Contacts of the helix formed by residues 54 - 74 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU 3.8 0.5 + - - +
50G GLN* 3.0 23.1 + - - -
51G ASP 4.8 0.2 - - - -
52G LEU 3.8 0.4 - - - -
53G HIS* 1.3 82.0 - - - +
55G PRO* 1.3 76.0 - - - +
56G SER* 3.3 3.5 + - - -
57G LEU* 3.4 2.3 + - - +
58G ARG 3.2 15.9 + - - -
925G LEU 5.4 0.2 - - - -
927G LYS* 5.1 9.9 - - - -
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Residues in contact with PRO 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G HIS* 4.3 12.6 - - + +
50G GLN* 3.7 31.4 - - + +
54G GLY* 1.3 85.4 - - - +
56G SER* 1.3 54.7 + - - +
58G ARG* 3.2 2.3 + - + +
59G GLU* 2.7 39.3 + - + +
927G LYS* 6.0 2.9 - - + -
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Residues in contact with SER 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLY 3.3 1.2 - - - -
55G PRO* 1.3 82.9 - - - +
57G LEU* 1.3 59.1 + - - +
59G GLU* 3.6 5.3 + - - +
60G PHE* 3.0 26.0 + - - +
925G LEU* 3.3 44.9 + - - +
927G LYS* 4.6 3.4 + - - -
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 4.9 7.4 - - + -
53G HIS* 4.1 15.0 - - + +
54G GLY 3.4 7.8 + - - +
55G PRO 3.2 0.2 - - - -
56G SER* 1.3 79.3 + - - +
58G ARG* 1.3 65.7 + - - +
60G PHE* 3.1 10.3 + - + -
61G VAL* 3.0 34.0 + - + +
90G LEU* 6.3 1.3 - - + -
94G ASP* 4.9 9.6 - - + +
97G LEU* 3.9 33.4 - - + -
98G VAL* 3.9 27.1 - - + -
101G SER* 6.1 0.4 - - - +
925G LEU* 4.6 15.2 + - + +
926G SER* 4.0 21.1 - - - +
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Residues in contact with ARG 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G HIS* 3.6 36.9 + - - +
14G HIS 4.1 12.5 + - - -
43G ASP* 4.8 7.3 + - - +
46G LEU* 3.4 41.8 + - + +
47G ASN* 2.9 26.0 + - - -
49G LEU* 4.2 11.9 - - - +
50G GLN* 2.8 52.9 - - + +
54G GLY 3.2 6.0 + - - +
55G PRO 3.2 6.9 + - - +
57G LEU* 1.3 78.9 - - - +
59G GLU* 1.3 63.0 + - - +
61G VAL* 3.2 2.4 + - - +
62G GLN* 3.0 50.3 + - - +
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Residues in contact with GLU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G HIS* 3.6 36.8 + - + +
14G HIS* 5.1 11.5 + - - -
55G PRO* 2.7 22.6 + - + +
56G SER* 3.9 6.1 - - - +
58G ARG* 1.3 75.1 - - - +
60G PHE* 1.3 63.2 + - - +
62G GLN* 3.4 11.6 + - - +
63G GLU* 2.9 49.3 + - - +
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Residues in contact with PHE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G SER 3.0 16.2 + - - +
57G LEU* 3.1 14.8 + - + +
59G GLU* 1.3 77.0 - - - +
61G VAL* 1.3 66.0 + - - +
63G GLU* 3.0 25.7 + - - +
64G CYS* 3.1 40.6 + - - -
86G LYS* 4.2 32.1 - - + -
87G LEU* 4.1 8.3 - - + -
90G LEU* 3.9 42.4 - - + -
98G VAL* 4.2 16.8 - - + -
922G GLN* 4.4 8.5 - - - -
925G LEU* 4.8 13.5 - - + -
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Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU* 4.0 8.7 - - + -
49G LEU* 4.0 15.7 - - + -
57G LEU* 3.0 33.4 + - + +
58G ARG 3.8 3.4 - - - +
60G PHE* 1.3 76.7 - - - +
62G GLN* 1.3 63.6 + - - +
64G CYS* 3.5 5.8 + - - +
65G TYR* 3.1 20.8 + - - +
98G VAL* 4.4 19.3 - - + -
101G SER* 4.4 15.9 - - - +
102G ILE* 4.1 13.3 - - + +
105G MET* 3.8 28.5 - - + -
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Residues in contact with GLN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G HIS* 5.3 1.4 - - - -
14G HIS* 3.0 51.5 + - + +
16G ILE* 3.9 27.9 - - + +
46G LEU* 3.9 14.2 - - + +
58G ARG* 3.0 47.1 + - - +
59G GLU* 3.9 12.6 - - - +
61G VAL* 1.3 77.0 - - - +
63G GLU* 1.3 62.3 + - - +
65G TYR* 3.5 6.9 + - - +
66G GLU* 3.0 33.7 + - - +
105G MET* 5.7 0.2 - - - -
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Residues in contact with GLU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G GLU* 2.9 41.8 + - - +
60G PHE* 3.0 18.6 + - + +
62G GLN* 1.3 73.9 - - - +
64G CYS* 1.3 61.1 + - - +
66G GLU* 2.9 17.5 + - - +
67G VAL* 2.9 36.3 + - + +
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Residues in contact with CYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G PHE* 3.1 47.3 + - - -
61G VAL* 3.9 6.1 - - - +
63G GLU* 1.3 72.8 - - - +
65G TYR* 1.3 66.0 + - - +
67G VAL* 3.4 9.9 - - - +
68G SER* 3.1 28.6 + - - -
83G LEU* 3.6 25.8 - - + -
87G LEU* 4.5 4.5 - - - -
98G VAL* 5.0 3.1 - - - -
102G ILE* 5.3 2.2 - - + -
900G THR* 4.0 18.8 - - + -
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Residues in contact with TYR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 3.3 40.2 - - + +
19G GLN* 4.0 20.4 + - + -
20G LEU* 3.1 40.2 + - + +
61G VAL 3.1 14.9 + - - +
62G GLN* 3.6 8.5 - - - +
63G GLU 3.3 0.2 - - - -
64G CYS* 1.3 76.0 - - - +
66G GLU* 1.3 65.1 + - + +
68G SER* 3.6 1.7 + - - -
69G ALA* 3.0 29.0 + - + +
102G ILE* 5.0 5.9 - - + +
105G MET* 4.5 11.4 - - + -
896G PRO* 3.3 28.5 - - + +
897G TYR* 3.5 36.3 - + - -
900G THR* 4.4 6.7 + - - -
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Residues in contact with GLU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G HIS* 2.5 37.4 + - - -
16G ILE* 5.2 0.2 - - - +
19G GLN* 3.6 25.6 + - - +
62G GLN* 3.0 28.9 + - + +
63G GLU* 2.9 19.0 + - - +
65G TYR* 1.3 85.2 - - + +
67G VAL* 1.3 63.4 + - + +
69G ALA* 3.2 5.6 + - - +
70G ASP* 2.6 37.3 + - - +
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Residues in contact with VAL 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLU* 2.9 16.9 + - + +
64G CYS* 3.4 13.0 - - - +
66G GLU* 1.3 75.7 - - + +
68G SER* 1.3 61.5 + - - +
70G ASP* 3.4 4.7 + - - -
71G TYR* 3.0 27.4 + - - +
79G LYS* 3.9 36.6 - - + +
80G LEU* 5.6 1.7 - - + +
83G LEU* 3.5 35.7 - - + -
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Residues in contact with SER 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G CYS 3.1 10.8 + - - -
65G TYR 3.9 1.3 - - - -
67G VAL* 1.3 74.8 - - - +
69G ALA* 1.3 64.4 + - - +
71G TYR* 3.3 7.9 + - - +
72G GLU* 3.3 28.7 + - - +
80G LEU* 4.9 2.3 - - - +
83G LEU* 3.8 9.0 - - - +
896G PRO* 3.1 26.7 - - - -
899G THR* 3.9 13.5 - - - +
900G THR* 2.6 30.8 + - - -
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLN* 3.9 32.7 - - + +
23G LEU* 3.7 10.0 - - + +
65G TYR* 3.0 22.8 + - + +
66G GLU 3.2 4.5 + - - +
68G SER* 1.3 76.5 - - - +
70G ASP* 1.3 62.3 + - - +
72G GLU* 3.5 7.8 + - - +
73G GLY* 3.3 14.7 + - - -
896G PRO* 4.0 23.9 - - + +
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Residues in contact with ASP 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLN* 4.9 11.7 - - - +
66G GLU* 2.6 29.7 + - - +
67G VAL* 4.0 5.9 + - - +
68G SER 3.2 0.4 - - - -
69G ALA* 1.3 76.3 - - - +
71G TYR* 1.3 66.3 + - - +
73G GLY* 2.9 12.7 + - - +
74G LYS 3.2 11.8 + - - +
79G LYS* 4.8 13.5 - - + -
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Residues in contact with TYR 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G VAL 3.0 14.1 + - - +
68G SER 3.3 8.0 + - - +
70G ASP* 1.3 76.6 - - - +
72G GLU* 1.3 78.9 + - - +
74G LYS 3.2 4.2 - - - -
75G GLY* 3.0 57.4 + - - -
76G ASP 3.6 20.6 - - - +
77G THR* 4.1 4.0 - - - -
79G LYS* 4.9 7.3 - - + +
80G LEU* 3.4 44.0 - - + -
837G ASP* 2.6 40.9 + - - -
839G GLY* 3.5 15.9 - - - -
840G ILE* 3.8 7.9 + - + -
899G THR* 4.3 3.6 - - + -
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Residues in contact with GLU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.5 25.5 - - + +
68G SER 3.3 15.5 - - - +
69G ALA* 3.6 3.1 - - - +
70G ASP 3.2 0.4 - - - -
71G TYR* 1.3 90.2 - - - +
73G GLY* 1.3 63.9 + - - +
74G LYS* 3.4 1.0 + - - -
75G GLY 4.7 0.9 + - - -
785G ARG* 4.2 7.3 + - - -
837G ASP* 5.2 3.5 - - - +
840G ILE* 4.8 0.2 - - - +
892G VAL* 5.2 2.0 - - + +
895G ASN* 3.0 39.4 + - + +
896G PRO 4.6 2.9 - - - -
899G THR* 2.5 30.2 + - - +
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Residues in contact with GLY 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLN 5.2 9.0 - - - -
23G LEU* 4.6 4.2 - - - +
69G ALA 3.3 8.9 + - - -
70G ASP* 2.9 11.5 + - - -
72G GLU* 1.3 78.8 - - - +
74G LYS* 1.3 69.5 + - - +
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Residues in contact with LYS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASP 3.2 8.8 + - - +
71G TYR* 3.2 3.8 - - - +
72G GLU 4.3 0.2 - - - -
73G GLY* 1.3 84.1 - - - +
75G GLY* 1.3 52.5 + - - +
76G ASP* 2.8 23.6 + - - +
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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