Contacts of the helix formed by residues 54 - 74 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 4.4 0.3 - - - +
50A GLN* 2.9 25.3 + - - -
52A LEU 3.9 0.4 - - - -
53A HIS* 1.3 80.0 - - - +
55A PRO* 1.3 77.9 - - - +
56A SER 3.4 2.6 + - - -
57A LEU* 3.5 2.8 + - - +
58A ARG 3.2 15.6 + - - -
925A LEU 5.4 0.9 - - - -
927A LYS* 4.0 14.6 - - - +
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Residues in contact with PRO 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 4.4 2.0 - - + -
50A GLN* 3.7 32.5 - - + +
54A GLY* 1.3 84.1 - - - +
56A SER* 1.3 55.5 + - - +
58A ARG* 3.2 2.6 + - - +
59A GLU* 2.7 53.9 + - - +
927A LYS* 5.2 3.1 - - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.4 0.8 - - - -
55A PRO* 1.3 80.6 - - - +
57A LEU* 1.3 57.4 - - - +
59A GLU* 3.9 12.9 + - - +
60A PHE* 2.9 28.9 + - - +
925A LEU* 3.9 20.8 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.0 12.6 - - + +
53A HIS* 3.3 32.1 - - + +
54A GLY 3.5 6.6 + - - +
55A PRO 3.3 0.4 - - - -
56A SER* 1.3 75.7 - - - +
58A ARG* 1.3 65.3 + - - +
60A PHE* 3.1 2.5 + - + +
61A VAL* 3.0 31.2 + - + +
94A ASP* 4.8 0.9 - - - +
97A LEU* 3.4 36.3 - - + -
98A VAL* 4.2 22.4 - - + -
925A LEU* 3.5 49.4 + - + +
926A SER* 4.4 2.5 - - - -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.8 27.0 + - - +
13A HIS 4.7 5.5 + - - +
14A HIS 4.1 12.9 + - - -
43A ASP* 4.8 6.1 + - - +
46A LEU* 3.4 45.4 + - + +
47A ASN* 2.9 26.5 + - - +
49A LEU* 4.0 11.2 - - + +
50A GLN* 2.9 46.6 + - + +
54A GLY 3.2 4.3 + - - +
55A PRO 3.2 8.1 + - - +
57A LEU* 1.3 80.8 - - - +
59A GLU* 1.3 65.9 + - - +
61A VAL* 3.4 2.3 + - - +
62A GLN* 2.9 49.0 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.4 41.3 + - - +
55A PRO* 2.7 30.6 + - - +
56A SER* 3.9 12.5 + - - +
58A ARG* 1.3 74.7 - - - +
60A PHE* 1.3 57.2 + - - +
62A GLN* 3.4 5.3 + - - +
63A GLU* 2.9 45.5 + - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER 2.9 19.8 + - - +
57A LEU* 3.1 6.3 + - + +
59A GLU* 1.3 75.5 - - - +
61A VAL* 1.3 64.1 + - - +
63A GLU* 3.0 20.4 + - - +
64A CYS* 3.1 36.7 + - - -
86A LYS* 3.3 51.6 - - + -
87A LEU* 4.1 5.2 - - + -
90A LEU* 3.6 41.1 - - + -
98A VAL* 4.1 18.2 - - + -
925A LEU* 3.7 20.6 - - + -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.7 1.8 - - + -
49A LEU* 3.8 21.3 - - + -
57A LEU* 3.0 26.3 + - + +
58A ARG 4.0 2.5 - - - +
60A PHE* 1.3 76.8 - - - +
62A GLN* 1.3 61.2 + - - +
64A CYS* 3.6 5.9 + - - +
65A TYR* 3.2 22.0 + - - +
98A VAL* 4.4 23.3 - - + -
101A SER* 4.1 18.8 - - - +
102A ILE* 3.8 29.0 - - + +
105A MET* 4.5 12.2 - - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS 5.1 2.4 + - - -
13A HIS 5.6 0.2 + - - -
14A HIS* 2.9 51.1 + - + +
15A SER 4.1 1.6 - - - -
16A ILE* 4.1 18.1 - - + +
46A LEU* 3.8 21.3 - - + +
58A ARG* 2.9 46.8 + - - +
59A GLU* 3.8 6.2 - - - +
61A VAL* 1.3 75.9 - - - +
63A GLU* 1.3 64.4 + - + +
65A TYR* 3.4 8.2 + - + +
66A GLU* 3.0 34.8 + - + +
105A MET* 6.4 0.2 - - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 2.9 30.5 + - + +
60A PHE* 3.0 10.6 + - - +
62A GLN* 1.3 77.1 - - + +
64A CYS* 1.3 58.1 + - - +
66A GLU* 2.9 17.2 + - - +
67A VAL* 2.8 35.0 + - + +
86A LYS* 2.5 38.0 + - + +
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Residues in contact with CYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.1 47.2 + - - +
61A VAL* 4.1 5.6 - - - +
63A GLU* 1.3 71.4 - - - +
65A TYR* 1.3 65.5 + - - +
67A VAL* 3.3 4.4 + - - +
68A SER* 2.8 31.4 + - - -
83A LEU* 3.6 29.8 - - + +
86A LYS* 4.5 7.4 - - - +
87A LEU* 4.4 6.7 - - - -
98A VAL* 5.0 2.7 - - - -
102A ILE* 5.1 1.6 - - + -
900A THR* 4.1 16.6 - - + -
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 30.9 + - + -
19A GLN* 4.0 22.5 - - + +
20A LEU* 2.9 43.5 + - + +
42A VAL* 6.3 1.1 - - + -
61A VAL 3.2 13.3 + - - +
62A GLN* 3.4 15.3 - - + +
64A CYS* 1.3 77.7 - - - +
66A GLU* 1.3 64.5 + - + +
68A SER* 3.9 2.0 - - - -
69A ALA* 3.0 31.1 + - + +
102A ILE* 4.9 2.6 - - + +
105A MET* 4.7 11.7 - - + -
896A PRO* 3.5 26.7 - - + -
897A TYR* 3.7 33.4 - + - -
900A THR* 4.4 7.2 + - - -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 2.6 37.3 + - - -
19A GLN* 3.7 31.9 + - + +
62A GLN* 3.0 29.1 + - - +
63A GLU* 2.9 18.4 + - - +
65A TYR* 1.3 82.4 - - + +
67A VAL* 1.3 65.3 + - + +
69A ALA* 3.2 3.0 + - - -
70A ASP* 2.6 34.3 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 2.8 29.4 + - + +
64A CYS* 3.3 8.3 + - - +
66A GLU* 1.3 73.6 - - + +
68A SER* 1.3 63.3 + - - +
70A ASP* 3.4 5.2 + - - +
71A TYR* 3.1 20.8 + - + +
79A LYS* 3.7 58.4 - - + +
83A LEU* 4.2 17.7 - - + -
86A LYS* 6.2 3.1 - - + -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A CYS 2.8 10.9 + - - -
65A TYR 3.9 2.0 - - - -
67A VAL* 1.3 76.2 - - - +
69A ALA* 1.3 62.9 + - - +
71A TYR* 3.1 18.8 + - - +
72A GLU* 3.3 17.3 + - - +
83A LEU* 3.4 15.3 - - - +
896A PRO* 3.2 26.5 - - - -
899A THR* 4.1 15.0 - - - -
900A THR* 2.4 23.0 + - - -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 4.1 28.5 - - + +
23A LEU* 3.3 23.7 - - + +
65A TYR* 3.0 23.9 + - + +
66A GLU 3.2 4.0 + - - +
68A SER* 1.3 76.0 - - - +
70A ASP* 1.3 65.3 + - - +
72A GLU* 3.5 0.7 + - - -
73A GLY* 3.4 7.1 + - - -
896A PRO* 4.1 24.2 - - + +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 4.0 15.2 + - - +
66A GLU* 2.6 27.7 + - - +
67A VAL* 3.9 5.4 - - - +
69A ALA* 1.3 79.9 - - - +
71A TYR* 1.3 66.7 + - - +
73A GLY* 3.0 12.2 + - - +
74A LYS* 3.3 11.8 + - - +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.1 13.1 + - + +
68A SER* 3.1 9.8 + - - +
70A ASP* 1.3 77.0 - - - +
72A GLU* 1.3 81.1 + - - +
74A LYS 3.1 23.4 - - - -
75A GLY* 3.2 37.0 + - - -
76A ASP* 3.8 11.4 - - - +
77A THR* 4.6 2.7 - - - -
79A LYS* 5.8 4.7 - - + -
80A LEU* 3.2 33.4 - - + -
837A ASP* 2.3 45.0 + - - -
839A GLY* 3.8 10.9 - - - -
840A ILE* 3.6 18.1 - - + +
899A THR* 4.0 12.3 - - + -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.5 25.1 - - + -
68A SER 3.3 15.0 + - - +
69A ALA* 3.8 0.4 - - - +
70A ASP 3.3 0.4 - - - -
71A TYR* 1.3 91.6 - - - +
73A GLY* 1.3 61.8 + - - +
74A LYS* 3.4 1.2 + - - -
75A GLY 4.8 0.9 + - - -
785A ARG* 3.9 6.6 + - - -
837A ASP* 4.7 3.7 - - - +
892A VAL* 4.8 5.6 - - + +
895A ASN* 2.9 40.5 + - + +
896A PRO 4.6 4.0 - - - -
899A THR* 2.6 28.2 + - - +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 5.2 9.2 - - - -
23A LEU* 4.3 6.5 - - - +
69A ALA 3.4 8.5 + - - -
70A ASP* 3.0 11.0 + - - -
72A GLU* 1.3 80.0 - - - +
74A LYS* 1.3 63.5 + - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP 3.3 9.3 + - - +
71A TYR* 3.1 6.1 + - - +
72A GLU 4.3 0.7 - - - -
73A GLY* 1.3 81.0 - - - +
75A GLY* 1.3 53.0 + - - +
76A ASP* 2.7 30.9 + - + +
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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
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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