Contacts of the helix formed by residues 80 - 90 (chain C) in PDB entry 6T90
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 ILE 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C LYS* 5.3 9.9 - - + -
78C ARG* 4.2 15.9 - - + +
79C ILE* 1.3 80.4 - - - +
81C PRO* 1.3 65.1 - - + +
82C ARG* 3.9 20.2 - - + +
83C HIS* 2.8 51.6 + - + +
84C LEU* 3.4 6.8 + - - +
56D SER* 3.8 12.6 - - - +
59D ALA* 4.1 4.9 - - - -
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Residues in contact with PRO 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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80C ILE* 1.3 89.4 - - + -
82C ARG* 1.3 62.4 + - - +
84C LEU* 3.2 9.4 + - + +
85C GLN* 3.1 20.8 + - - +
103C ILE* 4.4 2.4 - - - +
104C ALA 3.8 9.2 - - - +
105C GLN* 3.8 22.4 - - + +
106C GLY* 3.9 5.1 - - - +
56D SER* 4.0 11.2 - - - +
58D LYS* 3.9 23.1 - - + -
59D ALA 4.2 2.2 - - - +
62D ILE* 3.7 29.2 - - + -
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Residues in contact with ARG 82 (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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74C ASN* 5.7 1.3 - - - +
80C ILE* 2.9 18.9 + - + +
81C PRO* 1.3 80.9 - - - +
83C HIS* 1.3 67.2 - - + +
85C GLN* 3.2 1.8 + - - +
86C LEU* 3.0 54.0 + - + +
105C GLN 4.2 1.4 + - - -
106C GLY* 3.0 26.9 + - - +
108C VAL 3.3 25.9 + - - -
110C PRO* 4.8 7.9 - - - +
56E GLN 3.9 8.4 + - - -
57E LYS* 2.7 31.9 + - - +
58E SER 4.7 0.4 + - - -
59E THR* 4.0 19.4 - - + +
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Residues in contact with HIS 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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67C ALA* 3.8 20.7 - - - +
70C ALA* 4.2 14.0 - - + +
71C ALA* 3.6 22.2 - - - +
74C ASN* 3.0 29.9 + - - +
76C LYS* 4.1 16.9 - - + +
78C ARG 3.2 26.3 + - - -
79C ILE* 4.0 6.0 - - + -
80C ILE* 2.8 39.2 + - + +
82C ARG* 1.3 79.4 - - + +
84C LEU* 1.3 65.7 + - - +
86C LEU* 4.0 4.6 - - + +
87C ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 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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63C ILE* 3.7 26.5 - - + -
64C LEU* 5.1 3.1 - - + -
67C ALA* 3.9 16.4 - - + -
79C ILE* 4.0 14.4 - - + -
80C ILE 3.4 1.8 + - - +
81C PRO* 3.2 7.4 + - + +
82C ARG 3.2 0.6 - - - -
83C HIS* 1.3 78.4 - - - +
85C GLN* 1.3 62.7 + - - +
87C ALA* 3.3 3.1 + - - +
88C ILE* 3.1 35.5 + - + +
103C ILE* 4.8 3.6 - - + -
59D ALA* 3.7 35.0 - - + +
62D ILE* 3.8 31.0 - - + -
63D MET* 3.9 14.8 - - + -
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Residues in contact with GLN 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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81C PRO 3.1 10.8 + - - +
82C ARG* 3.2 6.0 + - - +
84C LEU* 1.3 77.9 - - - +
86C LEU* 1.3 62.9 + - - +
88C ILE* 3.9 1.0 - - - +
89C ARG* 3.0 61.0 + - - +
103C ILE* 3.6 27.1 + - + +
106C GLY* 3.4 32.3 - - - +
107C GLY 3.0 23.2 + - - +
108C VAL* 5.0 1.0 - - - +
109C LEU* 4.4 12.3 - - + +
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Residues in contact with LEU 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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70C ALA* 4.7 12.1 - - + -
74C ASN* 4.8 9.0 - - - +
82C ARG* 3.0 53.6 + - + +
83C HIS* 4.0 14.4 - - + +
85C GLN* 1.3 81.7 - - + +
87C ALA* 1.3 64.6 + - - +
90C ASN* 3.1 40.9 + - - +
109C LEU* 3.8 30.5 - - + -
110C PRO* 5.0 4.9 - - + -
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Residues in contact with ALA 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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63C ILE* 4.3 6.1 - - + +
66C LEU* 3.6 24.6 - - + +
67C ALA* 3.5 28.7 - - + +
70C ALA* 5.1 1.9 - - - +
83C HIS 3.0 19.0 + - - +
84C LEU* 3.5 5.6 - - - +
86C LEU* 1.3 78.2 - - - +
88C ILE* 1.3 64.9 + - + +
90C ASN* 4.2 2.1 - - - +
91C ASP* 3.5 20.3 + - - +
94C LEU* 4.8 0.4 - - - -
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Residues in contact with ILE 88 (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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63C ILE* 4.8 16.6 - - + -
84C LEU* 3.1 21.1 + - + +
85C GLN* 3.9 3.4 - - - +
87C ALA* 1.3 79.6 - - - +
89C ARG* 1.3 87.2 + - - +
91C ASP 3.1 21.5 + - - +
94C LEU* 4.1 36.3 - - + +
95C ASN* 3.6 4.7 + - - -
98C LEU* 3.6 27.4 - - + -
103C ILE* 3.7 24.7 - - + -
62D ILE* 6.4 0.4 - - + -
99F TYR* 6.3 0.9 - - + -
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Residues in contact with ARG 89 (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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85C GLN* 3.0 46.1 + - - +
86C LEU 4.4 0.2 - - - +
88C ILE* 1.3 100.4 - - - +
90C ASN* 1.3 62.5 + - - +
91C ASP 3.3 1.7 + - - -
95C ASN* 3.1 28.5 + - - +
98C LEU* 3.5 20.0 + - - +
99C GLY* 4.6 8.0 + - - -
101C VAL* 3.0 25.9 + - - +
103C ILE* 4.9 3.6 - - - +
109C LEU* 3.6 32.1 - - + +
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Residues in contact with ASN 90 (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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86C LEU* 3.1 33.2 + - - +
87C ALA* 4.2 2.2 - - - +
88C ILE 3.2 0.2 - - - -
89C ARG* 1.3 77.4 - - - +
91C ASP* 1.3 57.5 + - - +
92C GLU* 4.3 7.1 + - - +
109C LEU* 3.3 24.3 - - - +
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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