Contacts of the strand formed by residues 70 - 77 (chain C) in PDB entry 1SMK
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 VAL 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY* 4.9 0.2 - - - -
45C PHE 3.3 4.9 - - - +
47C VAL* 4.0 13.0 - - + -
64C MET* 3.8 42.8 - - + +
67C ASN* 3.1 20.8 + - + +
68C PRO 3.2 4.6 - - - +
69C LEU* 1.3 79.2 - - - +
71C SER* 1.3 58.9 + - - +
72C VAL 3.4 29.4 - - - +
73C LEU* 4.1 9.9 - - + -
94C GLY 4.3 0.5 - - - -
95C ALA* 3.2 32.9 + - + +
283C LEU* 4.0 5.2 - - + -
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Residues in contact with SER 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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44C GLY* 3.3 28.8 + - - -
45C PHE 2.7 19.7 + - - +
46C LYS* 4.1 5.2 + - - +
69C LEU 3.8 0.2 + - - -
70C VAL* 1.3 75.0 - - - +
72C VAL* 1.3 70.3 + - - +
94C GLY 4.3 2.8 - - - +
95C ALA* 3.5 2.6 - - - +
96C VAL* 2.9 29.1 + - - +
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Residues in contact with VAL 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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45C PHE 3.3 0.8 + - - -
46C LYS* 3.3 29.5 - - + -
47C VAL 2.7 31.7 + - - -
70C VAL* 3.4 6.5 - - - +
71C SER* 1.3 94.6 + - - +
73C LEU* 1.3 57.7 + - - +
74C HIS* 3.2 35.4 - - + +
96C VAL* 3.4 13.0 - - + +
98C ARG* 5.8 2.5 - - + -
113C MET* 4.6 6.1 - - + -
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Residues in contact with LEU 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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47C VAL* 3.2 21.5 - - + +
49C ILE* 3.9 17.9 - - + -
61C ALA 3.7 23.3 - - - +
64C MET* 4.1 9.0 - - + -
65C LYS* 3.8 24.9 - - + +
70C VAL* 4.1 10.3 - - + -
71C SER 4.3 0.2 - - - -
72C VAL* 1.3 74.3 - - - +
74C HIS* 1.3 63.1 + - - +
75C LEU* 3.8 25.1 - - + -
88C ILE* 4.6 1.6 - - + -
95C ALA* 4.6 5.4 - - + -
96C VAL 2.8 12.9 + - - +
97C VAL* 3.0 37.2 - - + +
98C ARG 3.0 4.9 + - - -
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Residues in contact with HIS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL 2.7 12.7 + - - +
48C ALA* 3.2 6.0 - - + +
49C ILE 2.9 27.7 + - - -
72C VAL* 3.2 26.9 - - + +
73C LEU* 1.3 77.6 - - - +
75C LEU* 1.3 65.0 + - - +
76C TYR* 3.9 1.0 + - - -
98C ARG* 3.5 25.1 + - + -
100C PHE* 3.3 34.6 - + + -
108C ALA 3.9 9.0 - - - -
109C ALA* 2.9 27.7 + - + +
111C THR 4.9 2.0 - - - -
113C MET* 3.6 22.8 - - + +
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Residues in contact with LEU 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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49C ILE* 3.7 28.7 - - + -
52C ALA* 3.6 14.4 - - + -
61C ALA* 3.7 22.2 - - + -
73C LEU* 3.8 9.6 - - + -
74C HIS* 1.3 79.3 - - - +
76C TYR* 1.3 53.8 + - - +
81C ALA* 4.2 6.4 - - + +
84C VAL* 4.1 12.6 - - + -
85C THR* 3.9 19.1 - - - +
88C ILE* 3.9 17.7 - - + -
97C VAL* 3.6 25.4 - - + -
98C ARG 2.8 9.4 + - - +
99C GLY* 3.2 1.2 - - - -
100C PHE* 2.7 33.9 + - - +
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Residues in contact with TYR 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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48C ALA* 6.2 0.2 - - + -
49C ILE 3.0 12.3 + - - +
50C LEU* 4.0 17.9 - - + -
51C GLY 2.7 33.5 + - - -
52C ALA* 3.0 7.1 + - - +
74C HIS 3.9 0.8 + - - +
75C LEU* 1.3 76.0 - - - +
77C ASP* 1.3 68.7 + - - +
78C VAL* 3.9 13.7 - - + +
81C ALA* 4.6 0.2 - - - -
100C PHE* 3.3 24.7 - - + +
102C GLY 3.2 28.6 - - - -
103C GLN* 3.3 26.2 + - - +
106C LEU* 3.8 42.2 - - + +
109C ALA* 3.8 16.6 - - + -
144C LEU* 4.1 14.1 - - + +
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Residues in contact with ASP 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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51C GLY* 3.2 18.8 - - - +
53C ALA* 2.8 34.3 + - + +
54C GLY* 3.8 3.3 + - - -
76C TYR* 1.3 86.2 - - - +
78C VAL* 1.3 87.9 + - - +
79C VAL* 3.3 25.8 + - - +
81C ALA* 4.1 5.8 - - + +
100C PHE 3.1 9.3 + - - +
101C LEU* 3.3 5.2 - - - +
102C GLY 3.0 20.3 + - - -
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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