Contacts of the helix formed by residues 70 - 81 (chain B) in PDB entry 6V99
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ALA 5.8 0.2 - - - +
34B ALA* 5.1 12.3 - - + +
66B THR* 3.9 28.0 - - - +
67B GLN 4.3 7.6 - - - +
68B TYR 3.1 5.9 + - - -
69B LYS* 1.3 75.7 - - - +
71B HIS* 1.3 53.9 + - - +
72B ASP 3.3 2.9 - - - -
73B LEU* 2.9 21.0 + - + -
74B ILE* 2.8 35.8 + - + +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.5 5.6 + - - +
70B ALA* 1.3 74.8 - - - +
72B ASP* 1.3 63.7 + - - +
74B ILE* 4.2 7.5 - - + +
75B ARG* 3.0 67.6 + - + +
94C ILE 4.0 19.4 + - - -
95C LEU* 4.5 8.9 - - + +
96C PRO* 4.9 11.0 - - + -
100C ARG* 4.9 23.4 + - + +
120C ILE* 4.9 17.7 - - + -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG 4.9 8.0 + - - +
33B ARG* 2.8 53.8 + - + +
37B ALA* 4.6 3.1 - - + -
45B ARG* 3.3 23.1 + - - +
70B ALA 3.3 0.6 - - - -
71B HIS* 1.3 78.2 + - - +
73B LEU* 1.3 61.6 + - - +
75B ARG* 3.7 28.6 + - - +
76B HIS* 3.1 22.7 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 3.8 27.8 - - + +
34B ALA* 4.7 8.5 - - + +
36B PRO* 4.4 5.8 - - + -
37B ALA* 3.9 29.0 - - + +
47B ILE* 4.0 30.5 - - + -
66B THR* 3.7 26.7 - - + -
70B ALA* 2.9 17.5 + - + +
72B ASP* 1.3 78.9 - - - +
74B ILE* 1.3 63.4 + - - +
76B HIS* 3.0 10.8 + - + +
77B LEU* 2.9 37.2 + - + +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR* 3.9 23.8 - - + +
68B TYR 4.1 14.8 - - - +
70B ALA* 2.8 26.1 + - + +
71B HIS* 4.2 6.3 - - + +
73B LEU* 1.3 70.8 - - - +
75B ARG* 1.3 57.5 + - - +
77B LEU* 3.1 9.4 + - - +
78B GLN* 2.8 54.4 + - + +
94B ILE* 3.8 20.8 - - + +
96B PRO* 3.9 19.3 - - + -
74C ILE* 6.1 1.1 - - + -
78C GLN* 4.2 7.4 - - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 5.4 1.6 - - - +
71B HIS* 3.0 63.0 + - + +
72B ASP* 3.7 29.7 + - - +
74B ILE* 1.3 77.4 - - - +
76B HIS* 1.3 64.0 + - - +
78B GLN* 3.6 15.8 - - - +
79B ARG* 3.1 65.9 + - - +
93C ASP* 4.7 10.5 - - - -
120C ILE* 6.4 1.1 - - - -
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.1 42.0 + - + +
47B ILE* 4.3 8.3 - - + -
48B ASP* 2.7 40.4 + - - -
72B ASP 3.1 13.9 + - - +
73B LEU* 3.0 12.6 + - + +
75B ARG* 1.3 77.4 - - - +
77B LEU* 1.3 73.8 + - + +
79B ARG* 4.3 2.6 - - - +
80B GLY* 2.8 29.5 + - - -
81B TRP* 4.1 4.4 + + - -
301B THR* 3.8 10.3 - - - -
302B TYR* 3.8 25.8 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.4 8.1 - - + -
51B LEU* 3.7 29.8 - - + -
64B VAL* 3.6 32.5 - - + -
66B THR* 4.7 1.1 - - + -
73B LEU* 2.9 32.8 + - + +
74B ILE* 3.1 5.3 + - - +
76B HIS* 1.3 84.1 - - + +
78B GLN* 1.3 60.2 + - - +
81B TRP* 2.9 44.5 + - + +
92B PHE* 4.0 12.1 - - + -
94B ILE* 3.7 30.9 - - + +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 2.8 27.8 + - - +
75B ARG* 3.6 24.2 + - - +
77B LEU* 1.3 77.4 - - - +
79B ARG* 1.3 62.7 + - + +
81B TRP 5.4 0.2 - - - -
82B ASP* 3.3 22.9 - - - +
94B ILE* 4.0 5.8 - - + +
74C ILE* 4.4 3.8 - - - +
78C GLN* 2.8 56.0 + - + +
82C ASP* 5.9 1.7 - - - +
94C ILE* 3.8 24.1 + - - +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 3.1 56.2 + - - +
76B HIS* 4.3 1.9 - - - +
78B GLN* 1.3 85.3 - - + +
80B GLY* 1.3 62.6 + - - +
82B ASP* 3.5 17.5 - - - +
302B TYR* 3.6 53.6 + - + +
304B GLU* 4.8 3.4 + - - -
84C PHE 6.1 1.6 - - - +
85C ARG* 4.9 4.2 + - - -
86C PRO* 4.6 16.0 - - + +
91C SER* 6.3 0.6 - - - -
92C PHE 5.7 5.5 + - - -
93C ASP* 4.7 8.7 + - - -
124C TYR* 5.6 2.8 + - - -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B HIS* 2.8 17.0 + - - -
79B ARG* 1.3 79.8 - - - +
81B TRP* 1.3 63.2 + - - +
82B ASP* 3.5 10.3 + - - +
83B PHE* 4.1 0.5 - - - -
300B TRP* 2.9 26.3 + - - -
301B THR 4.7 0.2 - - - -
302B TYR* 3.7 28.2 - - - -
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Residues in contact with TRP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.0 24.0 + - - -
51B LEU* 3.4 45.2 - - + +
52B SER* 3.6 21.8 - - - -
55B LEU* 3.9 21.1 - - + -
62B ILE* 4.9 1.1 - - + -
76B HIS* 4.1 7.1 + - - -
77B LEU* 2.9 29.0 + - + +
78B GLN* 5.4 0.3 - - - -
80B GLY* 1.3 78.1 - - - +
82B ASP* 1.3 57.7 + - - +
83B PHE* 3.7 22.2 + + - -
84B PHE* 4.2 9.0 - + - -
92B PHE* 3.6 52.7 - + + +
300B TRP* 3.5 38.7 + + + -
301B THR* 4.8 1.4 - - - +
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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