Contacts of the helix formed by residues 54 - 74 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU 4.1 0.9 - - - +
50H GLN* 3.0 26.3 + - - +
51H ASP 4.6 1.0 + - - -
52H LEU 3.6 1.2 - - - -
53H HIS* 1.3 84.7 - - - +
55H PRO* 1.3 80.7 - - - +
56H SER* 3.7 0.9 - - - -
57H LEU* 4.0 0.7 + - - +
58H ARG 4.0 3.5 + - - -
927H LYS* 4.8 6.9 - - - +
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Residues in contact with PRO 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H GLN* 3.9 32.7 - - + +
54H GLY* 1.3 80.7 - - - +
56H SER* 1.3 55.3 + - - +
57H LEU 2.5 2.5 + - - -
58H ARG* 2.4 37.5 + - + -
59H GLU* 2.8 24.5 - - - +
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Residues in contact with SER 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLY 3.7 0.6 - - - -
55H PRO* 1.3 75.3 - - - +
57H LEU* 1.3 61.9 + - - +
59H GLU* 3.1 18.6 - - - +
60H PHE* 3.3 17.5 + - - +
925H LEU* 4.2 31.6 - - - +
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Residues in contact with LEU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 4.0 24.7 - - + -
53H HIS* 3.7 33.3 + - + +
54H GLY 4.0 8.9 + - - +
55H PRO 2.5 5.5 + - - +
56H SER* 1.3 71.5 + - - +
58H ARG* 1.3 56.6 + - - +
60H PHE* 2.6 36.1 + - + +
61H VAL* 3.1 13.2 + - + +
90H LEU* 5.8 1.3 - - + -
94H ASP* 4.3 13.9 - - + +
97H LEU* 4.5 16.4 - - + -
98H VAL* 4.4 19.5 - - + -
925H LEU* 3.2 31.9 - - + +
926H SER* 5.4 1.6 - - - -
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Residues in contact with ARG 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H HIS 3.8 14.0 + - - +
43H ASP* 5.2 4.2 + - - +
46H LEU* 3.4 48.2 + - + +
47H ASN* 3.1 26.3 + - - -
49H LEU* 4.2 13.2 - - + -
50H GLN* 3.5 40.4 + - + +
54H GLY 4.0 0.4 + - - -
55H PRO 2.4 23.0 + - - +
57H LEU* 1.3 71.4 - - - +
59H GLU* 1.3 69.6 + - - +
61H VAL* 3.7 1.4 - - - +
62H GLN* 2.4 61.0 + - - +
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Residues in contact with GLU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H GLN* 6.1 0.2 - - - -
55H PRO* 2.8 42.5 - - - +
56H SER* 3.7 17.5 - - - +
58H ARG* 1.3 83.1 - - - +
60H PHE* 1.3 63.4 + - - +
62H GLN* 3.3 4.1 + - - +
63H GLU* 2.9 41.9 + - - +
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Residues in contact with PHE 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H SER 3.3 10.4 + - - +
57H LEU* 2.6 24.1 + - + +
59H GLU* 1.3 74.7 - - - +
61H VAL* 1.3 65.2 + - + -
63H GLU* 3.1 17.6 + - - +
64H CYS* 2.9 47.0 + - - -
86H LYS* 4.0 40.9 + - + -
87H LEU* 3.9 10.1 - - + -
90H LEU* 3.8 39.9 - - + -
98H VAL* 4.3 8.1 - - + -
925H LEU* 5.2 10.8 - - + -
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Residues in contact with VAL 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LEU* 3.7 14.8 - - + -
49H LEU* 3.6 31.6 - - + -
57H LEU* 3.1 13.9 + - + +
58H ARG* 3.7 7.9 - - - +
60H PHE* 1.3 76.6 - - + +
62H GLN* 1.3 64.6 + - - +
64H CYS* 3.5 8.6 - - - +
65H TYR* 2.8 28.6 + - - +
98H VAL* 3.6 41.1 - - + -
101H SER* 5.3 2.2 - - - -
102H ILE* 4.6 6.3 - - + +
105H MET* 4.3 14.6 - - + +
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Residues in contact with GLN 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H HIS* 3.0 57.6 + - + +
16H ILE* 4.2 16.1 - - + +
19H GLN* 5.3 2.7 + - - +
46H LEU* 4.0 17.3 - - + -
58H ARG* 2.4 59.9 + - - +
59H GLU* 3.7 4.2 - - - +
61H VAL* 1.3 77.8 - - - +
63H GLU* 1.3 64.7 + - + +
65H TYR* 3.5 8.7 - - + +
66H GLU* 3.1 23.4 + - - +
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Residues in contact with GLU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H GLU* 2.9 33.4 + - - +
60H PHE* 3.1 19.4 + - - +
62H GLN* 1.3 74.1 - - - +
64H CYS* 1.3 64.6 + - - +
66H GLU* 3.2 8.3 + - - +
67H VAL* 2.9 30.9 + - + +
86H LYS* 3.9 17.8 + - - +
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Residues in contact with CYS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H PHE* 2.9 46.0 + - - -
61H VAL* 3.3 11.4 + - - +
63H GLU* 1.3 76.5 - - - +
65H TYR* 1.3 63.4 + - - +
66H GLU 3.3 0.2 + - - -
67H VAL* 3.4 1.9 + - - +
68H SER* 3.1 26.5 + - - -
83H LEU* 3.4 29.4 - - + -
86H LYS* 4.4 1.5 - - - +
87H LEU* 4.1 11.9 - - - -
98H VAL* 4.7 3.6 - - - -
102H ILE* 4.8 2.9 - - + -
900H THR* 4.0 19.5 - - + -
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Residues in contact with TYR 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 3.3 53.4 - - + +
19H GLN* 3.7 18.6 - - + -
20H LEU* 3.1 33.1 + - - +
46H LEU* 6.0 0.4 - - + -
61H VAL 2.8 19.8 + - - +
62H GLN* 3.5 12.3 - - + +
64H CYS* 1.3 72.7 - - - +
66H GLU* 1.3 62.6 + - - +
68H SER* 3.6 2.4 + - - -
69H ALA* 3.0 26.0 + - + +
102H ILE* 5.0 6.7 - - + +
105H MET* 5.7 6.7 - - - -
896H PRO* 3.3 26.4 - - + +
897H TYR* 3.3 36.5 + + - -
900H THR* 4.5 6.3 - - - -
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Residues in contact with GLU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H HIS* 5.8 0.7 - - - -
19H GLN* 3.3 37.3 + - + +
62H GLN 3.1 16.7 + - - +
63H GLU* 3.2 7.2 + - - +
65H TYR* 1.3 76.2 - - - +
67H VAL* 1.3 68.9 + - - +
69H ALA* 2.9 6.2 + - - -
70H ASP* 2.6 53.0 + - - +
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLU* 2.9 22.1 + - + +
64H CYS 3.9 3.4 - - - +
66H GLU* 1.3 77.7 + - + +
68H SER* 1.3 59.2 + - - +
70H ASP* 3.2 7.8 + - - +
71H TYR* 3.0 25.6 + - - +
79H LYS* 3.9 41.9 - - + +
80H LEU* 6.1 1.3 - - + -
82H GLU* 6.0 2.0 - - + +
83H LEU* 4.4 15.9 - - + +
86H LYS* 4.2 15.5 - - - +
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Residues in contact with SER 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H CYS 3.1 8.1 + - - -
65H TYR 4.0 0.4 - - - -
66H GLU 3.2 0.6 - - - -
67H VAL* 1.3 74.8 - - - +
69H ALA* 1.3 67.0 + - - +
71H TYR* 3.1 12.0 + - - +
72H GLU* 3.1 21.1 + - - +
80H LEU* 5.2 3.2 - - - +
83H LEU* 3.9 10.4 - - - +
895H ASN 5.9 0.2 - - - -
896H PRO* 3.5 24.8 - - - +
899H THR* 3.8 22.4 + - - +
900H THR* 2.8 24.1 + - - -
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H GLN* 4.5 23.1 - - + +
22H GLN* 4.0 4.5 + - - +
23H LEU* 3.9 11.8 - - + +
65H TYR* 3.0 22.5 + - + +
66H GLU* 2.9 9.0 + - - +
68H SER* 1.3 76.2 - - - +
70H ASP* 1.3 65.7 + - - +
72H GLU* 3.4 7.7 + - - +
73H GLY 3.3 14.6 + - - -
896H PRO* 4.0 24.6 - - + +
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Residues in contact with ASP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H GLN* 5.0 0.7 - - - +
22H GLN* 4.1 14.0 + - - +
66H GLU* 2.6 57.7 + - - +
67H VAL* 3.6 6.3 - - - +
69H ALA* 1.3 73.6 - - - +
71H TYR* 1.3 66.3 + - - +
73H GLY* 3.2 3.2 + - - +
74H LYS* 3.1 23.7 + - - +
79H LYS* 4.1 25.6 + - - +
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Residues in contact with TYR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H VAL 3.0 13.9 + - - +
68H SER 3.1 9.2 + - - +
70H ASP* 1.3 77.5 - - - +
72H GLU* 1.3 70.2 + - + +
74H LYS 3.2 4.9 - - - -
75H GLY* 3.1 47.8 + - - -
76H ASP 3.4 26.5 - - - -
77H THR* 4.0 4.7 - - + +
79H LYS* 4.7 9.6 - - + +
80H LEU* 3.7 42.8 - - + -
837H ASP* 2.7 39.3 + - - -
839H GLY* 3.5 18.9 + - - -
840H ILE* 3.8 6.3 + - + -
899H THR* 4.3 11.4 - - + -
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Residues in contact with GLU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU* 4.5 12.8 - - + -
68H SER 3.1 11.5 + - - +
69H ALA* 3.5 11.9 - - - +
71H TYR* 1.3 83.4 - - + +
73H GLY* 1.3 62.1 + - - +
74H LYS 3.6 0.2 + - - -
75H GLY 4.8 1.2 + - - -
785H ARG* 4.6 2.4 + - - -
837H ASP* 5.1 5.5 - - - +
892H VAL* 3.0 29.1 - - + +
895H ASN* 2.3 51.1 + - + +
896H PRO* 5.6 1.6 - - + -
899H THR* 4.5 7.0 + - - +
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Residues in contact with GLY 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 4.4 16.4 - - - -
23H LEU* 5.2 2.8 - - - +
69H ALA 3.3 7.2 + - - -
70H ASP* 3.2 6.9 + - - -
71H TYR 3.2 0.8 - - - -
72H GLU* 1.3 79.6 - - - +
74H LYS* 1.3 63.5 + - - +
75H GLY 4.2 0.2 - - - -
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Residues in contact with LYS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ASP 3.1 12.1 + - - +
71H TYR* 3.2 6.2 - - - +
73H GLY* 1.3 80.8 - - - +
75H GLY* 1.3 52.8 + - - +
76H ASP* 2.3 35.5 + - + +
79H LYS* 5.3 3.8 - - - -
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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