Contacts of the helix formed by residues 54 - 72 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU 3.8 0.5 + - - +
50F GLN* 2.9 24.8 + - - -
51F ASP 5.1 0.2 + - - -
52F LEU 3.8 0.6 - - - -
53F HIS* 1.3 81.6 - - - +
55F PRO* 1.3 76.4 - - - +
56F SER 3.4 2.9 + - - -
57F LEU* 3.5 2.4 + - - +
58F ARG 3.3 15.1 + - - -
927F LYS* 4.9 8.5 - - - -
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Residues in contact with PRO 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LYS 4.7 1.3 - - - +
50F GLN* 3.8 33.0 - - + +
54F GLY* 1.3 82.6 - - - +
56F SER* 1.3 72.5 + - - +
58F ARG* 3.3 1.7 + - + +
59F GLU* 2.9 43.2 + - + +
927F LYS* 5.1 8.3 - - + +
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLY 3.4 0.6 - - - -
55F PRO* 1.3 81.2 - - - +
57F LEU* 1.3 57.3 + - - +
59F GLU* 4.0 10.4 - - - +
60F PHE* 3.1 27.2 + - - +
925F LEU* 4.0 25.9 - - - +
927F LYS* 4.3 17.8 - - - -
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 3.8 23.6 - - + +
53F HIS* 3.5 22.0 - - + +
54F GLY 3.5 7.0 + - - +
55F PRO 3.2 0.4 - - - -
56F SER* 1.3 76.6 - - - +
58F ARG* 1.3 65.8 + - - +
60F PHE* 3.1 4.0 + - - +
61F VAL* 2.9 25.1 + - + +
94F ASP* 4.9 1.8 - - - +
97F LEU* 3.5 36.3 - - + -
98F VAL* 4.2 18.6 - - + -
101F SER* 5.5 0.4 - - - +
925F LEU* 3.7 42.1 + - + +
926F SER* 4.0 6.3 - - - -
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Residues in contact with ARG 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LYS* 3.5 30.7 + - - +
13F HIS 5.2 2.8 + - - -
14F HIS 4.3 10.9 + - - -
43F ASP* 4.5 6.9 + - - +
46F LEU* 3.3 50.9 + - + +
47F ASN* 2.8 28.3 + - - +
49F LEU* 4.1 12.1 - - + -
50F GLN* 2.9 45.3 + - + +
54F GLY 3.3 5.2 + - - +
55F PRO 3.3 6.0 + - - +
57F LEU* 1.3 79.8 - - - +
59F GLU* 1.3 56.8 + - - +
61F VAL* 3.1 3.8 + - - +
62F GLN* 2.8 52.8 + - - +
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LYS* 3.2 41.1 + - + +
55F PRO* 2.9 26.8 + - - +
56F SER* 4.1 7.2 - - - +
58F ARG* 1.3 75.4 - - - +
60F PHE* 1.3 57.1 + - - +
62F GLN* 3.7 7.0 - - - +
63F GLU* 2.8 46.5 + - + +
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F SER 3.1 19.8 + - - +
57F LEU 3.1 4.9 + - - +
59F GLU* 1.3 76.4 - - - +
61F VAL* 1.3 62.8 + - - +
63F GLU* 3.3 11.2 + - - +
64F CYS* 3.1 38.6 + - - -
86F LYS* 3.5 49.3 - - + -
87F LEU* 4.0 7.6 - - + -
90F LEU* 3.8 38.4 - - + -
98F VAL* 4.0 19.1 - - + -
925F LEU* 3.7 21.3 - - + -
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LEU* 4.1 11.9 - - + -
49F LEU* 4.1 18.6 - - + -
57F LEU* 2.9 20.1 + - + +
58F ARG 3.6 7.0 - - - +
60F PHE* 1.3 77.7 - - - +
62F GLN* 1.3 63.1 + - - +
64F CYS* 3.3 7.7 + - - +
65F TYR* 3.1 20.6 + - - +
98F VAL* 4.1 35.9 - - + -
101F SER* 4.4 5.4 - - - +
102F ILE* 4.4 6.4 - - + +
105F MET* 3.4 32.8 - - + -
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Residues in contact with GLN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LYS* 3.8 6.0 - - + +
14F HIS* 3.0 50.2 + - + -
16F ILE* 3.4 30.1 - - + +
46F LEU* 3.6 13.0 - - + +
58F ARG* 2.8 44.6 + - - +
59F GLU* 3.8 6.3 - - - +
61F VAL* 1.3 77.8 - - - +
63F GLU* 1.3 62.6 + - + +
65F TYR* 3.3 7.1 + - - +
66F GLU* 3.0 34.5 + - - +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLU* 2.8 34.1 + - + +
60F PHE* 3.6 11.6 - - - +
61F VAL 3.3 0.2 - - - -
62F GLN* 1.3 75.0 - - + +
64F CYS* 1.3 65.0 + - - +
66F GLU* 3.1 14.1 + - - +
67F VAL* 3.0 32.6 + - + +
83F LEU* 5.3 0.7 - - - -
86F LYS* 2.7 36.6 + - - +
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Residues in contact with CYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F PHE* 3.1 47.1 + - - -
61F VAL* 3.3 9.6 + - - +
63F GLU* 1.3 76.7 - - - +
65F TYR* 1.3 62.4 + - - +
67F VAL* 3.5 1.9 + - - +
68F SER* 3.2 18.7 + - - -
83F LEU* 3.6 31.5 - - + +
86F LYS* 4.8 1.8 - - - -
87F LEU* 4.5 9.6 - - - -
98F VAL* 4.7 4.3 - - - -
102F ILE* 4.7 4.0 - - + -
900F THR* 3.5 26.4 + - + -
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Residues in contact with TYR 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.1 49.9 + - + +
19F GLN* 3.9 21.8 + - + +
20F LEU* 3.1 32.7 + - + +
42F VAL* 6.2 0.7 - - + -
61F VAL 3.1 13.3 + - - +
62F GLN* 3.5 8.3 - - - +
63F GLU 3.3 0.2 - - - -
64F CYS* 1.3 76.6 - - - +
66F GLU* 1.3 65.9 + - + +
68F SER* 3.4 1.6 + - - -
69F ALA* 2.9 30.8 + - + +
102F ILE* 4.8 9.1 - - + +
105F MET* 5.5 6.5 - - - -
896F PRO* 3.4 26.6 - - + +
897F TYR* 3.6 35.4 - + + -
900F THR* 4.4 6.5 + - - -
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F HIS* 2.6 37.5 + - - -
19F GLN* 3.6 32.9 + - + +
62F GLN* 3.0 31.7 + - - +
63F GLU* 3.1 15.6 + - - +
65F TYR* 1.3 81.6 - - + +
67F VAL* 1.3 61.6 + - + +
69F ALA* 3.3 4.1 + - - +
70F ASP* 2.9 40.0 + - - +
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLU* 3.0 20.4 + - + +
64F CYS 4.0 3.4 - - - +
66F GLU* 1.3 76.7 - - + +
68F SER* 1.3 59.8 + - - +
70F ASP* 3.3 7.8 + - - +
71F TYR* 3.0 25.8 + - - +
79F LYS* 3.7 40.3 - - + +
80F LEU* 5.3 2.7 - - + -
82F GLU* 5.8 2.2 - - + +
83F LEU* 4.2 25.6 - - + +
86F LYS* 5.9 4.5 - - + +
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F CYS 3.2 7.9 + - - -
65F TYR 3.9 1.3 - - - -
67F VAL* 1.3 77.1 - - - +
69F ALA* 1.3 64.5 + - - +
71F TYR* 3.3 10.3 + - - +
72F GLU* 3.3 20.8 + - - +
80F LEU* 5.0 3.3 - - - +
83F LEU* 3.9 9.2 - - - +
895F ASN 5.6 0.2 - - - -
896F PRO* 3.3 18.6 - - - +
899F THR* 3.8 15.1 - - - +
900F THR* 2.8 42.5 + - - -
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F GLN* 4.1 20.9 - - + +
22F GLN* 3.9 12.8 - - - +
23F LEU* 3.3 16.9 - - + +
65F TYR* 2.9 22.1 + - + +
66F GLU 3.3 4.2 + - - +
68F SER* 1.3 75.4 - - - +
70F ASP* 1.3 62.6 + - - +
72F GLU* 3.2 18.3 + - - +
896F PRO* 4.0 24.6 - - + +
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Residues in contact with ASP 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F GLN* 4.3 7.3 - - - +
22F GLN* 2.9 26.0 + - - +
66F GLU* 2.9 21.3 + - - +
67F VAL* 3.7 6.4 - - - +
68F SER 3.2 0.2 - - - -
69F ALA* 1.3 75.7 - - - +
71F TYR* 1.3 64.3 + - - +
72F GLU 3.4 3.7 - - - +
74F LYS* 3.2 28.2 - - + +
79F LYS* 4.3 23.2 - - + +
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Residues in contact with TYR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F VAL 3.0 13.9 + - - +
68F SER* 3.3 7.8 + - - +
70F ASP* 1.3 76.2 - - - +
72F GLU* 1.3 68.7 + - - +
73F GLY 3.4 0.3 + - - -
74F LYS 3.1 4.0 + - - -
75F GLY* 3.1 48.9 + - - -
76F ASP 3.6 25.4 - - - -
77F THR* 4.0 10.0 + - - -
79F LYS* 4.6 8.9 - - + +
80F LEU* 3.7 34.3 - - + -
837F ASP* 2.6 40.8 + - - -
839F GLY* 3.5 16.3 + - - -
840F ILE* 3.9 10.2 + - + -
899F THR* 4.3 11.7 - - + -
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Residues in contact with GLU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLN* 5.2 1.2 - - - +
23F LEU* 3.8 30.5 - - + +
68F SER 3.3 10.1 + - - +
69F ALA* 3.2 18.9 - - - +
70F ASP* 3.3 4.5 - - - +
71F TYR* 1.3 85.1 - - - +
73F GLY* 1.3 66.0 + - - +
74F LYS* 3.2 1.9 + - - +
785F ARG* 4.4 6.1 + - - -
837F ASP* 5.1 6.2 - - - +
892F VAL* 4.9 14.5 - - + +
895F ASN* 2.8 43.0 - - + +
896F PRO* 5.5 0.4 - - + -
899F THR* 4.4 4.9 + - - -
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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) + - + + + + + -
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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