Contacts of the helix formed by residues 171 - 179 (chain D) in PDB entry 4UC5
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 SER 171 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ARG* 3.3 20.3 + - - -
168C THR* 3.8 15.0 - - - +
171C SER* 5.0 1.8 - - - -
174C HIS* 4.8 0.4 - - - -
167D ARG 5.2 0.2 + - - -
168D THR* 3.3 21.5 + - - +
170D GLU* 1.3 74.3 - - - +
172D GLN* 1.3 64.4 + - - +
173D VAL* 3.6 8.5 - - - +
174D HIS* 2.7 34.2 + - - +
175D ARG* 3.2 24.4 + - - +
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Residues in contact with GLN 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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98C GLU* 2.9 28.9 + - - -
100C PRO* 3.2 19.0 - - + +
101C ARG 3.1 31.2 + - - +
107C LYS* 3.2 21.1 + - - +
147C LEU* 4.2 13.4 - - + +
167C ARG* 3.6 21.2 - - - +
168C THR* 4.8 4.4 - - - +
170D GLU 3.3 3.6 + - - -
171D SER* 1.3 72.5 + - - +
173D VAL* 1.3 63.0 + - - +
175D ARG* 3.2 8.1 + - + +
176D GLU* 2.9 44.0 + - + +
209D HIS* 6.3 1.3 - - + -
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Residues in contact with VAL 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU* 3.7 24.2 + - + +
148C ASP* 4.4 15.3 - - + +
149C MET* 4.9 1.3 - - + -
168C THR* 5.6 0.6 - - + +
174C HIS* 3.9 8.7 - - + -
149D MET* 3.7 39.9 - - + -
171D SER* 3.6 10.8 - - - +
172D GLN* 1.3 78.8 - - - +
174D HIS* 1.3 62.8 + - - +
176D GLU* 3.2 18.2 + - - +
177D LEU* 2.8 27.5 + - - +
211D PHE* 4.3 10.1 - - + -
212D LEU 5.5 2.2 - - - +
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Residues in contact with HIS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C SER* 4.0 4.0 - - - -
173C VAL* 3.9 19.7 - - + -
174C HIS* 4.1 6.5 - + - -
146D PHE 4.1 13.7 - - - -
147D LEU 3.0 25.8 + - - -
149D MET* 4.2 13.6 - - + -
164D ILE* 3.9 18.2 - - + +
168D THR* 3.4 49.8 - - + +
171D SER* 2.7 24.4 + - - +
172D GLN 3.2 0.8 - - - -
173D VAL* 1.3 85.7 - - + +
175D ARG* 1.3 57.9 + - - +
177D LEU* 3.4 9.9 + - + +
178D ALA* 2.9 26.3 + - - +
187D PHE* 5.2 1.1 - - - -
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Residues in contact with ARG 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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102C THR* 3.5 24.7 + - - +
167C ARG* 3.3 22.2 - - - +
169D THR 2.6 23.6 + - - +
170D GLU* 3.6 21.3 + - - +
171D SER 3.2 14.5 + - - +
172D GLN* 3.5 6.7 - - + +
174D HIS* 1.3 74.1 - - - +
176D GLU* 1.3 65.6 + - + +
178D ALA* 3.3 9.4 + - - +
179D SER* 3.1 21.7 + - - -
187D PHE* 4.3 5.4 - - + -
197D ILE* 2.8 35.6 + - - +
200D ASP* 3.7 12.1 + - - +
201D ALA* 3.6 28.6 - - + +
204D ALA* 4.5 17.5 - - + +
205D ALA* 3.9 6.0 - - - +
209D HIS* 4.9 2.2 - - - +
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Residues in contact with GLU 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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98C GLU* 4.7 1.6 - - - +
107C LYS* 4.2 11.3 + - - +
111C ASN* 5.8 1.2 + - - -
172D GLN* 2.9 43.5 + - + +
173D VAL* 3.4 20.1 - - - +
175D ARG* 1.3 74.3 - - + +
177D LEU* 1.3 64.9 + - - +
179D SER* 2.6 26.0 + - - -
180D GLY 3.7 1.6 + - - -
209D HIS* 3.9 32.7 + - + +
210D HIS 3.1 24.2 + - - +
211D PHE* 3.8 20.9 - - + +
225D THR* 3.9 0.2 - - - +
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Residues in contact with LEU 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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146D PHE* 4.0 25.1 - - + +
148D ASP 3.4 24.0 - - - +
149D MET* 4.0 21.3 - - + +
152D PRO* 4.0 20.2 - - + -
164D ILE* 4.7 4.9 - - + -
173D VAL 2.8 13.6 + - - +
174D HIS* 3.5 10.8 - - + +
176D GLU* 1.3 76.1 - - - +
178D ALA* 1.3 65.0 + - - +
180D GLY* 2.9 14.8 + - - -
181D LEU* 3.3 24.6 + - + +
211D PHE* 3.9 29.5 - - + -
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Residues in contact with ALA 178 (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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164D ILE* 4.5 3.6 - - + +
174D HIS 2.9 12.2 + - - +
175D ARG 3.4 6.7 - - - +
177D LEU* 1.3 76.3 - - - +
179D SER* 1.3 56.9 + - - +
180D GLY 3.0 5.5 + - - -
181D LEU* 3.3 17.1 + - - +
185D VAL* 4.3 12.3 - - + -
187D PHE* 3.4 35.2 - - + -
205D ALA* 4.1 4.0 - - + -
228D ASN* 3.1 25.9 + - - -
231D CYS* 5.0 0.2 - - - -
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Residues in contact with SER 179 (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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11C LYS* 4.2 1.0 - - - +
175D ARG 3.1 9.8 + - - -
176D GLU 2.6 20.9 + - - -
178D ALA* 1.3 75.3 - - - +
180D GLY* 1.3 54.8 + - - +
205D ALA* 3.0 31.6 - - - -
207D HIS 3.3 15.3 - - - -
209D HIS* 3.7 9.1 - - - +
225D THR* 2.8 20.9 + - - +
227D GLY 3.0 31.4 + - - +
228D ASN* 3.9 4.0 - - - +
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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