Contacts of the helix formed by residues 76 - 89 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41I ILE* 3.7 7.9 - - + -
75I ARG* 1.3 73.7 - - - +
77I VAL* 1.3 58.1 - - - +
79I ALA* 3.1 6.2 + - - +
80I ASN* 3.0 36.8 + - - +
100I LEU* 3.4 24.7 - - + -
102I GLY* 3.4 42.6 - - - +
103I VAL 3.7 5.2 - - - +
104I ASP* 3.8 16.4 - - + +
109I HIS* 3.3 35.4 + - + +
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Residues in contact with VAL 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR 3.6 3.5 - - - +
106A GLY* 4.3 19.7 - - - +
107A TYR* 4.9 6.3 - - + -
75I ARG* 4.3 12.3 - - + -
76I VAL* 1.3 76.9 - - - +
78I THR* 1.3 63.3 + - - +
80I ASN* 3.4 10.4 + - - +
81I ARG* 2.8 34.0 + - - +
106I THR* 5.6 0.4 - - - +
109I HIS* 4.0 23.1 - - + +
111I TYR* 3.6 20.4 - - - +
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Residues in contact with THR 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS 4.3 0.9 - - - +
105A TYR* 3.1 32.3 - - + +
107A TYR* 3.4 27.4 - - - -
63I LEU* 5.6 1.3 - - + -
66I HIS* 3.8 15.3 - - + +
74I PRO* 5.3 4.7 - - + -
75I ARG* 3.4 24.6 + - - +
77I VAL* 1.3 72.7 - - - +
79I ALA* 1.3 65.4 + - - +
81I ARG* 3.3 1.6 + - - +
82I MET* 3.1 47.7 + - + +
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ILE* 4.1 9.4 - - + -
59I ILE* 4.6 0.6 - - + +
63I LEU* 3.4 32.8 - - + -
75I ARG 3.6 0.8 + - - +
76I VAL 3.1 10.4 + - - +
78I THR* 1.3 77.6 - - - +
80I ASN* 1.3 59.4 - - - +
82I MET* 3.4 8.4 - - - +
83I LEU* 3.1 31.6 + - - +
100I LEU* 3.6 25.6 - - + -
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Residues in contact with ASN 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I VAL* 3.0 25.7 + - - +
77I VAL* 3.5 7.9 - - - +
79I ALA* 1.3 75.3 - - - +
81I ARG* 1.3 54.0 + - - +
83I LEU* 3.2 6.3 + - - +
84I LYS* 2.7 34.9 + - - +
100I LEU* 3.8 15.9 - - - +
111I TYR* 2.5 66.1 - - + +
113I ILE* 3.6 13.5 - - - +
119I THR* 3.7 12.9 - - + +
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Residues in contact with ARG 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 2.2 26.5 + - - +
103A TYR* 1.8 78.1 + - - +
104A LYS 3.5 19.5 - - - +
105A TYR 3.3 19.1 - - - +
106A GLY* 3.6 12.4 - - - -
57H ASP* 5.2 14.1 + - - +
77I VAL 2.8 13.4 + - - +
78I THR 3.3 1.3 + - - +
80I ASN* 1.3 70.5 - - - +
82I MET* 1.3 63.5 + - - +
84I LYS* 3.4 24.4 + - - +
85I GLN* 3.2 32.9 + - - +
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Residues in contact with MET 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 4.0 7.2 - - + +
105A TYR* 4.2 16.8 - - + -
59I ILE* 3.8 14.9 - - + +
62I ASN* 4.0 18.4 - - + +
63I LEU* 2.8 38.8 - - + -
66I HIS* 5.0 2.7 - - + +
78I THR* 3.1 43.4 + - + +
79I ALA 3.4 11.2 - - - +
81I ARG* 1.3 76.2 - - - +
83I LEU* 1.4 61.3 + - - +
85I GLN* 3.9 11.1 - - - +
86I MET* 2.9 32.3 + - + +
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ILE* 4.6 4.7 - - + -
43I CYS* 4.5 4.0 - - - -
55I THR* 4.3 7.4 - - + -
59I ILE* 3.7 26.9 - - + -
79I ALA 3.1 18.4 + - - +
80I ASN 3.2 5.8 + - - +
82I MET* 1.4 74.9 - - - +
84I LYS* 1.3 61.7 + - - +
86I MET* 4.2 1.1 - - + -
87I LEU* 3.1 35.9 + - + +
98I LEU* 3.5 31.4 - - + -
100I LEU* 3.4 33.9 - - + -
113I ILE* 3.5 28.3 - - + -
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Residues in contact with LYS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H GLN* 3.2 56.4 - - + +
54H ALA* 6.4 0.2 - - - -
57H ASP* 4.5 13.2 + - + +
80I ASN 2.7 17.8 + - - +
81I ARG* 3.5 26.5 - - - +
82I MET 3.3 0.4 - - - -
83I LEU* 1.3 72.7 - - - +
85I GLN* 1.4 61.5 + - + +
87I LEU 3.7 1.2 + - - -
88I PHE* 3.1 28.9 + - + +
113I ILE* 4.9 0.9 - - - -
117I GLY* 3.9 15.7 - - - +
119I THR* 3.2 34.9 + - + +
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Residues in contact with GLN 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 2.9 59.6 + - - +
104A LYS* 4.0 19.7 - - - +
81I ARG* 3.2 22.3 + - - +
82I MET* 3.9 8.9 - - - +
84I LYS* 1.4 80.9 - - + +
86I MET* 1.3 64.9 + - - +
88I PHE* 3.6 6.5 - - - +
89I ARG* 3.0 31.1 + - - +
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Residues in contact with MET 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I THR* 4.0 25.8 - - + -
58I LEU* 3.6 32.1 - - + -
59I ILE* 4.1 18.2 - - + -
62I ASN* 4.7 5.6 - - - +
82I MET* 2.9 23.7 + - + +
83I LEU* 3.9 6.1 - - + +
84I LYS 3.4 0.2 - - - -
85I GLN* 1.3 77.7 - - - +
87I LEU* 1.4 59.5 + - + +
89I ARG* 3.8 23.4 + - - +
90I TYR* 3.1 53.5 - - + -
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I THR* 4.3 18.2 - - + -
83I LEU* 3.1 26.2 + - + +
84I LYS 3.9 2.2 - - - +
86I MET* 1.4 73.8 - - - +
88I PHE* 1.3 62.0 + - - +
90I TYR* 4.7 4.4 - - - +
91I GLN* 4.5 5.7 + - - -
92I GLY 4.8 0.2 + - - -
94I ILE* 3.4 32.8 - - + +
96I ALA 3.9 10.1 - - - +
98I LEU* 4.4 10.1 - - + -
113I ILE* 3.5 38.1 - - + +
114I TYR 3.9 8.1 - - - +
115I PRO* 2.9 34.9 - - + +
116I HIS* 3.6 6.0 - - - -
117I GLY* 4.2 4.7 - - - -
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Residues in contact with PHE 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ALA* 3.3 28.7 - - + -
51H ASP* 3.6 23.6 - - - -
53H GLN* 5.9 0.7 - - + -
54H ALA* 3.4 30.7 - - + +
93H ASP 5.4 1.6 - - - -
94H LEU* 6.3 1.1 - - + -
84I LYS* 3.1 20.1 + - + +
85I GLN* 3.2 7.8 + - - +
87I LEU* 1.3 79.5 - - - +
89I ARG* 1.3 70.4 + - + +
90I TYR 3.2 0.9 - - - -
91I GLN* 3.0 42.4 + - + +
116I HIS 3.6 15.0 - - - +
117I GLY* 4.9 1.3 - - - +
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Residues in contact with ARG 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LEU* 5.9 0.4 - - - +
85I GLN* 3.0 14.3 + - - +
86I MET* 3.8 38.2 + - - +
87I LEU 3.6 0.4 - - - -
88I PHE* 1.3 85.9 - - + +
90I TYR* 1.3 93.3 + - + +
91I GLN* 3.4 10.0 + - - +
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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