Contacts of the strand formed by residues 58 - 68 (chain C) in PDB entry 6S1M
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 HIS 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C ARG* 4.4 1.3 - - - +
56C GLN* 5.2 1.2 - - - -
57C LEU* 1.3 90.9 + - - +
59C VAL* 1.3 64.4 + - - +
82C GLU* 5.3 8.1 - - - +
103C ILE* 3.1 8.4 - - - +
104C GLN* 2.9 40.1 + - + +
105C LYS 3.8 17.2 + - - -
106C ALA* 4.2 1.5 - - - -
107C MET* 3.4 65.9 + - + +
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Residues in contact with VAL 59 (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 VAL* 3.8 26.7 - - + -
49C ARG* 3.7 20.2 - - - +
57C LEU* 5.2 0.9 - - + -
58C HIS* 1.3 78.9 - - - +
60C THR* 1.3 69.9 + - - +
61C TYR* 3.6 36.3 - - + +
82C GLU* 3.5 34.3 + - + +
100C VAL* 5.4 5.8 - - + -
102C SER 3.4 4.5 - - - +
103C ILE* 3.7 19.5 - - + -
107C MET* 5.5 0.3 - - - +
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PHE* 4.6 17.5 - - + -
59C VAL* 1.3 80.5 - - - +
61C TYR* 1.3 65.1 + - - +
79C VAL* 4.9 6.1 - - - -
80C VAL 3.4 13.7 - - - +
81C ARG* 4.2 13.2 - - + -
100C VAL* 4.0 2.4 - - - +
101C TYR* 2.9 28.5 + - - +
102C SER* 2.9 34.1 + - - +
107C MET* 6.0 4.0 - - + -
108C LEU* 5.8 5.8 - - + -
114C LEU* 4.8 6.4 - - + +
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Residues in contact with TYR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.5 5.2 - - + -
49C ARG* 4.7 6.6 + - - -
59C VAL* 3.6 35.1 - - + +
60C THR* 1.3 76.4 - - - +
62C LEU* 1.3 63.7 + - - +
63C VAL* 5.2 0.4 - - + -
79C VAL* 3.5 8.3 - - - +
80C VAL* 2.9 31.8 + - + +
81C ARG 3.9 13.5 - - - +
82C GLU* 4.4 11.4 - - - -
85C LEU* 4.5 36.3 - - + -
98C ILE* 5.3 7.9 - - + -
99C HIS 3.6 17.5 - - - +
100C VAL* 4.3 18.6 - - + -
101C TYR* 4.1 5.4 - - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 4.6 1.6 - - + -
226B LEU* 3.7 37.2 - - + -
227B GLY* 5.4 0.9 - - - -
61C TYR* 1.3 76.0 - - - +
63C VAL* 1.3 76.8 + - - +
64C SER* 4.5 4.0 - - - -
77C VAL* 4.5 16.2 - - + -
78C ALA 3.4 10.1 - - - +
79C VAL* 3.7 24.2 - - + -
97C SER* 3.6 19.0 - - - +
98C ILE* 3.6 24.3 - - - +
99C HIS* 3.4 30.7 + - + +
101C TYR* 4.5 8.3 - - + +
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Residues in contact with VAL 63 (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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61C TYR* 5.2 0.7 - - + -
62C LEU* 1.3 80.6 - - - +
64C SER* 1.3 69.0 + - - +
76C LYS 4.1 1.2 - - - +
77C VAL* 3.7 0.7 - - - -
78C ALA* 2.9 33.0 + - - +
80C VAL* 3.9 19.7 - - + -
85C LEU* 3.7 31.2 - - + +
88C VAL* 4.6 16.8 - - + -
89C LYS* 5.0 15.0 - - + -
92C LEU* 4.5 14.8 - - + -
95C THR* 5.0 6.5 - - + -
97C SER 3.7 5.2 - - - +
98C ILE* 4.8 10.1 - - + -
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Residues in contact with SER 64 (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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231B GLU* 2.9 27.9 + - - -
62C LEU* 4.5 4.3 - - - -
63C VAL* 1.3 75.8 - - - +
65C GLY* 1.3 61.1 + - - +
75C HIS* 3.0 14.0 + - - -
76C LYS 3.4 5.2 - - - -
77C VAL* 3.3 22.6 - - - +
92C LEU* 3.9 10.2 - - - +
95C THR* 4.1 4.0 - - - +
96C ALA* 3.2 19.8 + - - -
97C SER* 3.2 18.9 + - - +
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Residues in contact with GLY 65 (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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3B SER* 4.6 0.2 - - - -
64C SER* 1.3 81.1 + - - +
66C SER* 1.3 66.1 + - - +
75C HIS* 3.6 13.0 - - - -
76C LYS* 2.9 32.8 + - - +
92C LEU* 3.8 4.7 - - - +
94C VAL 3.4 11.7 - - - -
96C ALA* 4.2 10.5 - - - -
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Residues in contact with SER 66 (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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3B SER* 3.3 25.4 + - - -
448B GLN* 5.6 0.2 + - - -
65C GLY* 1.3 77.0 - - - +
67C LEU* 1.3 77.3 + - - +
68C ILE* 5.4 1.4 - - - +
73C SER* 4.7 8.5 - - - -
74C CYS 3.5 11.8 + - - -
75C HIS* 4.4 0.4 - - - +
92C LEU* 3.5 15.9 - - - +
93C ALA* 3.5 12.9 + - - +
94C VAL* 3.2 30.5 + - - +
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Residues in contact with LEU 67 (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 SER* 1.3 80.0 + - - +
68C ILE* 1.3 78.1 + - - +
69C GLN* 4.2 8.7 - - + +
73C SER* 3.4 6.4 - - - -
74C CYS* 2.9 45.2 + - - +
76C LYS* 4.0 27.8 - - + +
91C LYS* 3.4 30.1 - - + +
92C LEU* 3.9 22.7 - - + -
93C ALA* 4.0 9.4 - - + +
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Residues in contact with ILE 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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66C SER* 5.4 1.3 - - - +
67C LEU* 1.3 91.7 - - - +
69C GLN* 1.3 66.9 + - - +
71C GLY* 3.5 39.5 - - - +
72C HIS 3.3 9.9 - - - +
73C SER* 4.0 11.9 - - - -
93C ALA* 5.1 2.2 - - - +
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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