Contacts of the helix formed by residues 54 - 64 (chain A) in PDB entry 1RGD
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 PRO 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.3 2.7 - - + -
35A TYR* 3.7 14.1 - - + -
51A LYS* 3.4 44.6 - - + +
52A ASN 4.5 0.4 - - - -
53A CYS* 1.3 84.8 - - + +
55A ALA* 1.3 63.5 + - + +
57A ARG* 3.0 19.7 + - + +
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Residues in contact with ALA 55 (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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35A TYR* 3.0 46.2 - - + +
37A CYS* 3.5 31.0 - - - +
53A CYS* 3.0 7.5 + - - -
54A PRO* 1.3 80.1 - - + +
56A CYS* 1.3 58.5 + - - +
57A ARG 3.0 6.8 + - - -
58A TYR 3.2 6.6 + - - -
59A ARG 3.6 0.7 + - - -
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Residues in contact with CYS 56 (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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37A CYS* 3.5 7.9 - - + -
43A CYS* 3.0 34.8 - - - -
45A ILE* 3.9 3.4 - - - -
53A CYS* 2.9 6.5 + - - +
55A ALA* 1.3 78.2 - - - +
57A ARG* 1.3 55.7 + - - +
59A ARG* 3.2 29.7 - - - +
60A LYS* 3.0 34.0 + - - +
73A ZN 2.0 38.1 - - - -
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Residues in contact with ARG 57 (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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3A VAL* 5.1 2.8 - - + +
4A CYS* 3.2 18.7 - - - +
6A ASP* 4.6 3.6 + - - +
18A CYS* 3.3 11.3 - - - -
20A SER* 4.1 5.7 + - - -
21A CYS* 3.1 20.9 - - - -
24A PHE* 3.7 21.9 - - + -
45A ILE* 4.1 31.4 + - + +
50A ARG 6.0 0.2 - - - -
51A LYS* 3.8 38.1 - - - +
53A CYS 3.6 1.8 + - - -
54A PRO* 3.0 15.3 + - + +
55A ALA 3.0 0.6 + - - -
56A CYS* 1.3 73.7 - - - +
58A TYR* 1.3 51.9 + - - +
60A LYS* 3.1 6.1 + - - +
61A CYS* 2.9 37.5 + - - -
72A ZN 3.1 23.7 - - - -
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Residues in contact with TYR 58 (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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24A PHE* 3.6 21.0 - + + -
25A PHE* 3.2 43.7 - + - -
28A ALA* 3.8 22.9 - - + -
29A VAL* 3.9 7.4 - - + +
33A HIS* 3.1 29.3 + - - -
34A ASN* 4.2 18.8 - - - -
35A TYR* 3.4 36.1 - + + -
55A ALA 3.2 3.5 + - - +
57A ARG* 1.3 76.0 - - - +
59A ARG* 1.3 60.0 + - - +
61A CYS* 2.8 30.2 + - - +
62A LEU* 3.2 27.4 + - + +
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Residues in contact with ARG 59 (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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35A TYR 4.0 12.3 + - - +
36A LEU* 5.1 13.0 - - + -
37A CYS* 4.0 23.5 - - - +
42A ASP* 3.5 32.3 - - - +
43A CYS 3.9 4.0 + - - +
55A ALA 3.6 1.2 + - - -
56A CYS* 3.2 42.0 + - - +
58A TYR* 1.3 81.1 - - - +
60A LYS* 1.3 72.7 + - - +
62A LEU* 3.1 23.5 + - + +
63A GLN* 2.9 58.0 + - - +
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Residues in contact with LYS 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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3A VAL* 3.3 23.1 - - + +
42A ASP* 6.2 0.4 - - + -
43A CYS 2.9 22.6 + - - +
44A ILE* 3.2 6.6 - - + +
45A ILE* 2.8 45.5 - - - +
46A ASP* 3.2 19.5 + - - +
56A CYS* 3.0 17.6 + - - +
57A ARG 3.5 2.0 - - - +
59A ARG* 1.3 86.3 - - - +
61A CYS* 1.3 54.0 + - - +
62A LEU 3.1 0.9 - - - -
63A GLN* 3.4 24.4 - - + +
64A ALA* 2.7 36.2 + - - +
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Residues in contact with CYS 61 (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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3A VAL* 4.6 2.5 - - - -
17A THR* 4.2 10.8 - - - -
21A CYS* 3.7 39.7 - - - -
24A PHE* 4.7 1.8 - - - -
25A PHE* 4.5 5.4 - - + -
57A ARG* 2.9 29.5 + - - -
58A TYR* 2.8 15.4 + - - +
60A LYS* 1.3 74.7 - - - +
62A LEU* 1.3 52.5 + - - +
64A ALA* 3.2 6.6 - - - +
65A GLY 2.9 10.7 + - - -
66A MET* 2.7 51.8 + - + +
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Residues in contact with LEU 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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25A PHE* 3.7 31.9 - - + -
34A ASN* 6.1 0.7 - - - +
58A TYR* 3.3 30.7 - - + +
59A ARG* 3.2 17.0 - - + +
60A LYS 3.1 0.2 - - - -
61A CYS* 1.3 78.3 - - - +
63A GLN* 1.3 62.1 + - + +
65A GLY* 3.1 19.2 - - - -
66A MET 4.0 6.5 - - - +
67A ASN* 5.5 0.4 - - + -
71A ARG* 3.4 22.0 + - - +
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Residues in contact with GLN 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 ARG* 2.9 71.8 + - - +
60A LYS* 3.4 20.8 - - + +
62A LEU* 1.3 78.1 - - + +
64A ALA* 1.3 62.8 + - - +
65A GLY* 3.2 0.4 - - - -
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Residues in contact with ALA 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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2A LEU* 3.9 28.0 - - + +
3A VAL* 3.4 21.1 - - + -
15A VAL* 4.7 5.6 - - + +
17A THR* 4.6 3.8 - - + -
60A LYS 2.7 18.0 + - - +
61A CYS* 3.2 7.2 - - - +
63A GLN* 1.3 76.3 - - - +
65A GLY* 1.3 58.8 + - - +
66A MET* 4.5 1.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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