Contacts of the helix formed by residues 80 - 94 (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 THR 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLY 3.1 11.8 + - - +
50A GLY* 3.9 12.5 - - - -
51A ASN* 2.7 30.3 + - - +
78A LYS* 4.6 9.6 - - - +
79A LYS* 1.3 75.2 - - - +
81A PRO* 1.3 68.1 - - + +
82A ASP 4.3 0.4 - - - -
83A CYS* 3.1 14.9 + - - +
84A GLU* 2.8 31.4 + - - +
493A NAD 4.4 7.6 - - - +
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Residues in contact with PRO 81 (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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79A LYS 4.5 1.1 - - - +
80A THR* 1.3 89.1 - - + +
82A ASP* 1.3 64.5 + - - +
84A GLU* 3.4 6.4 + - + +
85A TYR* 2.9 28.8 + - - +
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Residues in contact with ASP 82 (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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16A SER* 2.5 40.8 + - - +
17A ARG* 3.5 23.0 + - + +
20A MET* 3.5 29.7 - - + +
51A ASN* 3.9 10.2 + - - +
80A THR* 3.2 1.4 + - - -
81A PRO* 1.3 80.7 - - - +
83A CYS* 1.3 64.8 - - - +
85A TYR* 3.6 4.3 - - - +
86A ASN* 3.0 32.1 + - - +
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Residues in contact with CYS 83 (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* 4.4 0.2 - - - -
48A GLY 3.8 13.0 - - - -
49A GLY 3.9 9.9 - - - +
50A GLY 3.4 26.7 - - - +
51A ASN* 4.1 1.4 + - - -
54A GLY* 3.7 20.2 - - - -
57A PHE* 3.8 19.8 - - - -
79A LYS* 4.0 11.9 - - - -
80A THR* 3.1 16.9 + - - +
82A ASP* 1.3 77.7 - - - +
84A GLU* 1.3 53.0 + - - +
86A ASN* 3.2 2.1 + - - +
87A TYR* 2.8 35.9 + - - +
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Residues in contact with GLU 84 (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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79A LYS* 3.6 34.7 + - + +
80A THR 2.8 20.4 + - - +
81A PRO* 3.6 7.4 - - + +
83A CYS* 1.3 72.0 - - - +
85A TYR* 1.3 58.2 + - - +
87A TYR* 3.5 26.9 - - - +
88A GLY* 2.8 27.5 + - - -
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Residues in contact with TYR 85 (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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17A ARG* 3.4 51.7 + - + -
81A PRO 2.9 18.3 + - - +
82A ASP* 3.6 6.5 - - - +
83A CYS 3.3 0.2 - - - -
84A GLU* 1.3 75.5 - - - +
86A ASN* 1.3 74.2 + - - +
88A GLY* 3.3 4.1 + - - -
89A LEU* 3.0 62.8 + - + +
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Residues in contact with ASN 86 (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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17A ARG* 5.1 4.9 + - - +
20A MET* 3.3 26.3 - - - +
21A GLU* 4.3 2.1 - - - +
54A GLY 4.0 6.7 - - - +
57A PHE* 3.7 21.4 - - + +
58A VAL* 3.5 20.9 - - + +
61A ARG* 3.7 7.3 + - - +
82A ASP* 3.0 24.7 + - - +
83A CYS 4.0 1.3 - - - +
85A TYR* 1.3 90.5 - - - +
87A TYR* 1.3 57.6 + - - +
89A LEU* 3.2 23.3 + - - +
90A TYR* 2.9 29.3 + - - +
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Residues in contact with TYR 87 (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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57A PHE* 3.7 41.0 - + + -
74A PHE* 5.8 0.7 - + + -
79A LYS* 3.7 28.6 + - + -
83A CYS 2.8 21.6 + - - +
84A GLU* 3.5 27.4 - - - +
86A ASN* 1.3 69.6 - - - +
88A GLY* 1.3 66.9 + - - +
90A TYR* 3.2 2.1 + - - +
91A LYS* 2.9 67.3 + - + +
97A VAL* 3.9 18.3 - - + +
99A GLU* 5.7 1.2 + - - -
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Residues in contact with GLY 88 (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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84A GLU* 2.8 19.6 + - - -
85A TYR* 3.5 5.4 - - - -
86A ASN 3.3 0.2 - - - -
87A TYR* 1.3 79.2 - - - +
89A LEU* 1.3 58.1 + - - +
91A LYS* 3.5 5.2 + - - +
92A LYS* 3.0 35.0 + - - +
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Residues in contact with LEU 89 (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* 5.4 0.9 - - - +
61A ARG* 3.7 27.6 - - - +
85A TYR* 3.0 54.7 + - + +
86A ASN* 3.6 19.3 - - - +
87A TYR 3.2 0.4 - - - -
88A GLY* 1.3 73.3 - - - +
90A TYR* 1.3 57.0 + - - +
92A LYS* 3.1 8.7 + - + +
93A PHE* 2.7 53.9 + - + -
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Residues in contact with TYR 90 (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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57A PHE* 4.0 21.1 - + + +
60A ALA* 3.4 25.6 - - + -
61A ARG* 3.6 30.9 - - - +
64A LEU* 3.8 9.4 - - + +
70A VAL* 3.9 15.5 + - + +
72A VAL* 3.4 23.6 + - + +
86A ASN 2.9 17.6 + - - +
87A TYR 3.2 4.0 + - - +
89A LEU* 1.3 76.9 - - - +
91A LYS* 1.3 66.0 + - + +
93A PHE* 3.1 8.1 + - - +
94A GLY 3.3 0.5 + - - -
95A GLY* 3.0 40.7 + - - -
96A LYS 2.8 33.3 + - - -
97A VAL* 3.7 20.2 - - + -
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Residues in contact with LYS 91 (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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87A TYR* 2.9 61.1 + - + +
88A GLY* 3.9 4.9 - - - +
90A TYR* 1.3 78.2 - - + +
92A LYS* 1.3 60.9 + - - +
94A GLY* 3.1 13.3 + - - -
95A GLY 3.9 14.9 + - - +
97A VAL* 4.1 29.7 + - + +
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Residues in contact with LYS 92 (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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88A GLY* 3.0 23.9 + - - +
89A LEU* 3.1 11.4 + - + +
91A LYS* 1.3 75.6 - - - +
93A PHE* 1.4 67.2 + - + +
94A GLY* 3.2 1.8 + - - -
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Residues in contact with PHE 93 (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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61A ARG* 3.7 40.6 - - + -
64A LEU* 3.5 28.3 - - + +
89A LEU* 2.7 39.7 + - + +
90A TYR 3.1 0.8 + - - +
92A LYS* 1.4 81.7 - - + +
94A GLY* 1.3 56.8 + - - +
95A GLY 3.7 0.2 - - - -
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Residues in contact with GLY 94 (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 LEU* 4.2 8.1 - - - +
91A LYS 3.1 10.1 + - - -
92A LYS 3.2 2.7 - - - -
93A PHE* 1.3 77.7 - - - +
95A GLY* 1.3 64.0 + - - +
96A LYS* 3.9 1.2 + - - +
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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