Contacts of the helix formed by residues 11 - 33 (chain A) in PDB entry 2RMH
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.2 16.2 - - - +
10A VAL* 1.3 91.3 - - - +
12A THR* 1.3 53.8 - - - +
13A ASN* 3.1 11.4 - - + +
14A ILE* 2.7 37.4 + - + +
15A MET* 2.4 35.9 + - - -
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Residues in contact with THR 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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11A PRO* 1.3 72.6 - - - +
13A ASN* 1.3 63.9 + - - +
15A MET* 4.1 7.0 - - + -
16A ASN* 2.6 53.0 + - - +
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Residues in contact with ASN 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 PRO* 3.1 10.5 + - + +
12A THR* 1.3 82.7 + - - +
14A ILE* 1.3 60.4 + - + +
16A ASN* 4.6 2.3 - - - +
17A LEU* 3.1 32.2 + - + +
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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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4A PHE* 4.2 20.9 - - + -
9A ASP* 3.5 32.3 - - - +
10A VAL* 3.6 14.6 - - + -
11A PRO* 2.7 36.6 + - + +
13A ASN* 1.3 75.1 - - + +
15A MET* 1.3 55.9 + - - +
16A ASN 3.3 1.3 - - - -
17A LEU* 3.0 8.7 + - + +
18A LEU* 2.5 41.7 + - + +
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Residues in contact with MET 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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10A VAL* 3.5 28.7 - - + +
11A PRO 2.4 19.6 + - - +
12A THR* 4.0 7.9 - - + +
14A ILE* 1.3 73.4 - - - +
16A ASN* 1.3 55.4 + - - +
18A LEU* 3.6 10.3 - - + +
19A PHE* 2.5 73.7 + - + +
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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 THR* 2.6 45.8 + - - +
13A ASN* 4.9 2.5 - - - +
15A MET* 1.3 79.0 - - - +
17A LEU* 1.3 60.7 + - + +
19A PHE* 3.4 7.1 + - - +
20A ASN* 2.8 31.4 + - - +
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Residues in contact with LEU 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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13A ASN 3.1 22.9 + - - +
14A ILE* 3.0 14.1 + - + +
16A ASN* 1.3 77.5 - - + +
18A LEU* 1.3 56.3 + - - +
20A ASN* 3.0 7.7 + - + +
21A ILE* 2.6 46.0 + - + +
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Residues in contact with LEU 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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10A VAL* 3.8 27.8 - - + -
14A ILE* 2.5 24.6 + - + +
15A MET* 4.0 13.9 - - + +
17A LEU* 1.3 71.2 - - - +
19A PHE* 1.3 60.3 + - + +
21A ILE* 3.6 7.7 - - + +
22A ALA* 2.8 45.0 + - + +
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Residues in contact with PHE 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 MET* 2.5 51.1 + - + +
16A ASN* 3.6 6.5 - - - +
18A LEU* 1.3 79.5 - - + +
20A ASN* 1.3 58.6 + - - +
22A ALA* 3.9 4.6 - - + +
23A LYS* 2.9 36.9 + - + +
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Residues in contact with ASN 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 2.8 18.7 + - - +
17A LEU* 3.4 8.5 - - + +
19A PHE* 1.3 74.9 - - - +
21A ILE* 1.3 56.5 + - + +
23A LYS* 2.9 11.2 + - - +
24A ALA* 2.7 40.6 + - - +
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Residues in contact with ILE 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 LEU* 2.6 29.6 + - + +
18A LEU* 3.6 8.3 - - + +
20A ASN* 1.3 74.1 - - + +
22A ALA* 1.3 57.6 + - - +
24A ALA* 3.1 4.0 + - + +
25A LYS* 2.6 51.1 + - + +
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Residues in contact with ALA 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 LEU* 2.8 28.1 + - + +
19A PHE* 4.0 5.2 - - + +
21A ILE* 1.3 77.1 - - + +
23A LYS* 1.3 50.2 + - - +
25A LYS* 4.3 5.2 - - - -
26A ASN* 2.7 43.4 + - - +
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Residues in contact with LYS 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 PHE* 2.9 23.3 + - + +
20A ASN* 2.9 19.9 + - - +
22A ALA* 1.3 76.5 - - - +
24A ALA* 1.3 57.0 + - - +
26A ASN* 2.7 27.7 + - - +
27A LEU* 2.9 47.0 + - + +
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Residues in contact with ALA 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 ASN* 2.7 21.2 + - - +
21A ILE* 4.0 4.7 - - + +
23A LYS* 1.3 70.5 - - - +
25A LYS* 1.3 59.4 + - - +
27A LEU* 3.6 11.6 - - + +
28A ARG* 3.0 31.7 + - - +
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Residues in contact with LYS 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 ILE* 2.6 36.2 + - + +
22A ALA* 4.1 4.5 - - - +
24A ALA* 1.3 73.7 - - - +
26A ASN* 1.3 57.5 + - - +
28A ARG* 3.7 3.7 - - - +
29A ALA* 2.8 37.0 + - + +
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Residues in contact with ASN 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 ALA* 2.7 27.5 + - + +
23A LYS* 2.7 33.4 + - - +
25A LYS* 1.3 73.8 - - - +
27A LEU* 1.3 57.6 + - - +
29A ALA* 3.4 6.7 - - - +
30A GLN* 2.6 68.2 + - - +
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Residues in contact with LEU 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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23A LYS* 2.9 51.9 + - + +
24A ALA* 3.6 9.4 - - + +
25A LYS 3.3 0.2 - - - -
26A ASN* 1.3 84.2 - - - +
28A ARG* 1.3 57.0 + - - +
30A GLN* 3.4 16.9 + - - +
31A ALA* 2.9 31.0 + - - +
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Residues in contact with ARG 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 ALA 3.0 14.3 + - - +
25A LYS* 4.0 3.6 - - - +
27A LEU* 1.3 77.9 - - - +
29A ALA* 1.3 58.4 + - - +
31A ALA* 4.1 5.8 - - + -
32A ALA* 2.7 67.5 + - + +
39A ALA* 4.2 15.3 + - + +
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Residues in contact with ALA 29 (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 LYS* 2.8 28.7 + - + +
26A ASN* 3.1 9.4 + - - +
28A ARG* 1.3 77.1 - - - +
30A GLN* 1.3 57.3 + - - +
33A ALA* 2.8 42.4 + - + +
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Residues in contact with GLN 30 (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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26A ASN* 2.6 57.2 + - - +
27A LEU* 3.4 15.6 - - - +
29A ALA* 1.3 72.8 - - - +
31A ALA* 1.3 53.5 + - + +
34A ASN* 2.8 41.0 + - + +
38A MET* 4.2 4.4 - - + +
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Residues in contact with ALA 31 (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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27A LEU 2.9 19.8 + - - +
28A ARG* 3.9 5.4 - - + +
30A GLN* 1.3 82.3 - - + +
32A ALA* 1.3 63.4 + - + +
33A ALA 3.5 0.4 - - - -
34A ASN* 3.9 5.7 + - - +
35A ALA 4.4 0.5 + - - -
38A MET* 2.8 48.7 + - + +
39A ALA* 4.5 6.7 - - + -
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Residues in contact with ALA 32 (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 ARG* 2.7 58.0 + - - +
31A ALA* 1.3 75.0 - - - +
33A ALA* 1.3 57.6 + - + +
34A ASN 3.6 0.7 - - - -
36A HIS* 3.9 18.4 - - - +
37A LEU 5.6 0.2 - - - +
38A MET 5.3 0.9 - - - +
39A ALA* 3.9 12.8 - - + +
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Residues in contact with ALA 33 (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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29A ALA* 2.8 25.4 + - + +
32A ALA* 1.3 77.9 - - + +
34A ASN* 1.3 63.5 + - - +
35A ALA 3.9 0.2 - - - -
36A HIS* 4.4 3.9 - - - +
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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