Contacts of the strand formed by residues 78 - 87 (chain C) in PDB entry 3SHD
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 PRO 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C PHE* 4.0 32.8 - - + -
3C LYS 5.2 0.9 - - - +
4C PRO* 4.4 9.2 - - + -
5C HIS* 3.1 34.1 + - + +
70C GLN* 6.5 0.2 - - + -
71C TRP 3.5 7.2 - - - +
72C ILE* 4.3 18.4 - - + -
76C LYS 3.7 7.0 - - - +
77C THR* 1.3 89.0 - - + +
79C PHE* 1.3 60.1 + - - +
41G ASP 6.1 1.6 - - - +
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Residues in contact with PHE 79 (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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4C PRO* 4.9 0.4 - - - -
5C HIS* 3.1 18.8 - - + +
7C THR* 3.8 25.1 - - + +
37C HIS* 3.8 28.5 - + - -
69C HIS 3.8 0.2 - - - +
70C GLN* 3.5 6.6 - - - +
71C TRP* 2.9 59.5 + + + +
73C ALA* 4.1 11.9 - - + -
77C THR* 3.5 40.8 - - + -
78C PRO* 1.3 72.9 - - - +
80C LEU* 1.3 71.3 + - - +
81C ARG* 4.6 5.8 - - + +
119C ARG* 6.3 1.6 - - - -
158C SO4 4.5 13.5 - - - -
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Residues in contact with LEU 80 (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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4C PRO* 4.1 16.8 - - + -
5C HIS 2.7 10.8 + - - +
6C VAL* 3.2 12.1 - - + +
7C THR* 2.8 34.0 + - - +
68C MET* 3.6 22.2 - - + -
69C HIS 3.7 4.5 - - - -
70C GLN* 3.8 28.7 - - + +
79C PHE* 1.3 79.3 - - - +
81C ARG* 1.3 54.4 + - - +
82C PHE* 3.9 8.3 - - + -
6G VAL* 4.0 35.9 - - + -
38G LEU* 4.9 1.3 - - + -
44G LEU* 4.7 6.7 - - + -
80G LEU* 4.7 3.8 - - + -
82G PHE* 4.1 16.8 - - + -
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Residues in contact with ARG 81 (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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7C THR* 3.4 11.0 - - - +
9C ALA* 3.5 19.2 - - + +
32C ASN* 3.3 15.6 + - - -
33C GLN* 2.7 28.3 + - - -
67C ARG 4.2 0.2 - - - +
68C MET* 3.4 4.8 - - - +
69C HIS* 3.0 38.9 + - - +
71C TRP* 6.1 1.1 - - - -
79C PHE* 4.9 7.0 - - + -
80C LEU* 1.3 73.6 - - - +
82C PHE* 1.3 66.6 + - - +
83C LEU* 3.5 14.7 + - - +
122C LEU* 3.6 37.5 - - + +
123C VAL* 4.7 4.8 - - - +
126C SER* 2.8 21.4 + - - -
158C SO4 2.8 34.1 + - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.3 28.0 - - + -
7C THR 3.1 14.8 + - - +
8C VAL* 3.3 2.7 - - + -
9C ALA* 2.8 32.9 + - - +
44C LEU* 3.5 29.6 - - + -
65C PHE* 4.0 7.9 - + + -
67C ARG 4.0 2.2 - - - -
68C MET* 3.8 36.8 - - + -
80C LEU* 4.0 7.6 - - + -
81C ARG* 1.3 74.0 - - - +
83C LEU* 1.3 53.9 + - - +
84C PHE* 3.9 20.1 - - + -
141C ILE* 3.8 21.3 - - + -
68G MET* 3.9 24.2 - - - -
80G LEU* 4.4 4.0 - - + -
82G PHE* 4.1 7.0 - + - -
141G ILE* 5.9 0.2 - - + -
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Residues in contact with LEU 83 (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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9C ALA* 3.4 20.4 - - + +
10C CYS 4.5 0.4 - - - +
11C VAL* 4.1 10.8 - - + -
33C GLN* 4.7 1.1 - - + -
65C PHE* 3.5 4.0 - - - -
66C ILE* 2.7 63.7 + - + +
67C ARG 3.0 18.1 + - - +
69C HIS* 4.9 10.1 - - + +
81C ARG* 3.5 16.6 - - - +
82C PHE* 1.3 74.8 - - - +
84C PHE* 1.3 56.2 + - - +
126C SER* 3.3 50.3 - - - +
129C CYS* 4.5 3.8 - - + -
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Residues in contact with PHE 84 (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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8C VAL* 3.9 18.6 - - + -
9C ALA 2.8 20.5 + - - +
10C CYS* 3.3 6.9 - - - -
11C VAL* 2.6 34.0 + - - +
44C LEU* 4.1 23.3 - - + -
45C VAL* 4.6 6.7 - - + -
48C ALA* 3.7 27.1 - - + -
62C PRO* 4.1 17.7 - - + -
64C HIS 3.1 11.2 - - - +
65C PHE* 3.9 20.9 - + - -
66C ILE* 3.7 7.9 - - - +
82C PHE* 3.9 20.6 - - + -
83C LEU* 1.3 71.7 - - - +
85C ALA* 1.3 54.3 + - - +
138C LEU* 3.7 26.9 - - + -
141C ILE* 3.9 11.9 - - + -
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Residues in contact with ALA 85 (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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11C VAL 3.5 5.8 - - - +
62C PRO 4.0 0.2 - - - -
63C GLN* 3.0 27.7 + - - +
64C HIS* 2.9 22.3 + - + +
66C ILE* 3.7 19.9 - - + +
84C PHE* 1.3 72.8 - - - +
86C ILE* 1.3 63.2 + - - +
87C GLU* 4.3 2.7 - - - +
130C TYR* 4.5 10.8 - - + -
135C ARG* 3.9 21.8 - - - +
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Residues in contact with ILE 86 (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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10C CYS* 4.1 20.9 - - + -
11C VAL 2.8 13.9 + - - +
12C VAL* 3.3 8.5 - - + +
13C HIS* 3.0 25.7 + - - +
52C LEU* 4.1 24.5 - - + -
60C ALA* 4.2 8.7 - - + +
61C GLN 3.4 27.1 - - - +
62C PRO* 3.7 14.4 - - + -
63C GLN* 3.4 7.4 - - + +
85C ALA* 1.3 81.1 - - - +
87C GLU* 1.3 66.0 + - - +
88C LEU* 3.8 28.8 + - + -
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Residues in contact with GLU 87 (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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13C HIS* 3.0 36.8 - - - +
63C GLN* 2.6 33.3 - - - +
64C HIS* 6.1 2.0 - - + +
85C ALA* 5.2 2.6 - - + +
86C ILE* 1.3 73.2 - - - +
88C LEU* 1.3 67.1 + - - +
89C GLU* 5.1 2.4 - - - +
130C TYR* 2.6 32.2 + - - -
135C ARG* 4.4 6.2 + - - -
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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