Contacts of the helix formed by residues 11 - 28 (chain A) in PDB entry 1RC9
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 LYS 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASP 4.1 8.1 - - - +
6A SER* 2.8 42.7 + - - +
8A SER* 3.0 19.6 + - - +
10A ARG* 1.3 79.2 - - - +
12A PRO* 1.3 71.6 - - + +
13A GLU* 4.3 19.8 + - - +
14A ILE* 2.9 27.2 + - + +
15A GLN* 2.9 15.0 + - - +
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Residues in contact with PRO 12 (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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10A ARG 3.5 8.0 - - - +
11A LYS* 1.3 82.7 - - + +
13A GLU* 1.3 61.6 + - - +
15A GLN* 3.3 18.9 + - + +
16A ASN* 3.0 35.1 + - - +
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Residues in contact with GLU 13 (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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11A LYS* 3.1 22.1 + - - -
12A PRO* 1.3 80.7 - - - +
14A ILE* 1.3 61.5 + - + +
16A ASN* 3.5 9.3 + - - +
17A GLU* 3.1 26.1 + - - +
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Residues in contact with ILE 14 (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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6A SER 3.6 24.5 - - - +
7A GLU* 3.9 24.0 - - - +
8A SER 3.4 26.5 - - - +
9A PRO* 3.8 9.2 - - + -
11A LYS* 2.9 17.8 + - + +
13A GLU* 1.3 81.0 - - + +
15A GLN* 1.3 65.3 + - - +
17A GLU* 3.2 15.9 + - + +
18A ILE* 3.0 26.1 + - + +
86A TRP* 3.5 30.5 - - + -
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Residues in contact with GLN 15 (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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9A PRO 3.0 28.8 + - - +
10A ARG* 3.6 18.8 + - - +
11A LYS 2.9 13.4 + - - +
12A PRO* 3.3 18.1 + - - +
14A ILE* 1.3 75.5 - - - +
16A ASN* 1.3 59.4 + - - +
18A ILE* 3.3 2.7 + - - +
19A VAL* 3.0 35.1 + - - +
41A TRP* 3.5 56.2 - - + +
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Residues in contact with ASN 16 (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 PRO* 3.0 25.5 + - - +
13A GLU* 3.7 8.7 - - - +
14A ILE 3.2 0.2 - - - -
15A GLN* 1.3 75.2 - - - +
17A GLU* 1.3 55.7 + - - +
19A VAL* 4.6 5.2 - - - +
20A ASP* 2.7 51.2 + - - +
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Residues in contact with GLU 17 (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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7A GLU* 4.3 14.6 - - - +
13A GLU* 3.1 14.8 + - - +
14A ILE* 3.5 24.4 - - - +
16A ASN* 1.3 76.9 - - - +
18A ILE* 1.3 62.6 + - - +
20A ASP* 4.0 5.2 - - - +
21A LEU* 3.0 25.4 + - + +
85A LYS* 5.0 8.9 + - - +
86A TRP* 4.4 5.1 + - + -
87A THR* 2.7 41.8 + - - +
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Residues in contact with ILE 18 (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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9A PRO* 4.3 2.7 - - + -
14A ILE* 3.0 25.7 + - + +
15A GLN 3.6 6.3 - - - +
17A GLU* 1.3 76.9 - - - +
19A VAL* 1.3 62.7 + - - +
21A LEU* 3.9 1.4 - - - +
22A HIS* 2.9 49.6 + - + +
41A TRP* 4.0 24.5 - - + -
86A TRP* 3.7 49.6 - - + -
90A ILE* 4.0 11.2 - - + -
127A ILE* 4.0 15.7 - - + -
129A CYS* 4.0 12.3 - - - -
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Residues in contact with VAL 19 (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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15A GLN 3.0 20.8 + - - +
16A ASN* 3.9 5.8 - - - +
18A ILE* 1.3 72.6 - - - +
20A ASP* 1.3 73.3 + - - +
22A HIS* 3.2 7.2 + - - +
23A ASN* 3.0 29.3 + - - +
39A MET* 3.4 28.9 - - + +
40A GLU* 4.0 6.3 - - - -
41A TRP* 3.7 33.4 - - + +
127A ILE* 4.1 14.4 - - + -
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Residues in contact with ASP 20 (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 ASN* 2.7 39.0 + - - +
17A GLU* 4.0 4.4 - - - +
19A VAL* 1.3 77.6 - - - +
21A LEU* 1.3 57.2 + - - +
23A ASN* 3.4 8.0 + - - +
24A SER* 3.0 28.8 + - - -
27A ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 21 (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 GLU 3.0 19.2 + - - +
18A ILE 3.9 3.8 - - - +
20A ASP* 1.3 72.1 - - - +
22A HIS* 1.3 67.7 + - - +
24A SER* 3.2 10.8 + - - +
25A LEU* 3.0 39.9 + - + +
87A THR* 3.5 45.1 - - + +
90A ILE* 3.6 28.5 - - + -
91A HIS* 3.8 24.7 - - + +
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Residues in contact with HIS 22 (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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18A ILE* 2.9 28.7 + - + +
19A VAL* 3.6 8.7 - - - +
21A LEU* 1.3 77.0 - - - +
23A ASN* 1.3 57.8 + - - +
25A LEU* 3.3 8.2 + - - +
26A ARG* 2.9 34.8 + - - +
39A MET* 3.7 26.7 - - + -
90A ILE* 3.5 33.4 - - + +
93A TRP* 4.9 1.6 - + - -
119A ILE* 3.9 25.7 - - + +
127A ILE* 3.4 18.3 - - + +
147A TYR* 2.8 38.9 + + - -
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Residues in contact with ASN 23 (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 VAL* 3.0 29.0 + - - +
20A ASP* 3.8 7.5 + - - +
22A HIS* 1.3 72.6 - - - +
24A SER* 1.3 65.0 + - - +
26A ARG* 3.3 5.0 + - - +
27A ARG* 2.9 41.5 + - - +
38A ARG* 3.7 9.6 - - - +
39A MET* 2.8 50.3 + - - +
178A LEU* 3.6 23.3 - - + +
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Residues in contact with SER 24 (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 ASP 3.0 15.0 + - - -
21A LEU* 3.2 19.4 + - - +
23A ASN* 1.3 75.1 - - - +
25A LEU* 1.3 62.6 + - - +
27A ARG* 3.2 13.4 + - - +
28A SER* 2.9 30.1 + - - -
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Residues in contact with LEU 25 (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 LEU* 3.0 30.3 + - + +
22A HIS* 3.6 3.6 - - - +
24A SER* 1.3 79.0 - - - +
26A ARG* 1.3 62.2 + - - +
28A SER* 3.1 17.9 + - - -
29A VAL* 3.4 15.1 + - - +
90A ILE* 3.7 29.4 - - + +
91A HIS* 4.1 21.3 - - + +
94A HIS* 3.7 53.2 + - + +
119A ILE* 4.2 11.9 - - + -
120A VAL* 4.4 3.2 - - - +
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Residues in contact with ARG 26 (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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22A HIS 2.9 24.6 + - - +
23A ASN* 3.3 9.1 + - - +
25A LEU* 1.3 76.6 - - - +
27A ARG* 1.3 60.8 + - - +
28A SER 3.5 0.2 + - - -
29A VAL* 3.6 24.9 - - - +
36A MET* 3.4 33.5 - - + +
37A LEU* 2.8 30.9 + - - +
39A MET* 3.4 28.4 - - - +
119A ILE* 2.9 32.2 + - + +
120A VAL* 3.5 4.6 - - + -
121A TRP 2.9 35.9 + - - +
122A TYR 3.2 15.6 + - - -
124A SER 3.5 14.1 + - - -
177A GLY 5.4 0.2 - - - +
178A LEU* 4.0 6.8 - - + +
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Residues in contact with ARG 27 (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 ASP 5.6 0.4 + - - -
23A ASN* 2.9 39.8 + - - +
24A SER* 3.6 9.2 - - - +
25A LEU 3.2 0.2 - - - -
26A ARG* 1.3 77.9 - - - +
28A SER* 1.3 60.5 + - - +
29A VAL* 3.5 3.9 + - - +
32A THR* 6.1 0.9 - - - +
38A ARG* 4.6 3.8 - - - +
175A ASP* 2.9 41.2 + - - +
176A ASN* 2.7 44.0 + - - +
177A GLY* 4.8 4.5 - - - -
178A LEU* 3.5 27.9 - - + +
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Residues in contact with SER 28 (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 SER* 2.9 20.0 + - - -
25A LEU* 3.1 13.9 + - - -
27A ARG* 1.3 78.7 - - - +
29A VAL* 1.3 66.3 + - - +
30A ASN* 3.6 4.9 + - - +
94A HIS* 6.1 2.9 - - - -
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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
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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