Contacts of the strand formed by residues 67 - 78 (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 ILE 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C VAL* 4.0 19.1 - - + -
61C SER 3.5 10.8 - - - +
62C SER* 3.6 20.6 - - - -
65C GLY 3.6 17.3 - - - +
66C ALA* 1.3 72.4 - - - +
68C THR* 1.3 66.7 + - - +
107C TRP* 3.1 49.4 - - + +
248C ILE 4.0 0.3 - - - +
249C GLN* 3.6 2.3 - - - -
250C MET* 2.9 48.1 + - + +
253C PRO* 5.6 3.6 - - + -
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Residues in contact with THR 68 (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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59C ALA 3.3 1.7 - - - +
60C VAL* 3.2 5.2 - - - +
61C SER* 2.8 43.8 + - - -
63C SER* 5.6 4.2 - - - -
66C ALA* 5.0 4.2 - - - +
67C ILE* 1.3 76.8 + - - +
69C VAL* 1.3 64.7 + - - +
70C LEU* 4.8 5.6 - - + -
113C LEU* 4.7 7.6 - - + +
247C THR* 3.8 23.3 - - + -
248C ILE 3.2 17.0 - - - +
249C GLN* 4.6 9.8 + - + +
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Residues in contact with VAL 69 (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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58C PRO* 5.0 1.6 - - + -
59C ALA 3.2 3.8 - - - +
60C VAL* 3.7 27.6 - - + -
67C ILE 4.3 0.4 + - - -
68C THR* 1.3 72.8 - - - +
70C LEU* 1.3 75.0 + - - +
71C HIS* 4.3 1.8 - - + -
99C TRP* 4.3 20.2 - - + -
100C LEU* 5.0 4.9 - - + -
103C VAL* 4.5 11.0 - - + -
246C TYR* 4.0 17.9 - - + +
247C THR* 3.3 5.4 - - - +
248C ILE* 3.0 45.1 + - + +
250C MET* 3.6 24.0 - - + +
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Residues in contact with LEU 70 (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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57C ASN 4.9 0.3 - - - +
58C PRO* 3.6 2.4 - - - +
59C ALA* 2.9 42.2 + - + +
68C THR* 4.8 6.1 - - + -
69C VAL* 1.3 72.8 - - - +
71C HIS* 1.3 65.3 + - - +
245C THR* 5.6 6.3 - - + -
246C TYR 3.3 10.3 - - - +
247C THR* 3.0 39.9 - - + +
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Residues in contact with HIS 71 (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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55C ILE* 3.9 9.3 - - + +
56C ARG 3.3 24.6 + - - -
57C ASN 4.5 0.2 - - - -
58C PRO* 3.6 29.7 - - + +
69C VAL* 4.3 5.8 - - + -
70C LEU* 1.3 77.7 - - - +
72C CYS* 1.3 88.8 + - - +
73C GLU* 4.0 7.7 - - + +
99C TRP* 3.9 24.3 - + + +
245C THR* 3.4 3.8 - - - +
246C TYR* 2.9 64.8 + - + +
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Residues in contact with CYS 72 (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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55C ILE* 3.7 29.4 - - + +
71C HIS* 1.3 92.4 + - - +
73C GLU* 1.3 70.6 + - - +
170C PHE 4.4 0.2 - - - -
171C ILE* 3.8 31.2 - - + +
243C TYR* 5.7 0.7 - - + -
244C ASP 3.2 5.2 - - - +
245C THR* 3.0 43.7 - - - -
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Residues in contact with GLU 73 (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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55C ILE* 4.5 3.4 - - - -
71C HIS* 4.0 6.1 - - + +
72C CYS* 1.3 82.7 - - - +
74C LEU* 1.3 67.6 + - - +
75C THR* 3.3 0.4 + - - -
96C VAL 5.0 2.2 - - - +
97C GLY* 3.7 13.0 - - - -
98C THR* 3.0 14.6 + - - +
99C TRP* 2.8 35.0 + - + +
100C LEU* 3.0 19.8 + - - +
243C TYR* 3.4 7.1 - - - -
244C ASP* 2.8 33.5 + - + +
246C TYR* 2.5 31.9 + - + +
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Residues in contact with LEU 74 (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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55C ILE* 4.8 2.0 - - - +
73C GLU* 1.3 78.4 - - - +
75C THR* 1.3 63.0 + - - +
76C ALA* 3.6 26.2 - - - +
77C GLU* 4.4 20.0 - - + +
96C VAL 5.2 1.0 - - - +
97C GLY* 5.5 2.1 - - - -
98C THR* 5.4 3.8 + - - -
241C ARG* 4.5 8.3 - - + -
242C ILE 4.1 3.4 - - - +
243C TYR* 3.5 42.4 - - + +
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Residues in contact with THR 75 (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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73C GLU 3.3 1.2 + - - -
74C LEU* 1.3 78.1 - - - +
76C ALA* 1.3 67.6 + - + +
89C GLU* 2.9 27.6 + - - +
95C THR 4.6 0.3 + - - -
96C VAL 2.8 25.6 + - - -
117C TYR* 4.0 13.4 - - + -
224C LEU* 5.9 1.1 - - + -
242C ILE* 2.8 37.9 + - + +
244C ASP* 4.0 17.2 - - + +
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Residues in contact with ALA 76 (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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74C LEU* 3.6 6.2 - - - +
75C THR* 1.3 91.8 - - + +
77C GLU* 1.3 65.8 + - - +
78C ILE* 4.9 4.0 - - + -
89C GLU* 5.2 5.6 - - + +
226C ILE* 5.1 7.9 - - + -
241C ARG* 3.4 6.6 - - - +
242C ILE* 2.8 41.0 + - + +
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Residues in contact with GLU 77 (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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74C LEU* 4.4 14.2 - - + +
76C ALA* 1.3 78.0 - - - +
78C ILE* 1.3 71.7 + - - +
238C ALA* 5.9 3.3 - - - +
240C GLY 3.9 9.7 - - - +
241C ARG* 3.6 25.2 - - - +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ALA* 4.7 3.8 - - + +
77C GLU* 1.3 87.2 + - - +
79C GLY* 1.3 56.3 + - - +
119C TYR* 4.0 14.6 - - + -
131C ILE* 4.6 2.2 - - + -
226C ILE* 4.3 13.2 - - + -
228C LEU* 3.3 42.6 - - + -
238C ALA* 3.7 4.9 - - - +
239C ALA* 2.8 36.9 + - + -
240C GLY 2.8 25.1 + - - +
241C ARG* 4.5 1.3 - - - -
242C ILE* 4.1 33.9 - - + -
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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