Contacts of the strand formed by residues 70 - 77 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F PHE 3.5 5.8 - - - +
47F VAL* 4.1 14.4 - - + -
64F MET* 3.4 41.5 - - + +
67F ASN* 2.9 24.7 + - + +
68F PRO 3.1 6.5 - - - +
69F LEU* 1.3 79.1 - - - +
71F SER* 1.3 56.7 + - - +
72F VAL 3.4 24.0 - - - +
73F LEU* 4.2 7.9 - - + -
94F GLY* 4.1 1.2 - - - -
95F ALA* 3.1 34.5 + - + +
283F LEU* 3.7 11.4 - - + -
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLY* 3.6 23.0 + - - -
45F PHE 2.8 28.3 + - - -
46F LYS* 3.9 5.7 + - - +
69F LEU 3.6 1.8 + - - -
70F VAL* 1.3 72.5 - - - +
72F VAL* 1.3 79.5 + - - +
94F GLY 3.8 4.1 - - - +
95F ALA* 3.0 5.1 - - - +
96F VAL* 2.8 26.2 + - - +
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LYS* 3.3 43.1 - - + -
47F VAL 2.9 19.4 + - - -
70F VAL* 3.4 6.6 - - - +
71F SER* 1.3 95.8 + - - +
73F LEU* 1.3 60.3 + - - +
74F HIS* 4.6 11.0 - - + +
96F VAL* 3.4 15.0 - - + +
113F MET* 3.9 13.0 - - + -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 3.2 27.8 - - + +
49F ILE* 3.9 23.1 - - + -
61F ALA 3.8 22.2 - - - +
64F MET* 4.2 6.5 - - + -
65F LYS* 3.9 24.2 - - + +
70F VAL* 4.2 8.5 - - + -
72F VAL* 1.3 74.7 - - - +
74F HIS* 1.3 70.8 + - - +
75F LEU* 3.8 15.7 - - + -
88F ILE* 4.8 1.1 - - + -
95F ALA* 4.3 6.1 - - + -
96F VAL 2.7 14.1 + - - +
97F VAL* 3.2 14.9 - - + +
98F ARG 2.8 26.0 + - - -
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Residues in contact with HIS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL 2.8 13.9 + - - +
48F ALA* 3.5 6.2 - - + +
49F ILE* 2.8 29.3 + - - +
72F VAL* 4.6 8.4 - - + +
73F LEU* 1.3 85.2 - - - +
75F LEU* 1.3 64.5 + - - +
76F TYR* 3.9 0.7 - - - -
96F VAL 5.5 0.4 - - - -
98F ARG* 3.2 27.5 + - + -
100F PHE* 3.2 35.5 - + + -
108F ALA 3.8 9.2 - - - -
109F ALA* 2.7 31.2 + - + +
111F THR 4.7 2.5 - - - -
113F MET* 3.6 25.1 - - + +
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 3.9 9.2 - - + -
52F ALA* 3.7 15.0 - - + -
61F ALA* 3.7 20.9 - - + -
73F LEU* 3.8 15.9 - - + -
74F HIS* 1.3 81.2 - - - +
76F TYR* 1.3 53.6 + - - +
81F ALA* 4.0 6.2 - - + +
84F VAL* 3.9 16.8 - - + -
85F THR* 3.6 27.4 - - - +
88F ILE* 3.8 26.0 - - + -
97F VAL* 3.9 17.5 - - + -
98F ARG 2.7 8.5 + - - -
99F GLY* 3.2 1.6 - - - -
100F PHE* 2.7 34.5 + - - +
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Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE 3.0 6.8 + - - +
50F LEU* 3.6 26.5 - - + -
51F GLY 2.9 24.2 + - - -
52F ALA* 2.9 7.3 + - - +
74F HIS 3.9 1.0 + - - +
75F LEU* 1.3 75.3 - - - +
77F ASP* 1.3 94.4 + - - +
78F VAL* 3.8 15.2 - - + +
81F ALA* 4.5 1.1 - - - -
100F PHE* 3.2 19.7 - - + -
102F GLY 3.2 41.0 - - - -
103F GLN* 3.3 11.6 + - - +
105F GLN 4.2 0.2 - - - -
106F LEU* 3.5 45.8 - - + +
109F ALA* 4.1 11.2 - - + -
144F LEU* 4.3 10.4 - - + +
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Residues in contact with ASP 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLY* 3.0 18.5 - - - +
53F ALA* 2.6 40.9 + - + +
54F GLY 3.6 3.1 + - - -
76F TYR* 1.3 93.9 - - - +
78F VAL* 1.3 84.9 + - - +
79F VAL* 3.2 20.1 + - - +
81F ALA* 4.1 6.1 - - + -
100F PHE 3.1 3.3 + - - +
101F LEU* 3.3 9.2 - - - +
102F GLY 3.1 19.2 + - - -
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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