Contacts of the strand formed by residues 84 - 92 (chain H) in PDB entry 6A3W
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 ALA 84 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLN* 3.7 28.0 - - + -
38H GLN 3.3 16.6 - - - +
39H LYS* 4.0 9.2 - - + +
40H PRO* 5.4 3.4 - - - -
82H ASP 3.1 8.6 + - - +
83H GLU* 1.3 77.4 - - - +
85H ASP* 1.3 58.4 + - - +
86H TYR* 3.5 9.2 - - + -
105H LYS* 3.9 10.5 - - - +
106H LEU 2.8 32.8 + - - -
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Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 5.8 0.2 + - - -
36H TYR 3.8 0.2 - - - +
37H GLN* 3.5 2.9 - - - -
38H GLN* 2.9 44.2 + - + +
40H PRO* 6.2 0.2 - - - +
84H ALA* 1.3 76.5 - - - +
86H TYR* 1.3 60.8 + - - +
87H TYR* 3.8 29.5 + - + +
103H GLY* 5.9 0.4 - - - -
104H THR 3.3 4.4 - - - +
105H LYS* 3.3 34.1 + - - +
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Residues in contact with TYR 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLN* 3.0 9.8 + - - -
21H ILE* 3.6 29.2 - - + -
35H TRP* 4.6 4.9 - + + -
36H TYR 3.3 8.1 - - - +
37H GLN* 2.8 45.1 + - + -
47H VAL* 4.7 2.0 - - + -
62H PHE* 3.8 16.6 - + - -
73H LEU* 3.5 22.7 - - + -
75H ILE* 3.8 9.0 - - + +
82H ASP* 2.6 37.7 + - - +
84H ALA* 3.5 21.1 - - + -
85H ASP* 1.3 72.9 - - - +
87H TYR* 1.3 62.1 + - - +
103H GLY* 3.3 0.9 - - - -
104H THR 2.8 32.7 + - - +
106H LEU* 3.7 14.4 - - + -
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Residues in contact with TYR 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 3.3 18.4 + - - -
43G LYS 3.7 3.1 + - - -
44G GLY* 3.5 28.9 - - - -
45G LEU* 3.5 34.1 - - + -
7H GLN* 3.5 2.0 - - - -
34H HIS 3.7 0.3 - - - +
35H TRP* 3.4 6.5 - - - -
36H TYR* 2.9 48.2 + - + +
38H GLN* 3.6 23.7 + - + -
85H ASP* 3.8 30.3 + - + +
86H TYR* 1.3 75.3 - - - +
88H CYS* 1.3 66.7 + - - +
100H PHE* 4.3 6.7 - - + -
101H GLY 3.7 11.9 - - - -
102H GLY 3.8 1.6 - - - -
103H GLY* 3.4 23.6 - - - -
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Residues in contact with CYS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 4.0 3.4 - - + -
7H GLN* 3.0 25.5 + - - -
23H CYS* 2.0 54.7 - - + -
28H ILE* 5.7 0.4 - - + -
33H ALA* 5.7 5.4 - - + -
34H HIS 3.3 5.8 - - - +
35H TRP* 3.7 20.3 - - + -
87H TYR* 1.3 76.0 - - - +
89H ALA* 1.3 59.3 + - - +
100H PHE* 3.3 5.2 - - - -
101H GLY* 2.7 40.1 + - - -
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G GLY 4.9 5.8 - - - +
103G PHE* 5.0 2.5 - - + -
5H LEU* 4.5 2.5 - - - -
33H ALA* 3.6 3.7 - - - +
34H HIS* 2.8 34.4 + - + -
36H TYR* 3.7 23.6 - - + -
88H CYS* 1.3 78.6 - - - +
90H THR* 1.3 63.9 + - - +
98H ALA* 6.3 0.9 - - + -
99H VAL 3.1 10.1 - - - +
100H PHE* 3.6 24.9 - - + -
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Residues in contact with THR 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G GLY* 5.2 2.0 - - - -
3H TYR* 4.3 11.0 - - + -
5H LEU* 3.7 23.3 - - + -
28H ILE* 5.1 7.2 - - + -
31H GLN* 2.9 36.5 + - - +
32H TYR 2.9 21.4 + - - -
33H ALA* 4.9 1.8 - - - -
34H HIS* 4.6 3.6 - - - -
89H ALA* 1.3 77.0 - - - +
91H TYR* 1.3 59.7 + - - +
92H THR* 4.4 4.0 - - - +
97H LEU 3.9 0.3 - - - +
98H ALA* 3.4 5.1 - - - +
99H VAL* 2.9 38.9 + - + +
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Residues in contact with TYR 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 4.3 5.2 - - - -
100G TYR* 3.9 33.7 - + + +
101G GLY* 3.9 19.9 - - - -
31H GLN* 3.6 14.9 + - - +
32H TYR 4.4 3.6 + - - +
34H HIS* 5.1 4.2 + - - +
90H THR* 1.3 77.2 + - - +
92H THR* 1.3 60.8 + - - +
93H GLY* 3.8 20.0 + - - -
96H SER* 2.7 50.9 + - - -
97H LEU 3.4 12.6 - - - -
98H ALA* 4.4 0.4 - - - +
111I GLU* 4.5 7.5 + - - -
132I ILE* 3.4 33.6 - - + +
133I CYS 5.5 0.3 + - - -
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Residues in contact with THR 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H TYR* 3.4 26.5 - - + +
31H GLN* 3.1 26.2 + - - +
90H THR* 4.4 3.1 - - - +
91H TYR* 1.3 73.0 - - - +
93H GLY* 1.3 60.8 + - - +
94H PHE* 3.3 27.5 + - + +
96H SER* 3.0 23.0 + - - -
97H LEU* 2.8 27.9 + - - -
99H VAL* 5.1 3.2 - - - +
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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
------------------------------------------------------------
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