 - - + -
184D VAL* 4.5 21.1 - - + -
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Residues in contact with ASP 175 (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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171D ARG* 2.9 18.8 + - - +
172D ASP* 3.4 14.0 - - - +
173D ILE 3.2 0.2 - - - -
174D ALA* 1.3 76.4 - - - +
176D ARG* 1.3 58.3 + - - +
178D ASN* 2.8 29.8 + - - +
179D VAL 5.1 0.3 - - - +
181D HIS* 2.6 34.3 + - - -
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Residues in contact with ARG 176 (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 GLY* 2.8 25.5 + - - -
138D THR* 5.1 0.6 - - - +
172D ASP 3.2 9.1 + - - +
173D ILE 3.0 7.0 + - - +
175D ASP* 1.3 79.2 - - - +
177D PHE* 1.3 97.9 + - - +
178D ASN* 3.5 5.7 + - - -
331D THR* 5.1 1.0 + - - -
333D GLY* 2.9 36.6 + - - -
334D GLY 3.6 2.4 + - - -
335D ILE 2.4 28.7 + - - -
336D GLY* 3.7 7.9 - - - +
337D ASP* 5.6 2.0 + - - -
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Residues in contact with PHE 177 (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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102D THR* 5.9 2.7 - - + -
104D GLY* 4.4 6.3 - - - -
138D THR* 4.7 2.0 - - + -
141D VAL* 4.2 11.0 - - + -
142D THR* 3.8 26.0 - - + -
145D LEU* 3.5 35.9 - - + +
173D ILE* 3.0 41.2 + - + +
174D ALA 4.5 0.9 - - - +
176D ARG* 1.3 120.3 - - - +
178D ASN* 1.3 69.9 + - - +
179D VAL* 3.3 12.2 - - + +
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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