Contacts of the helix formed by residues 54 - 74 (chain C) in PDB entry 6V3O
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 GLY 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU 4.4 0.3 - - - +
50C GLN* 2.9 25.2 + - - -
52C LEU 3.8 0.6 - - - -
53C HIS* 1.3 80.8 - - - +
55C PRO* 1.3 75.1 - - - +
56C SER 3.4 3.1 + - - -
57C LEU* 3.5 2.6 + - - +
58C ARG 3.3 15.9 + - - -
925C LEU 5.4 0.9 - - - -
927C LYS* 5.9 1.8 - - - -
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Residues in contact with PRO 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLN* 3.8 35.0 - - + +
54C GLY* 1.3 82.4 - - - +
56C SER* 1.3 64.2 + - - +
58C ARG* 3.7 2.5 - - + +
59C GLU* 2.9 39.3 + - - +
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY 3.4 1.2 - - - -
55C PRO* 1.3 81.0 - - - +
57C LEU* 1.3 58.5 + - - +
59C GLU* 4.0 4.6 - - - +
60C PHE* 3.1 26.0 + - - +
925C LEU* 3.8 28.3 + - - +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.5 7.4 - - + -
53C HIS* 3.7 23.8 - - + +
54C GLY 3.5 7.2 + - - +
55C PRO 3.3 0.2 - - - -
56C SER* 1.3 77.2 - - - +
58C ARG* 1.3 65.8 + - - +
60C PHE* 3.2 5.9 + - + +
61C VAL* 2.9 31.3 + - + +
90C LEU* 5.8 1.1 - - + -
94C ASP* 4.2 26.0 - - + +
97C LEU* 3.4 37.9 - - + -
98C VAL* 5.4 4.0 - - + -
925C LEU* 3.6 40.8 + - + +
926C SER* 4.1 2.7 - - - +
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS* 3.9 34.2 + - - -
43C ASP* 4.5 5.5 + - - +
46C LEU* 3.3 47.6 + - + +
47C ASN* 3.1 27.3 + - - +
49C LEU* 4.2 12.2 - - + +
50C GLN* 2.8 47.3 + - + +
54C GLY 3.3 6.4 + - - +
55C PRO* 3.7 7.2 - - + +
57C LEU* 1.3 78.2 - - - +
59C GLU* 1.3 66.0 + - - +
61C VAL* 3.3 2.8 + - - +
62C GLN* 2.9 53.6 + - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS* 6.5 0.9 - - - -
55C PRO* 2.9 22.4 + - - +
56C SER* 4.1 4.0 - - - +
58C ARG* 1.3 82.1 - - - +
60C PHE* 1.3 66.6 + - - +
62C GLN* 3.2 7.1 + - + +
63C GLU* 2.8 52.1 + - + +
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Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 3.1 16.6 + - - +
57C LEU* 3.4 11.2 - - + +
59C GLU* 1.3 75.9 - - - +
61C VAL* 1.3 68.9 + - + +
63C GLU* 3.2 13.1 + - - +
64C CYS* 3.1 42.7 + - - -
86C LYS* 4.0 30.3 - - + -
87C LEU* 3.8 19.7 - - + -
90C LEU* 3.8 33.2 - - + -
98C VAL* 4.3 9.6 - - + -
925C LEU* 3.7 21.1 - - + -
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.0 12.1 - - + -
49C LEU* 3.9 19.5 - - + -
57C LEU* 2.9 25.9 + - + +
58C ARG 3.7 4.3 - - - +
60C PHE* 1.3 77.9 - - + +
62C GLN* 1.3 63.6 + - - +
64C CYS* 3.4 7.5 + - - +
65C TYR* 3.2 19.8 + - - +
98C VAL* 3.8 33.2 - - + -
101C SER* 4.4 4.3 - - - +
102C ILE* 4.4 7.2 - - + +
105C MET* 3.4 33.2 - - + -
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C HIS 3.3 9.7 + - - -
14C HIS* 3.0 29.3 + - - +
15C SER 4.4 1.2 - - - -
16C ILE* 4.0 17.2 - - + +
46C LEU* 3.7 19.9 - - + +
58C ARG* 2.9 49.0 + - - +
59C GLU* 3.7 8.9 - - + +
61C VAL* 1.3 77.8 - - - +
63C GLU* 1.3 64.2 + - + +
65C TYR* 3.2 7.6 + - + +
66C GLU* 3.0 51.4 + - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 2.8 49.1 + - + +
60C PHE* 3.8 10.8 - - - +
62C GLN* 1.3 78.2 - - + +
64C CYS* 1.3 57.9 + - - +
66C GLU* 3.0 13.9 + - - +
67C VAL* 2.9 39.7 + - + +
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Residues in contact with CYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE* 3.1 45.7 + - - -
61C VAL* 3.6 9.9 - - - +
62C GLN 3.3 0.2 - - - -
63C GLU* 1.3 76.1 - - - +
65C TYR* 1.3 63.0 + - - +
67C VAL* 3.2 9.0 - - - +
68C SER* 3.1 21.5 + - - -
83C LEU* 3.5 30.3 - - + -
86C LYS* 5.8 0.4 - - - -
87C LEU* 4.0 11.7 - - - -
98C VAL* 5.0 2.9 - - + -
102C ILE* 4.9 2.9 - - + -
900C THR* 4.0 17.0 - - + -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.6 39.5 + - + +
19C GLN* 3.9 24.4 - - + +
20C LEU* 3.1 35.0 + - + +
61C VAL* 3.2 10.1 + - + +
62C GLN* 3.2 9.8 + - - +
64C CYS* 1.3 78.6 - - - +
66C GLU* 1.3 67.6 + - + +
68C SER* 3.5 1.6 + - - -
69C ALA* 2.9 31.2 + - + +
102C ILE* 4.9 9.1 - - + +
105C MET* 5.5 7.0 - - - -
896C PRO* 3.3 31.0 - - + -
897C TYR* 3.6 32.5 - + + -
900C THR* 4.3 7.6 - - - -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C HIS* 3.4 15.8 + - - +
16C ILE* 5.5 0.6 - - + +
19C GLN* 3.5 37.9 + - + +
62C GLN* 3.0 46.4 + - - +
63C GLU* 3.0 12.8 + - - +
65C TYR* 1.3 85.8 - - + +
67C VAL* 1.3 65.9 + - + +
69C ALA* 3.2 2.0 + - - +
70C ASP* 2.8 34.6 + - - +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 2.9 23.4 + - + +
64C CYS* 3.2 13.0 - - - +
66C GLU* 1.3 75.1 - - + +
68C SER* 1.3 63.8 + - - +
70C ASP* 3.3 10.3 + - - +
71C TYR* 3.0 26.0 + - - +
79C LYS* 5.0 16.7 - - + +
83C LEU* 3.5 41.5 - - + -
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C CYS 3.1 8.1 + - - -
65C TYR 4.0 0.7 - - - -
67C VAL* 1.3 76.1 - - - +
69C ALA* 1.3 66.3 + - - +
71C TYR* 3.1 20.3 + - - +
72C GLU* 3.2 12.6 + - - +
80C LEU* 5.7 1.1 - - - -
83C LEU* 3.4 17.4 - - - +
896C PRO* 3.5 25.7 - - - +
899C THR* 3.7 19.7 - - - +
900C THR* 2.8 21.0 + - - -
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Residues in contact with ALA 69 (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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19C GLN* 4.2 30.2 - - + +
23C LEU* 3.6 17.0 - - + +
65C TYR* 2.9 24.1 + - + +
66C GLU 3.6 5.8 - - - +
68C SER* 1.3 77.3 - - - +
70C ASP* 1.3 61.5 + - - +
72C GLU* 3.5 2.3 + - - +
73C GLY* 3.4 13.3 + - - -
896C PRO* 4.0 25.2 - - + +
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Residues in contact with ASP 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLN* 3.1 21.8 - - - +
66C GLU* 2.8 22.7 + - - +
67C VAL* 3.7 7.6 - - - +
69C ALA* 1.3 77.3 - - - +
71C TYR* 1.3 65.7 + - - +
73C GLY* 3.0 11.3 + - - +
74C LYS* 3.1 14.2 + - - +
79C LYS* 6.4 2.2 - - + -
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL 3.0 13.9 + - - +
68C SER* 3.1 11.6 + - - +
70C ASP* 1.3 76.4 - - - +
72C GLU* 1.3 71.0 + - + +
74C LYS 3.2 4.4 + - - -
75C GLY* 3.1 47.6 + - - -
76C ASP 3.6 24.9 - - - +
77C THR* 4.1 2.9 + - - -
79C LYS* 5.2 8.9 - - + +
80C LEU* 3.6 37.9 - - + -
837C ASP* 2.5 41.9 + - - -
839C GLY* 3.6 16.6 + - - -
840C ILE* 3.8 9.5 + - + -
899C THR* 4.3 11.7 - - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.5 27.3 - - + +
68C SER 3.2 8.9 + - - +
69C ALA* 3.6 4.9 - - - +
70C ASP 3.2 0.2 - - - -
71C TYR* 1.3 88.6 - - + +
73C GLY* 1.3 62.3 + - - +
74C LYS 3.5 0.2 + - - -
75C GLY 4.7 1.2 + - - -
785C ARG* 4.4 4.2 + - - -
837C ASP* 5.3 6.1 - - - +
892C VAL* 4.2 14.5 - - + +
895C ASN* 3.0 45.0 + - + +
896C PRO* 5.7 1.3 - - + -
899C THR* 4.4 7.6 + - - -
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 5.3 7.2 - - - -
23C LEU* 4.0 8.9 - - - +
69C ALA 3.4 7.2 + - - -
70C ASP* 3.0 9.7 + - - -
72C GLU* 1.3 81.4 - - - +
74C LYS* 1.3 75.8 + - - +
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 6.3 0.4 - - - +
70C ASP 3.1 12.1 + - - +
71C TYR* 3.2 5.1 - - - +
73C GLY* 1.3 88.0 + - - +
75C GLY* 1.3 52.7 + - - +
76C ASP* 2.5 28.3 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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