Contacts of the helix formed by residues 55 - 78 (chain C) in PDB entry 1R5V
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 GLU 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 1.3 91.9 - - - +
56C ALA* 1.3 63.9 + - - +
57C GLN* 2.8 35.4 + - - +
58C GLY* 3.2 33.1 + - - -
4F LEU* 3.8 21.8 - - + +
7F TYR* 5.0 2.1 - - + -
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Residues in contact with ALA 56 (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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34C VAL* 4.0 14.4 - - + -
39C SER* 3.5 33.9 - - - +
40C GLU* 4.2 5.2 - - - +
41C THR* 4.5 6.5 - - - +
54C PHE* 3.5 15.9 + - - -
55C GLU* 1.3 69.8 + - - +
57C GLN* 1.3 67.3 + - - +
58C GLY 3.0 2.9 - - - -
59C ALA* 2.7 17.2 + - - +
60C LEU* 3.0 12.1 + - + +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 3.2 24.2 + - - +
55C GLU* 2.8 27.7 + - - +
56C ALA* 1.3 73.6 - - - +
58C GLY* 1.3 61.3 + - - +
60C LEU* 3.1 21.2 + - - +
61C ALA* 2.9 23.4 + - - +
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLU* 3.2 15.8 + - - -
56C ALA 2.9 1.4 + - - -
57C GLN* 1.3 75.3 - - - +
59C ALA* 1.3 61.0 + - - +
61C ALA* 3.3 5.8 + - - +
62C ASN* 3.2 15.9 + - - +
7F TYR* 3.3 46.4 + - - -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.4 48.9 - - + -
34C VAL* 3.7 19.3 - - + -
36C ILE* 6.0 0.2 - - + -
54C PHE* 3.8 6.2 - - + -
55C GLU 4.1 1.8 + - - -
56C ALA 2.7 15.6 + - - +
58C GLY* 1.3 69.4 - - - -
60C LEU* 1.3 64.5 + - - +
62C ASN* 3.2 4.3 + - - +
63C ILE* 3.0 26.9 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.4 9.9 - - + -
36C ILE* 3.7 49.8 - - + +
39C SER* 3.5 29.6 - - - +
56C ALA 3.0 15.4 + - - +
57C GLN* 3.1 28.2 + - - +
59C ALA* 1.3 78.1 - - - +
61C ALA* 1.3 60.9 - - - +
63C ILE* 3.3 7.1 + - - +
64C ALA* 3.0 21.3 + - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN 2.9 12.6 + - - +
58C GLY* 3.5 11.7 - - - +
59C ALA 3.2 0.2 - - - -
60C LEU* 1.3 75.6 - - - +
62C ASN* 1.3 66.3 + - - +
64C ALA* 3.0 9.9 + - - +
65C VAL* 3.0 26.4 + - + +
7F TYR* 4.9 3.6 - - - +
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 3.0 34.1 + - - +
22C PHE* 4.2 5.0 - - + -
58C GLY 3.2 4.2 + - - +
59C ALA 3.2 10.4 + - - +
61C ALA* 1.3 80.2 - - - +
63C ILE* 1.3 63.4 + - - +
65C VAL* 3.1 6.7 + - - +
66C ASP* 2.9 26.2 + - - +
7F TYR* 3.3 26.6 + - - -
8F PRO 3.0 23.8 + - - -
9F LYS* 4.0 2.3 - - - +
10F ALA* 3.3 28.1 + - - +
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Residues in contact with ILE 63 (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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11C GLU* 4.2 6.1 - - + -
12C PHE 4.1 7.9 - - - +
13C TYR* 4.0 24.0 - - + -
20C GLY* 4.5 7.0 - - - -
21C GLU 3.3 31.2 - - - +
22C PHE* 4.3 4.0 - - + -
36C ILE* 4.1 28.9 - - + -
59C ALA 3.0 17.0 + - - +
60C LEU* 3.6 8.1 - - - +
61C ALA 3.2 0.2 - - - -
62C ASN* 1.3 75.5 - - - +
64C ALA* 1.3 58.9 + - - +
66C ASP* 2.9 16.5 + - - +
67C LYS* 2.8 37.7 + - - +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU 3.0 13.5 + - - +
61C ALA* 3.0 12.5 + - - +
63C ILE* 1.3 76.2 - - - +
65C VAL* 1.3 63.7 + - + +
67C LYS* 3.3 16.5 + - + +
68C ALA* 3.2 21.8 + - - +
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Residues in contact with VAL 65 (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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61C ALA* 3.0 19.4 + - + +
62C ASN* 3.1 7.6 + - - +
64C ALA* 1.3 77.7 - - + +
66C ASP* 1.3 58.3 + - - +
68C ALA* 3.3 6.3 + - + +
69C ASN* 2.8 45.5 + - - +
10F ALA* 3.9 24.2 - - + +
11F ALA 3.5 16.4 - - - +
12F THR* 3.7 20.6 - - - +
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 2.6 41.7 - - - +
12C PHE* 4.6 2.0 + - - -
13C TYR* 4.2 19.2 - - + +
62C ASN 2.9 16.3 + - - +
63C ILE* 2.9 14.4 + - - +
65C VAL* 1.3 78.4 - - - +
67C LYS* 1.3 62.3 + - - +
69C ASN* 3.3 10.6 + - - +
70C LEU* 2.9 24.3 + - - +
36D GLU* 3.9 23.3 - - + +
38D SER* 4.9 5.5 + - - -
57D TYR* 6.0 1.9 - - - -
10F ALA* 4.4 5.7 - - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.3 60.1 - - + +
15C LEU* 6.0 0.5 - - - +
36C ILE* 6.1 3.0 - - - +
63C ILE* 2.8 25.7 + - - +
64C ALA* 3.5 16.7 - - + +
66C ASP* 1.3 74.0 - - - +
68C ALA* 1.3 64.6 + - - +
70C LEU* 3.3 13.7 + - - +
71C ASP* 3.5 11.8 + - - +
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Residues in contact with ALA 68 (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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64C ALA 3.2 9.2 + - - +
65C VAL* 3.7 9.0 - - + +
67C LYS* 1.3 81.4 - - - +
69C ASN* 1.3 65.0 + - - +
71C ASP* 3.1 20.4 + - - +
72C VAL* 3.3 14.0 + - - +
12F THR* 5.9 6.1 - - + +
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Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 2.8 33.7 + - - +
66C ASP* 3.8 9.7 + - - +
68C ALA* 1.3 73.4 - - - +
70C LEU* 1.3 56.7 + - - +
72C VAL* 3.0 9.1 + - - +
73C MET* 2.8 32.5 + - - +
36D GLU* 4.1 17.5 + - + +
57D TYR* 6.0 1.4 - - - -
11F ALA 2.8 24.9 + - - -
12F THR* 3.5 6.4 - - - +
13F LYS* 2.8 44.6 + - + +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.8 21.8 - - + +
15C LEU* 3.4 39.9 - - + -
66C ASP 2.9 13.8 + - - +
67C LYS* 3.4 10.5 - - - +
68C ALA 3.2 0.2 - - - -
69C ASN* 1.3 76.6 - - - +
71C ASP* 1.3 58.5 + - - +
73C MET* 3.1 2.7 + - - +
74C LYS* 2.8 34.6 + - + +
34D PHE* 3.6 35.4 - - + +
35D LEU 3.9 1.1 - - - +
36D GLU* 3.8 28.2 - - + +
59D TYR* 4.0 14.1 - - + -
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.0 20.8 - - - +
67C LYS 3.5 9.5 + - - +
68C ALA* 3.1 12.8 + - - +
70C LEU* 1.3 80.5 - - - +
72C VAL* 1.3 62.4 - - + +
74C LYS* 3.4 12.5 + - - +
75C GLU* 3.3 21.7 + - - +
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Residues in contact with VAL 72 (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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68C ALA 3.3 11.6 + - - +
69C ASN* 3.0 11.5 + - - +
71C ASP* 1.3 76.8 - - + +
73C MET* 1.3 59.3 + - - +
75C GLU* 3.3 6.3 + - - +
76C ARG* 2.9 41.1 + - + +
13F LYS* 3.7 22.0 - - + +
14F PHE* 3.3 42.0 - - - +
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Residues in contact with MET 73 (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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69C ASN 2.8 20.3 + - - +
70C LEU* 3.5 5.8 - - - +
72C VAL* 1.3 77.2 - - - +
74C LYS* 1.3 62.5 + - - +
76C ARG* 3.9 26.0 - - - +
77C SER* 3.2 25.1 + - - -
36D GLU* 3.3 18.2 - - - +
59D TYR* 3.7 28.5 + - + -
64D ASN* 3.6 28.9 - - - +
80D LEU* 3.8 30.4 - - + +
13F LYS* 3.4 25.6 - - + +
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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
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15C LEU* 4.1 23.2 - - + +
70C LEU* 2.8 24.1 + - + +
71C ASP* 3.8 14.3 + - - +
72C VAL 3.3 0.2 - - - -
73C MET* 1.3 74.2 - - - +
75C GLU* 1.3 61.6 + - - +
77C SER* 3.5 2.6 + - - -
78C ASN* 3.3 18.4 + - - -
79C ASN 5.2 0.5 + - - -
34D PHE* 3.6 63.3 - - + -
59D TYR* 3.6 10.1 - - - +
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Residues in contact with GLU 75 (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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71C ASP 3.3 9.9 + - - +
72C VAL* 3.3 9.3 + - - +
74C LYS* 1.3 79.7 - - - +
76C ARG* 1.3 64.5 + - - +
77C SER 3.3 0.9 + - - -
78C ASN* 3.7 8.5 + - - +
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Residues in contact with ARG 76 (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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72C VAL* 2.9 24.1 + - + +
73C MET* 3.9 18.9 - - - +
74C LYS 3.4 0.2 - - - -
75C GLU* 1.3 76.7 - - - +
77C SER* 1.3 60.5 + - - +
80D LEU* 3.0 40.3 + - + +
81D GLY* 4.4 0.2 - - - -
83D PRO* 3.6 30.0 - - + +
84D ASP* 2.8 44.6 + - - -
13F LYS* 3.9 3.8 - - - +
14F PHE 2.6 30.7 + - - -
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Residues in contact with SER 77 (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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73C MET 3.2 15.6 + - - -
74C LYS 3.5 4.5 + - - -
75C GLU 4.3 0.2 - - - -
76C ARG* 1.3 80.6 - - - +
78C ASN* 1.3 72.0 + - - +
80C THR* 3.6 24.3 + - - -
59D TYR* 3.6 12.3 + - - -
80D LEU* 3.9 26.5 - - - -
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Residues in contact with ASN 78 (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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74C LYS 3.3 11.6 + - - -
75C GLU* 3.7 7.4 + - - +
76C ARG 3.7 1.0 - - - -
77C SER* 1.3 91.3 + - - +
79C ASN* 1.3 64.0 + - - +
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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