Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 3RSG
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLY 3.3 2.8 - - - -
49A GLY* 1.3 80.3 - - - +
51A ASN* 1.3 61.1 + - - -
52A ASN 3.3 2.0 - - - -
53A GLY* 3.2 3.5 + - - +
54A GLY 3.0 20.8 + - - -
80A THR* 3.9 13.2 - - - -
83A CYS* 3.4 5.9 - - - +
116A ILE 5.3 0.6 + - - -
493A NAD 3.4 34.2 + - - -
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Residues in contact with ASN 51 (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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20A MET* 3.6 24.7 - - + +
50A GLY* 1.3 69.8 - - - -
52A ASN* 1.3 64.5 - - - +
54A GLY* 4.5 0.2 - - - -
55A ASP* 2.9 28.2 + - - +
80A THR* 2.7 30.5 + - - +
82A ASP* 3.9 11.4 + - - +
83A CYS 4.1 0.3 + - - -
493A NAD 2.8 44.8 + - - +
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Residues in contact with ASN 52 (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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51A ASN* 1.3 75.3 - - - +
53A GLY* 1.3 64.3 + - - +
55A ASP* 3.0 8.4 + - - +
56A GLY 3.0 16.3 + - - -
115A ALA* 3.0 29.1 - - - +
116A ILE 4.2 2.0 - - - +
117A PHE 3.3 4.3 - - - -
118A GLY* 3.4 25.7 - - - +
146A VAL* 3.0 26.4 + - - +
147A ASP* 3.8 0.6 - - - +
491A K 2.9 19.6 - - - -
493A NAD 3.0 45.0 + - - +
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Residues in contact with GLY 53 (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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47A CYS* 3.5 5.5 - - - -
48A GLY 3.3 22.9 + - - +
50A GLY 3.2 5.2 + - - -
52A ASN* 1.3 80.8 - - - +
54A GLY* 1.3 55.6 + - - +
56A GLY* 2.9 3.6 + - - -
57A PHE* 2.9 31.1 + - - -
83A CYS* 4.0 6.1 - - - -
115A ALA* 3.2 17.8 + - - -
116A ILE 4.7 0.2 + - - -
493A NAD 4.4 0.4 + - - -
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Residues in contact with GLY 54 (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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20A MET* 3.5 21.2 - - - +
50A GLY 3.0 10.7 + - - -
51A ASN 3.2 3.5 + - - -
52A ASN 3.2 0.6 - - - -
53A GLY* 1.3 73.2 - - - +
55A ASP* 1.3 64.4 + - - +
57A PHE* 3.2 8.0 + - - +
58A VAL* 3.2 23.7 + - - +
82A ASP 4.7 0.4 - - - -
83A CYS* 3.7 23.2 - - - -
86A ASN* 4.0 0.9 - - - +
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Residues in contact with ASP 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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20A MET* 3.3 27.5 - - - +
23A ALA* 3.6 21.2 - - + +
24A GLY* 4.0 3.1 - - - +
51A ASN 2.9 15.8 + - - +
52A ASN 3.2 8.1 - - - +
54A GLY* 1.3 73.7 - - - +
56A GLY* 1.3 63.0 + - - +
58A VAL* 3.1 9.5 + - - +
59A VAL* 3.0 25.9 + - + +
146A VAL* 3.7 14.6 - - + -
172A PHE* 3.4 11.7 - - + -
493A NAD 2.7 33.9 + - - -
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Residues in contact with GLY 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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45A VAL* 3.5 12.1 - - - +
47A CYS* 3.8 9.0 - - - -
52A ASN 3.0 6.7 + - - -
53A GLY 2.9 9.3 + - - -
55A ASP* 1.3 77.9 - - - +
57A PHE* 1.3 56.1 + - - +
59A VAL* 3.2 10.1 + - - +
60A ALA* 2.9 23.7 + - - +
113A VAL* 5.3 0.4 - - - -
115A ALA* 3.6 21.9 - - - +
146A VAL* 4.9 2.0 - - - -
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Residues in contact with PHE 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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47A CYS* 3.9 13.5 - - + -
53A GLY 2.9 22.0 + - - -
54A GLY 3.2 6.9 + - - +
56A GLY* 1.3 71.5 - - - +
58A VAL* 1.3 60.6 + - - +
60A ALA* 3.7 3.7 - - - +
61A ARG* 2.8 31.7 + - - +
72A VAL* 3.7 35.7 - - + -
74A PHE* 4.0 19.1 - + + -
79A LYS* 4.7 0.4 - - - -
83A CYS* 3.8 28.0 - - - -
86A ASN* 3.7 20.4 - - + -
87A TYR* 3.7 45.8 - + + -
90A TYR* 4.0 23.1 - + + +
97A VAL* 4.3 2.2 - - + -
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Residues in contact with VAL 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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20A MET* 3.8 17.3 - - + +
21A GLU* 3.4 27.1 - - - +
24A GLY* 3.6 20.6 - - - -
54A GLY 3.2 12.9 + - - +
55A ASP 3.1 7.7 + - - +
57A PHE* 1.3 72.7 - - - +
59A VAL* 1.3 66.3 + - - +
61A ARG* 3.4 7.2 + - - +
62A ASN* 2.9 48.7 + - - +
86A ASN* 3.5 29.6 - - - +
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Residues in contact with VAL 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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24A GLY* 3.4 21.8 - - - +
27A VAL* 3.7 22.0 - - + -
28A VAL* 4.2 9.6 - - + +
31A MET* 4.1 17.3 - - + -
45A VAL* 4.9 1.8 - - + -
55A ASP 3.0 20.6 + - - +
56A GLY* 3.2 11.4 + - - +
58A VAL* 1.3 77.9 - - - +
60A ALA* 1.3 63.4 + - - +
62A ASN* 3.2 2.3 + - - +
63A LEU* 3.1 40.1 + - + +
113A VAL* 4.3 15.9 - - + -
146A VAL* 4.8 4.9 - - + -
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Residues in contact with ALA 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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45A VAL* 4.1 9.4 - - + +
56A GLY 2.9 14.5 + - - +
57A PHE* 3.7 2.7 - - - +
59A VAL* 1.3 76.2 - - - +
61A ARG* 1.3 65.2 + - - +
63A LEU* 3.2 13.1 + - - +
64A LEU* 3.2 14.6 + - - +
70A VAL* 3.9 15.9 - - + +
72A VAL* 3.6 20.9 - - + -
90A TYR* 3.4 25.2 - - + -
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Residues in contact with ARG 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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21A GLU* 2.7 44.2 + - - -
57A PHE 2.8 21.4 + - - +
58A VAL* 3.9 6.9 - - - +
60A ALA* 1.3 72.9 - - - +
62A ASN* 1.3 84.4 + - - +
64A LEU* 3.2 21.3 + - - +
86A ASN* 3.7 17.1 + - - +
89A LEU* 3.7 32.7 - - - +
90A TYR* 3.6 19.9 - - - +
93A PHE* 3.7 50.1 - - + -
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Residues in contact with ASN 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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21A GLU* 3.2 23.3 + - - +
25A ILE* 3.8 15.3 - - - +
28A VAL* 4.2 19.4 - - + +
58A VAL* 2.9 37.2 + - - +
59A VAL 3.8 3.8 - - - +
61A ARG* 1.3 95.3 + - - +
63A LEU* 1.3 59.8 + - - +
64A LEU 3.4 3.4 - - - +
66A VAL* 4.7 9.0 - - - +
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Residues in contact with LEU 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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28A VAL* 4.3 15.7 - - + -
31A MET* 4.1 3.1 - - + -
38A LEU* 4.0 23.3 - - + -
43A PHE* 3.8 35.7 - - + -
45A VAL* 5.0 2.5 - - + -
59A VAL* 3.1 32.6 + - + +
60A ALA* 3.2 9.4 + - - +
62A ASN* 1.3 75.2 - - - +
64A LEU* 1.3 67.8 + - - +
65A GLY 3.2 0.5 + - - -
66A VAL* 3.0 20.5 + - + -
67A VAL* 3.3 33.6 + - + +
70A VAL* 3.9 12.3 - - + -
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Residues in contact with LEU 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 ALA 3.2 14.2 + - - +
61A ARG* 3.2 14.6 + - - +
62A ASN 4.4 2.9 - - - +
63A LEU* 1.3 75.2 - - - +
65A GLY* 1.3 60.2 + - - +
66A VAL* 3.1 9.7 + - - +
70A VAL* 4.1 22.4 - - + +
90A TYR* 3.8 17.0 - - + +
93A PHE* 3.5 40.6 - - + +
94A GLY 4.4 4.3 - - - +
95A GLY* 3.7 33.7 - - - +
96A LYS 5.3 0.2 - - - +
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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