Contacts of the helix formed by residues 167 - 179 (chain D) in PDB entry 3S52
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 PRO 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D GLN* 3.6 24.7 - - + +
164D MSE 4.5 6.0 - - + +
165D ILE 3.7 7.2 - - - +
166D THR* 1.3 88.6 - - + +
168D ILE* 1.3 61.5 + - - +
169D ILE 3.3 1.4 + - - +
170D PRO* 3.4 26.6 - - + +
171D LEU* 2.8 26.7 + - - +
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Residues in contact with ILE 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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73D LEU* 3.6 19.1 - - + -
75D VAL* 4.3 9.2 - - + -
93D ILE* 4.3 16.2 - - + -
96D TYR* 4.3 3.4 - - + +
142D ALA* 3.5 39.5 - - + +
143D GLN* 3.0 22.2 + - - +
164D MSE 3.8 22.3 - - + -
167D PRO* 1.3 70.7 - - - +
169D ILE* 1.3 62.8 + - + +
171D LEU* 3.3 7.1 - - - +
172D ILE* 2.9 51.6 + - + +
189D THR* 4.2 7.4 - - + -
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Residues in contact with ILE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLU* 3.2 42.8 - - + +
89D VAL* 3.8 10.2 - - + +
90D ALA* 3.7 31.4 - - + +
93D ILE* 4.0 20.6 - - + -
96D TYR* 5.6 0.7 - - - +
143D GLN* 4.8 0.9 + - - +
167D PRO* 4.7 0.2 - - - +
168D ILE* 1.3 78.3 - - + +
170D PRO* 1.3 71.4 - - + +
172D ILE* 3.2 2.3 + - - -
173D SER* 3.0 21.7 + - - -
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Residues in contact with PRO 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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86D GLU* 3.5 30.5 - - - +
166D THR* 4.3 9.1 - - + +
167D PRO* 3.4 38.8 - - + +
169D ILE* 1.3 96.6 - - + +
171D LEU* 1.3 60.3 - - - +
173D SER* 3.5 4.0 - - - -
174D TYR* 2.9 24.6 + - - +
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Residues in contact with LEU 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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22D VAL* 3.9 43.1 - - + -
25D ASN* 4.0 13.0 - - - +
41D PRO* 4.1 20.9 - - + -
43D LEU* 4.4 2.2 - - + -
164D MSE 5.4 0.2 - - - -
166D THR* 3.8 15.6 - - + +
167D PRO 2.8 20.1 + - - +
168D ILE* 3.3 5.4 - - - +
170D PRO* 1.3 79.1 - - - +
172D ILE* 1.3 62.1 + - + +
174D TYR* 3.2 4.6 + - + +
175D MSE 3.0 46.8 + - + +
187D VAL* 4.9 1.8 - - + -
189D THR* 4.3 21.3 - - + -
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Residues in contact with ILE 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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75D VAL* 4.0 22.0 - - + -
77D ILE* 4.2 9.9 - - + -
81D LEU* 3.8 13.2 - - + -
89D VAL* 3.6 25.7 - - + +
93D ILE* 4.4 3.4 - - + -
168D ILE* 2.9 37.6 + - + +
171D LEU* 1.3 73.7 - - + +
173D SER* 1.3 65.6 + - - +
175D MSE 3.5 7.8 + - - +
176D SER* 3.2 21.0 + - - -
181D LEU* 3.6 23.5 - - + +
187D VAL* 4.0 24.7 - - + -
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Residues in contact with SER 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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84D ALA 2.6 23.6 + - - +
85D SER* 4.0 5.0 - - - -
86D GLU* 4.0 16.1 + - - +
89D VAL* 3.8 15.4 - - - +
169D ILE 3.0 15.7 + - - -
170D PRO* 3.5 6.5 - - - -
171D LEU 3.2 0.2 - - - -
172D ILE* 1.3 77.4 - - - +
174D TYR* 1.3 61.7 + - - +
176D SER* 2.6 23.2 + - - -
177D ARG* 3.6 8.8 + - - +
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Residues in contact with TYR 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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120A LYS* 2.7 26.5 + - - +
40D GLU* 3.7 12.8 - - + +
41D PRO* 3.6 43.5 - - + -
43D LEU* 3.7 25.4 - - + -
166D THR* 6.1 0.4 - - + -
170D PRO 2.9 13.6 + - - +
171D LEU* 3.5 10.3 - - - +
173D SER* 1.3 76.1 - - - +
175D MSE 1.3 65.4 + - - +
177D ARG* 2.9 54.3 + - - +
178D PHE* 3.8 20.1 - + - -
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Residues in contact with MSE 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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20D VAL* 3.7 29.6 - - + +
21D CYS* 3.7 30.1 - - - +
22D VAL 3.9 3.1 - - - +
43D LEU* 3.8 35.9 - - + -
171D LEU* 3.0 32.4 + - + +
172D ILE* 3.7 11.9 - - - +
174D TYR* 1.3 76.3 - - - +
176D SER* 1.3 58.0 + - - +
178D PHE* 3.0 6.8 + - - +
179D PHE* 2.9 31.2 + - - +
181D LEU* 4.6 7.6 - - + -
187D VAL* 3.7 36.1 - - + -
188D LEU 4.1 2.0 - - - +
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Residues in contact with SER 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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125A ASP* 5.4 0.2 - - - +
81D LEU* 3.9 25.4 - - - -
82D LYS* 3.7 7.4 + - - +
83D GLN* 2.7 27.8 + - - +
84D ALA* 3.1 21.8 + - - +
172D ILE 3.2 9.7 + - - -
173D SER* 2.6 23.5 + - - -
174D TYR 3.2 0.2 - - - -
175D MSE 1.3 75.0 - - - +
177D ARG* 1.3 63.3 + - - +
178D PHE 3.1 0.8 - - - -
179D PHE 3.4 16.9 + - - +
181D LEU* 4.7 4.0 - - - -
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Residues in contact with ARG 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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63A ASP* 5.4 6.5 + - - +
64A PHE* 3.6 44.8 - - + -
82D LYS* 5.6 3.4 + - - -
83D GLN* 4.1 26.2 - - + +
173D SER* 3.8 9.6 - - - +
174D TYR* 2.9 47.0 + - - +
176D SER* 1.3 79.2 + - - +
178D PHE* 1.3 65.7 + - + +
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Residues in contact with PHE 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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64A PHE* 3.5 49.8 - + - -
107A LEU* 4.3 10.3 - - + -
120A LYS* 3.6 54.7 - - + -
124A PHE* 3.6 9.7 - - + +
125A ASP* 3.2 29.5 + - - +
43D LEU* 4.6 2.5 - - + -
174D TYR* 3.8 39.7 - + - -
175D MSE 3.0 5.4 + - - +
176D SER 4.5 0.4 - - - -
177D ARG* 1.3 87.5 - - + +
179D PHE* 1.3 80.5 + - + +
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Residues in contact with PHE 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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47A PRO* 5.3 0.4 - - + -
49A THR* 4.8 2.5 - - - +
119A GLU* 3.4 42.2 - - + -
120A LYS* 3.9 9.4 - - + -
123A ALA* 3.5 28.3 - - + -
124A PHE 4.1 1.1 - - - -
125A ASP* 3.4 4.9 - - - +
18D LYS* 4.3 18.6 - - - -
20D VAL* 4.1 20.4 - - + -
43D LEU* 3.8 24.5 - - + -
45D ILE* 3.9 13.9 - - + -
175D MSE 2.9 13.4 + - + +
176D SER* 3.4 20.9 - - - -
178D PHE* 1.3 96.3 - - + +
180D THR* 1.3 64.8 + - - +
181D LEU* 3.3 10.3 + - + +
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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