Contacts of the helix formed by residues 166 - 181 (chain D) in PDB entry 5IRC
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 GLY 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D MET* 4.9 0.7 - - - +
158D GLU 4.1 12.0 - - - +
159D CYS* 3.7 4.4 - - - +
164D LYS 3.1 2.4 + - - -
165D ASP* 1.3 77.8 + - - +
167D VAL* 1.3 63.1 + - - +
169D GLU* 3.2 26.9 + - - +
170D VAL* 3.2 24.6 + - - +
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Residues in contact with VAL 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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21D LEU* 3.8 18.2 - - + +
24D VAL* 3.5 34.3 - - + -
25D ASN 4.3 8.3 - - - -
159D CYS* 4.1 9.6 - - + -
160D SER 3.6 22.4 - - - +
161D ALA* 3.9 5.8 - - - +
164D LYS* 3.2 19.4 + - + +
165D ASP 4.2 0.9 - - - +
166D GLY* 1.3 74.2 - - - +
168D ARG* 1.3 67.9 - - - +
169D GLU* 3.8 0.2 + - - -
170D VAL* 3.0 19.1 + - - +
171D PHE* 3.4 17.3 + - + -
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Residues in contact with ARG 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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25D ASN 6.1 1.6 - - - -
46D ILE* 5.0 0.5 - - - +
164D LYS 4.7 1.8 + - - -
166D GLY 3.5 0.2 - - - -
167D VAL* 1.3 79.0 - - - +
169D GLU* 1.3 66.0 + - - +
171D PHE* 3.1 7.8 + - - +
172D GLU* 2.8 46.5 + - + +
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Residues in contact with GLU 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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157D MET* 3.5 26.9 - - + +
166D GLY* 3.2 31.5 + - - +
168D ARG* 1.3 82.9 + - - +
170D VAL* 1.3 61.6 + - - +
172D GLU* 3.7 18.5 - - - +
173D MET* 3.0 19.9 + - - +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.5 6.5 - - + -
81D LEU* 4.1 22.6 - - + +
113D ILE* 5.1 3.1 - - + +
115D VAL* 4.1 23.6 - - + -
157D MET* 3.7 29.6 - - + -
158D GLU 4.9 0.4 - - - +
159D CYS* 4.1 23.6 - - + -
166D GLY 3.2 15.0 + - - +
167D VAL* 3.0 10.3 + - - +
169D GLU* 1.3 76.1 - - - +
171D PHE* 1.3 64.3 + - + +
173D MET* 3.3 2.9 + - - +
174D ALA* 2.9 26.2 + - - +
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Residues in contact with PHE 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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8D LEU* 4.2 13.7 - - + -
21D LEU* 3.6 48.5 - - + -
22D LEU* 3.8 27.4 - - + -
25D ASN 3.7 26.7 - - - +
46D ILE* 3.8 11.7 - - + -
55D LEU* 4.3 11.2 - - + -
57D LEU* 4.1 14.8 - - + -
81D LEU* 3.9 18.4 - - + -
167D VAL* 3.4 13.9 - - + -
168D ARG* 3.1 8.0 + - - +
170D VAL* 1.3 76.1 - - + +
172D GLU* 1.3 57.8 + - - +
174D ALA* 3.8 3.5 - - - +
175D THR* 2.7 38.6 + - - +
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Residues in contact with GLU 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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46D ILE* 3.7 19.0 - - + +
47D GLU 5.4 1.6 - - - +
48D VAL* 4.0 10.1 - - + +
168D ARG* 2.8 37.7 + - - +
169D GLU* 3.7 20.2 - - - +
170D VAL 3.3 0.2 - - - -
171D PHE* 1.3 77.7 - - - +
173D MET* 1.3 62.7 + - - +
175D THR* 3.8 2.3 - - - -
176D ARG* 3.1 46.8 + - - +
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Residues in contact with MET 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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113D ILE* 3.9 15.9 - - + -
154D PHE* 4.0 14.5 - - + -
155D GLY* 3.9 26.2 - - - -
156D TYR 5.0 1.3 - - - +
157D MET* 3.5 39.7 - - + -
169D GLU 3.0 17.0 + - - +
170D VAL 3.8 3.4 - - - +
172D GLU* 1.3 74.0 - - - +
174D ALA* 1.3 61.1 + - - +
176D ARG* 3.2 10.5 + - + +
177D ALA* 2.9 28.1 + - - +
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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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8D LEU* 3.8 30.1 - - + -
55D LEU* 5.2 0.7 - - + -
79D VAL* 3.6 16.4 - - + +
81D LEU* 3.8 16.4 - - + -
113D ILE* 4.1 5.4 - - - +
170D VAL 2.9 17.6 + - - +
171D PHE* 3.8 7.0 - - - +
173D MET* 1.3 76.8 - - - +
175D THR* 1.3 58.1 - - - +
177D ALA* 3.4 2.9 + - - +
178D ALA* 2.9 28.6 + - - +
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Residues in contact with THR 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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46D ILE* 3.2 31.3 - - + +
48D VAL* 3.6 23.6 - - + -
53D VAL* 3.7 25.4 - - + -
55D LEU* 3.5 15.5 - - + +
171D PHE 2.7 22.2 + - - -
172D GLU 3.8 3.6 - - - -
174D ALA* 1.3 73.3 - - - +
176D ARG* 1.3 66.9 + - - +
178D ALA* 3.2 7.5 + - + +
179D LEU* 3.1 23.4 + - + +
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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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48D VAL* 4.1 16.0 - - + +
49D ASP* 2.8 48.0 + - - +
154D PHE* 4.7 7.4 - - + -
172D GLU* 3.1 46.7 + - - +
173D MET* 3.6 12.0 - - + +
175D THR* 1.3 75.9 - - - +
177D ALA* 1.3 63.1 + - - +
179D LEU* 3.3 18.4 + - + +
180D GLN* 3.4 14.0 + - - +
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Residues in contact with ALA 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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79D VAL* 4.1 14.1 - - + -
111D PRO* 3.7 10.0 - - + +
113D ILE* 4.1 2.7 - - + -
154D PHE* 3.7 40.1 - - + -
173D MET 2.9 17.0 + - - +
174D ALA 3.5 5.2 - - - +
176D ARG* 1.3 78.1 - - - +
178D ALA* 1.3 51.0 + - - +
180D GLN* 3.6 2.8 + - - +
181D ALA* 2.8 36.9 + - - -
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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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6D LYS* 3.8 31.8 + - + +
55D LEU* 5.0 0.9 - - + -
78D ASP* 3.8 18.0 - - + +
79D VAL* 3.8 17.9 - - + +
174D ALA 2.9 16.4 + - - +
175D THR* 3.2 9.6 + - - +
177D ALA* 1.3 76.4 - - - +
179D LEU* 1.3 60.4 + - - +
181D ALA* 3.1 23.2 - - - +
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Residues in contact with LEU 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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4D ILE* 4.4 11.0 - - + -
6D LYS* 4.2 27.3 + - + +
48D VAL* 3.9 25.4 - - + -
51D LYS* 4.4 31.0 - - + +
53D VAL* 4.0 24.0 - - + -
175D THR* 3.1 20.9 + - + +
176D ARG* 3.7 7.6 - - + +
177D ALA 3.2 0.4 - - - -
178D ALA* 1.3 76.5 - - - +
180D GLN* 1.3 64.6 + - - +
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Residues in contact with GLN 180 (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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154D PHE* 5.1 12.3 - - + -
176D ARG 3.4 11.5 + - - +
177D ALA* 4.3 3.8 - - - +
179D LEU* 1.3 80.2 - - - +
181D ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 181 (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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77D THR 5.0 0.2 - - - +
78D ASP* 2.7 36.0 - - - +
110D VAL* 5.2 1.0 - - - +
111D PRO* 3.7 17.6 - - - +
177D ALA 2.8 21.4 + - - -
178D ALA 3.1 15.1 - - - +
179D LEU 3.3 0.6 - - - -
180D GLN* 1.3 84.0 - - - +
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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