Contacts of the helix formed by residues 76 - 89 (chain V) in PDB entry 5A0Q
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 76 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41V ILE* 3.9 12.3 - - + -
74V PRO 4.8 1.6 - - - +
75V LEU* 1.4 76.4 - - + +
77V HIS* 1.4 59.0 + - - +
79V ALA* 3.1 5.7 + - - +
80V ALA* 3.0 24.7 + - - +
100V ILE* 4.5 4.7 - - + +
101V ALA* 3.6 25.4 - - - +
102V GLY* 3.7 4.0 - - - -
103V TRP 3.7 31.6 - - - +
110V GLN* 3.7 38.1 - - + +
112V TYR* 3.8 16.4 - - + -
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Residues in contact with HIS 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U PHE 4.4 9.0 - - - -
103U GLY* 4.9 3.6 - - - -
104U TYR* 3.6 24.4 + - + +
75V LEU* 3.7 37.1 - - + +
76V VAL* 1.4 76.0 + - - +
78V THR* 1.3 56.2 + - - +
79V ALA 3.4 0.2 - - - -
80V ALA* 3.6 8.7 - - - +
81V SER* 2.8 37.8 + - - -
110V GLN* 4.5 5.6 + - - -
112V TYR* 3.8 27.8 + - + +
120V MET* 3.7 13.9 - - + +
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Residues in contact with THR 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U ASN 4.4 0.2 - - - +
102U PHE* 3.0 53.3 + - + -
104U TYR* 3.1 20.6 - - - -
63V LEU* 4.4 7.6 - - + -
66V HIS* 3.8 16.4 - - + +
75V LEU* 3.1 22.8 + - - +
77V HIS* 1.3 77.8 - - - +
79V ALA* 1.3 60.7 + - - +
81V SER* 3.2 3.6 + - - -
82V LEU* 3.0 26.2 + - + +
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Residues in contact with ALA 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 4.7 0.7 - - + -
41V ILE* 3.9 21.3 - - + -
59V VAL* 4.0 4.8 - - + +
63V LEU* 3.5 39.0 - - + +
75V LEU 3.2 2.0 + - - -
76V VAL 3.1 10.3 + - - +
78V THR* 1.3 77.4 - - - +
80V ALA* 1.3 57.1 + - - +
82V LEU* 3.1 10.2 + - - +
83V PHE* 3.0 31.3 + - - -
100V ILE* 4.6 3.8 - - + -
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Residues in contact with ALA 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V VAL 3.0 15.9 + - - +
77V HIS* 3.7 5.6 - - - +
79V ALA* 1.3 76.5 - - - +
81V SER* 1.4 54.4 + - - +
83V PHE* 3.2 4.5 + - - +
84V LYS* 2.9 22.3 + - - +
100V ILE* 3.9 19.7 - - + -
112V TYR* 3.9 20.9 - - + -
114V VAL* 4.3 0.9 - - - +
120V MET* 3.2 34.9 - - + +
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Residues in contact with SER 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U SER 4.9 3.4 - - - -
101U ASN 4.0 13.5 - - - -
102U PHE 4.0 15.0 + - - -
103U GLY* 4.2 7.0 + - - -
77V HIS* 2.8 23.7 + - - +
78V THR 3.2 6.7 + - - -
80V ALA* 1.4 72.1 - - - +
82V LEU* 1.4 59.6 + - - +
84V LYS* 3.2 14.6 + - - +
85V GLU* 3.0 31.8 + - - +
120V MET* 3.8 15.1 - - - +
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Residues in contact with LEU 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U ASN* 3.4 23.6 - - + +
102U PHE* 4.2 20.0 - - + -
59V VAL* 4.1 23.6 - - + +
62V GLN* 3.6 42.0 - - + +
63V LEU* 4.2 21.3 - - + +
66V HIS* 5.9 0.2 - - + -
78V THR 3.0 15.7 + - - +
79V ALA 3.1 7.2 + - - +
81V SER* 1.4 75.1 - - - +
83V PHE* 1.4 57.3 + - - +
85V GLU* 3.2 9.0 + - + +
86V MET* 2.9 33.9 + - - +
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Residues in contact with PHE 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 3.5 26.2 - - + -
43V CYS* 3.6 17.7 - - - -
55V VAL* 3.5 32.1 - - + -
56V ALA* 3.7 9.2 - - - -
59V VAL* 3.7 23.1 - - + -
79V ALA 3.0 25.2 + - - -
80V ALA 3.2 6.5 + - - +
82V LEU* 1.4 73.1 - - - +
84V LYS* 1.3 62.8 + - - +
86V MET* 4.5 1.8 - - - +
87V CYS* 3.0 32.7 + - - +
98V ILE* 3.9 16.8 - - + -
100V ILE* 2.8 42.6 - - + -
114V VAL* 3.8 11.4 - - + -
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Residues in contact with LYS 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80V ALA 2.9 13.6 + - - +
81V SER* 3.2 17.2 + - - +
83V PHE* 1.3 75.3 - - - +
85V GLU* 1.4 58.5 + - - +
87V CYS* 4.9 0.2 - - - -
88V TYR* 2.6 55.1 + - + +
114V VAL* 4.7 7.1 - - - +
118V GLY 4.2 11.6 - - - +
120V MET* 3.8 37.2 - - + +
61b GLN* 4.2 29.0 + - + +
65b GLN* 3.5 36.2 + - - +
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Residues in contact with GLU 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U SER* 3.0 30.0 - - - +
101U ASN* 3.7 19.2 - - + +
81V SER 3.0 22.1 + - - +
82V LEU* 3.2 14.1 + - + +
84V LYS* 1.4 81.8 + - - +
86V MET* 1.4 66.0 + - + +
88V TYR* 3.8 7.1 - - - +
89V ARG* 3.0 28.1 + - - +
65b GLN* 3.9 17.8 + - - +
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Residues in contact with MET 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V ALA 4.5 2.7 - - - +
55V VAL* 4.0 30.0 - - + +
58V ALA* 4.1 20.4 - - + -
59V VAL* 4.1 16.6 - - + -
62V GLN* 4.5 21.3 - - - +
82V LEU* 2.9 20.5 + - + +
83V PHE* 4.1 4.9 - - - +
85V GLU* 1.4 76.9 - - + +
87V CYS* 1.3 65.0 + - - +
89V ARG* 3.9 41.7 + - - +
90V TYR* 3.6 16.5 + - - +
94V LEU* 4.0 4.5 - - - +
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Residues in contact with CYS 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V VAL* 4.7 9.4 - - - -
83V PHE* 3.0 27.4 + - - +
86V MET* 1.3 80.2 - - - +
88V TYR* 1.3 62.3 + - - +
90V TYR 2.7 22.7 - - - +
91V ARG* 3.3 11.3 + - - +
94V LEU* 3.4 23.1 - - + -
96V ALA* 4.2 16.8 - - - -
98V ILE* 5.3 1.3 - - - -
114V VAL* 4.2 12.1 - - + -
116V MET 4.4 5.1 - - - +
117V GLY 3.9 3.0 - - - +
118V GLY* 4.1 17.7 - - - -
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Residues in contact with TYR 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V LYS* 2.6 39.9 + - + +
85V GLU* 3.8 7.4 - - - +
87V CYS* 1.3 78.3 - - - +
89V ARG* 1.3 61.4 + - - +
90V TYR 3.5 0.5 + - - -
91V ARG* 3.7 23.4 + - - -
117V GLY 4.4 6.5 - - - -
118V GLY* 3.7 17.2 - - - +
58b ALA* 3.3 26.4 + - + -
59b ASP* 3.7 9.3 + - - -
61b GLN* 6.4 0.2 - - + -
62b TYR* 1.9 73.4 - + + +
65b GLN* 5.3 3.8 - - - -
99b ARG* 5.6 7.4 - - - -
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Residues in contact with ARG 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85V GLU 3.0 18.1 + - - +
86V MET* 3.9 46.0 + - - +
88V TYR* 1.3 78.3 - - - +
90V TYR* 1.3 98.1 + - + +
91V ARG* 4.0 9.5 + - - +
92V GLU* 5.4 0.5 - - - +
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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