Contacts of the helix formed by residues 167 - 179 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLN* 3.5 26.9 - - + +
164A MSE 4.4 6.3 - - + +
165A ILE 3.6 8.5 - - - +
166A THR* 1.3 89.0 - - + +
168A ILE* 1.3 66.1 + - - +
169A ILE 3.4 1.0 + - - +
170A PRO* 3.4 25.1 - - + +
171A LEU* 3.0 18.9 + - - +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.6 28.5 - - + -
75A VAL* 4.3 8.1 - - + -
93A ILE* 4.2 16.6 - - + -
96A TYR* 4.5 4.0 - - + +
142A ALA* 3.6 29.4 - - + +
143A GLN* 2.9 23.7 + - - +
164A MSE 3.8 18.5 - - - -
166A THR 3.9 0.4 + - - -
167A PRO* 1.3 70.3 - - - +
169A ILE* 1.3 61.3 + - + +
171A LEU* 3.3 8.6 + - - +
172A ILE* 2.9 49.7 + - + +
189A THR* 4.1 10.1 - - + -
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 3.4 44.2 - - + +
89A VAL* 3.9 18.2 - - + +
90A ALA* 4.2 21.8 - - + -
93A ILE* 4.8 5.2 - - + -
143A GLN* 4.8 0.4 + - - -
167A PRO* 4.8 0.2 - - - +
168A ILE* 1.3 84.3 - - + +
170A PRO* 1.3 76.0 - - + +
171A LEU 3.1 0.2 + - - -
172A ILE* 3.2 2.4 + - - -
173A SER* 2.9 21.3 + - - -
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLU* 3.6 26.5 - - + +
166A THR* 4.4 8.6 - - + +
167A PRO* 3.4 40.4 - - + +
169A ILE* 1.3 98.6 - - + +
171A LEU* 1.3 55.4 + - - -
173A SER* 3.6 6.4 - - - -
174A TYR* 2.9 29.6 + - - +
79C THR* 6.0 0.9 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.8 32.1 - - + -
25A ASN* 4.4 7.9 - - - +
41A PRO* 3.8 31.6 - - + -
43A LEU* 4.5 1.3 - - + -
164A MSE 5.8 0.2 - - - -
166A THR* 3.9 16.5 - - + +
167A PRO 3.0 19.7 + - - +
168A ILE* 3.4 6.5 - - - +
170A PRO* 1.3 76.2 - - - +
172A ILE* 1.3 60.0 + - + +
174A TYR* 3.1 6.6 + - - +
175A MSE 2.9 56.5 + - + +
187A VAL* 4.6 3.1 - - + -
188A LEU 4.5 0.2 - - - +
189A THR* 4.3 21.1 - - + -
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.0 21.8 - - + -
77A ILE* 4.1 11.4 - - + -
81A LEU* 3.9 14.6 - - + -
89A VAL* 3.8 18.8 - - + -
93A ILE* 4.2 9.0 - - + -
168A ILE* 2.9 38.0 + - + +
171A LEU* 1.3 73.7 - - + +
173A SER* 1.3 66.0 + - - +
175A MSE 3.7 6.9 - - - +
176A SER* 3.1 22.3 + - - -
181A LEU* 3.7 22.8 - - + +
187A VAL* 4.0 26.5 - - + -
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 2.7 23.9 + - - +
85A SER* 4.4 0.7 - - - -
86A GLU* 4.1 17.6 + - - +
89A VAL* 3.7 15.1 - - - +
169A ILE 2.9 16.8 + - - -
170A PRO* 3.6 9.9 - - - -
172A ILE* 1.3 76.9 - - - +
174A TYR* 1.3 63.1 + - - +
176A SER* 2.7 21.3 + - - -
177A ARG* 3.5 8.2 + - - +
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU* 3.3 29.5 + - + +
41A PRO* 3.5 44.6 - - + -
43A LEU* 3.8 19.5 - - + -
166A THR* 6.0 0.2 - - + -
170A PRO 2.9 19.3 + - - +
171A LEU* 3.4 6.3 - - - +
173A SER* 1.3 76.5 + - - +
175A MSE 1.3 64.1 + - - +
177A ARG* 2.9 42.6 + - - +
178A PHE* 3.7 13.3 - + - -
13C ASP* 2.7 27.8 + - - -
14C PHE* 5.6 2.5 - + - -
120D LYS* 2.7 21.4 + - - +
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Residues in contact with MSE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.7 32.5 - - + +
21A CYS 3.8 21.3 - - - +
22A VAL 4.0 0.4 - - - +
43A LEU* 3.8 33.9 - - + -
171A LEU* 2.9 42.3 + - + +
172A ILE* 3.7 11.2 - - - +
174A TYR* 1.3 71.8 - - - +
176A SER* 1.3 57.7 + - - +
177A ARG 3.1 0.2 - - - -
178A PHE* 3.0 6.2 + - - -
179A PHE* 2.9 30.7 + - - +
181A LEU* 4.4 8.3 - - + -
187A VAL* 3.6 42.8 - - + -
188A LEU 4.0 1.3 - - - +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.0 26.0 - - - -
82A LYS* 3.8 5.4 + - - +
83A GLN* 2.8 25.7 + - - +
84A ALA* 2.9 24.2 + - - -
89A VAL* 5.6 0.2 - - - -
172A ILE 3.1 12.8 + - - -
173A SER* 2.7 20.5 + - - -
174A TYR 3.1 0.2 - - - -
175A MSE 1.3 76.4 - - - +
177A ARG* 1.3 59.8 + - - +
178A PHE 3.2 0.6 - - - -
179A PHE 3.2 18.1 + - - +
181A LEU* 4.6 3.8 - - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU* 4.3 0.6 + - - -
82A LYS* 5.7 2.4 + - - -
83A GLN* 4.3 27.7 + - + +
173A SER* 3.9 9.2 - - - +
174A TYR* 2.9 35.6 + - - +
176A SER* 1.3 79.5 + - - +
178A PHE* 1.3 66.1 + - + +
13C ASP* 2.8 48.6 + - - -
14C PHE* 4.3 15.7 - - - +
15C PRO* 4.8 5.0 - - - +
183C ALA* 6.5 0.2 - - - -
63D ASP* 4.5 9.1 + - - +
64D PHE* 3.5 35.1 - - + -
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.7 2.7 - - + -
174A TYR* 3.6 31.6 - + - -
175A MSE 3.0 6.0 + - - +
176A SER 4.5 0.4 - - - -
177A ARG* 1.3 85.9 - - + +
179A PHE* 1.3 79.5 + - + +
180A THR 4.3 0.2 - - - -
13C ASP* 3.3 22.0 - - + -
64D PHE* 3.5 46.7 - + - -
107D LEU* 4.0 9.9 - - + -
120D LYS* 3.6 53.6 - - + -
124D PHE* 3.5 7.4 - - + +
125D ASP* 3.1 30.0 + - - +
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Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 4.2 19.3 - - - -
20A VAL* 4.0 21.3 - - + -
43A LEU* 4.0 22.7 - - + -
45A ILE* 3.9 20.2 - - + -
175A MSE 2.9 13.3 + - - +
176A SER* 3.2 24.2 - - - -
178A PHE* 1.3 97.4 - - + +
180A THR* 1.3 64.4 + - - +
181A LEU* 3.2 10.0 + - + +
47D PRO* 5.3 0.9 - - + -
49D THR* 5.1 1.1 - - - +
119D GLU* 3.6 33.2 - - + -
120D LYS* 3.9 6.3 - - + -
123D ALA* 3.4 33.9 - - + -
124D PHE* 3.8 2.2 - - - -
125D ASP* 3.6 3.6 - - - +
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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