Contacts of the strand formed by residues 240 - 251 (chain C) in PDB entry 1SMV
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 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C GLU* 3.9 6.3 - - - +
78C ILE* 2.8 29.2 + - - +
119C TYR* 3.3 8.6 + - - -
120C ILE 3.5 12.1 - - - -
122C SER* 3.4 16.3 + - - -
238C ALA* 5.4 0.4 - - - +
239C ALA* 1.3 81.9 - - - +
241C ARG* 1.3 62.6 + - - +
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA 4.3 7.5 + - - -
53C VAL* 4.0 16.8 - - - +
74C LEU* 4.5 10.5 - - + -
76C ALA 3.4 13.2 - - - +
77C GLU* 3.6 20.9 - - - +
78C ILE* 4.3 2.7 - - - +
118C THR 4.1 0.3 - - - +
119C TYR* 3.6 4.7 - - - -
120C ILE* 3.0 50.0 + - - +
121C PRO 3.9 6.7 + - - -
122C SER* 3.4 29.4 - - - -
240C GLY* 1.3 76.8 - - - +
242C ILE* 1.3 63.4 + - - +
243C TYR* 3.3 34.6 + - + -
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 3.8 3.5 - - - +
75C THR* 2.8 44.5 + - + -
76C ALA* 2.8 19.3 + - + +
78C ILE* 4.1 20.2 - - + -
117C TYR* 4.0 18.4 - - + -
118C THR 3.4 7.4 - - - +
119C TYR* 4.1 13.5 - - + -
131C ILE* 4.3 7.2 - - + -
133C MET* 3.9 20.4 - - - -
224C LEU* 5.2 0.2 - - + -
226C ILE* 3.7 28.9 - - + -
241C ARG* 1.3 77.7 - - - +
243C TYR* 1.3 71.8 + - - +
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 3.8 36.1 - - + +
55C ILE* 4.2 16.4 - - + -
73C GLU 3.4 5.4 - - - +
74C LEU* 3.5 42.9 - - + +
75C THR* 4.6 0.2 - - - -
116C ARG 3.7 0.9 - - - +
117C TYR* 3.5 3.1 - - - -
118C THR* 2.9 34.8 + - - +
120C ILE* 4.0 9.6 - - + -
171C ILE* 3.7 39.7 - - + -
241C ARG* 3.3 38.6 + - + -
242C ILE* 1.3 78.2 - - - +
244C ASP* 1.3 62.4 + - - +
245C THR* 4.2 1.3 + - - +
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Residues in contact with ASP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C HIS 3.8 0.9 - - - +
72C CYS* 3.2 4.7 - - - -
73C GLU* 2.8 35.7 + - + +
75C THR* 4.0 21.2 - - - +
96C VAL* 3.4 18.5 - - + +
115C VAL* 3.7 7.0 - - - +
116C ARG 3.3 6.3 - - - +
117C TYR* 2.9 38.4 + - + -
243C TYR* 1.3 74.3 - - - +
245C THR* 1.3 67.9 + - - +
246C TYR* 3.1 26.9 - - + +
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Residues in contact with THR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 5.6 5.6 - - + -
71C HIS 3.4 5.6 - - - +
72C CYS* 3.0 29.5 - - - -
114C SER* 4.1 3.0 + - - +
115C VAL* 3.7 1.2 + - - -
116C ARG* 2.9 44.2 + - - +
118C THR* 4.5 6.2 + - - -
170C PHE 3.9 20.4 + - - +
171C ILE* 4.3 9.5 - - - +
243C TYR 4.8 0.3 + - - -
244C ASP* 1.3 74.6 + - - +
246C TYR* 1.3 64.4 + - - +
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C VAL* 4.1 10.0 - - + +
70C LEU* 3.3 9.2 - - - +
71C HIS* 2.9 70.0 + - + +
73C GLU* 2.5 36.5 + - + -
96C VAL* 4.0 13.9 - - + -
99C TRP* 4.6 2.4 - - - -
100C LEU* 3.5 28.3 + - + +
112C TRP* 3.9 20.4 - + + -
114C SER* 3.2 15.5 - - - +
115C VAL* 4.4 3.6 - - + -
244C ASP* 3.1 25.6 - - - +
245C THR* 1.3 76.1 - - - +
247C THR* 1.3 62.1 + - - +
248C ILE* 4.3 13.2 - - + -
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 3.8 17.5 - - + -
69C VAL 3.3 4.3 - - - -
70C LEU* 3.0 40.6 - - + +
112C TRP* 3.8 2.3 - - - -
113C LEU* 2.8 54.6 + - + -
114C SER* 2.9 22.6 + - - +
246C TYR* 1.3 71.0 - - - +
248C ILE* 1.3 57.0 + - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE 4.0 0.2 - - - +
68C THR* 3.2 9.3 - - - +
69C VAL* 3.0 50.9 + - + +
93C PRO* 3.9 22.0 - - + -
100C LEU* 4.2 22.9 - - + -
104C ALA* 4.8 1.3 - - + -
110C TYR* 3.9 19.5 - - + -
111C SER 3.6 11.7 - - - +
112C TRP* 4.0 22.2 - - + -
113C LEU 4.4 0.4 - - - +
246C TYR* 4.3 5.2 - - + -
247C THR* 1.3 75.6 - - - +
249C GLN* 1.3 74.0 + - - +
250C MET* 4.1 12.6 - - + -
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA* 4.7 16.8 - - + +
67C ILE 3.6 5.6 - - - +
68C THR* 4.6 10.1 + - - +
110C TYR* 3.0 7.1 - - - +
111C SER* 2.9 37.0 + - - +
113C LEU* 3.5 38.6 - - + +
195C LYS* 2.9 30.5 + - - -
196C TRP* 3.9 18.1 - - + -
248C ILE* 1.3 74.3 - - - +
250C MET* 1.3 59.8 + - - +
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Residues in contact with MET 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA* 3.6 0.5 - - - -
67C ILE* 2.9 49.2 + - + +
69C VAL* 3.6 31.9 - - + +
100C LEU* 5.1 1.6 - - - -
103C VAL* 4.2 4.9 - - + -
104C ALA* 3.7 35.0 - - + +
107C TRP* 3.7 45.8 - - + -
109C LYS 3.6 5.2 - - - +
110C TYR* 4.7 2.2 - - + -
248C ILE* 4.1 20.6 - - + -
249C GLN* 1.3 79.5 - - - +
251C ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLU* 3.7 30.7 - - + +
65C GLY 4.4 7.6 - - - +
66C ALA* 4.0 17.9 - - + +
107C TRP* 3.5 9.3 - - - +
108C SER 3.1 14.6 + - - -
109C LYS* 3.0 20.9 + - + +
196C TRP* 3.5 48.2 - - + -
250C MET* 1.3 80.0 - - - +
252C GLU* 1.3 96.2 + - + +
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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