Contacts of the helix formed by residues 31 - 50 (chain C) in PDB entry 1RM1
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 ASP 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.4 2.5 - - - -
29C GLY 3.7 4.7 + - - +
30C ILE* 1.3 76.6 - - - +
32C GLU* 1.3 65.1 + - - +
33C GLN* 3.5 12.9 + - - +
34C THR* 3.0 37.1 + - - -
35C LEU* 3.4 6.9 + - - -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 2.9 44.7 + - - +
25C PHE* 6.3 0.2 - - - -
26C GLU* 5.1 2.1 - - - +
30C ILE 4.2 0.2 + - - -
31C ASP* 1.3 73.7 - - - +
33C GLN* 1.3 62.3 + - - +
35C LEU* 3.1 13.7 + - - +
36C GLN* 2.8 51.3 + - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 3.1 11.8 + - - +
32C GLU* 1.3 77.6 - - - +
34C THR* 1.3 58.0 + - - +
36C GLN* 3.2 16.3 + - - +
37C ASP* 2.8 56.9 + - - +
40C ASN* 4.9 3.6 + - - -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.1 8.4 - - + +
31B ARG* 4.0 27.0 + - + +
32B ILE* 3.9 17.9 - - + -
25C PHE* 4.2 1.1 - - + -
30C ILE* 3.4 32.2 - - + +
31C ASP* 3.0 16.6 + - - -
33C GLN* 1.3 74.5 - - - +
35C LEU* 1.3 66.3 + - - +
37C ASP* 3.2 11.2 + - + +
38C LEU* 3.0 21.8 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.4 40.3 - - + +
21C VAL* 3.5 26.0 - - + -
22C ARG* 3.5 37.2 - - + +
25C PHE* 3.5 32.0 - - + -
31C ASP 3.4 2.6 + - - -
32C GLU* 3.1 20.2 + - - +
34C THR* 1.3 76.9 - - - +
36C GLN* 1.3 63.0 + - - +
38C LEU* 3.1 14.1 + - + +
39C LYS* 3.1 19.2 + - - +
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.5 5.9 - - - +
22C ARG* 3.7 11.7 - - - +
32C GLU* 2.8 46.5 + - + +
33C GLN* 3.4 23.1 - - - +
35C LEU* 1.3 74.2 - - - +
37C ASP* 1.3 58.3 + - - +
39C LYS* 3.0 33.7 + - - +
40C ASN* 2.9 40.6 + - - +
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.6 4.0 - - + -
31B ARG* 2.6 35.0 + - - +
33C GLN* 2.8 44.7 + - - +
34C THR* 3.2 15.6 + - - +
36C GLN* 1.3 76.4 - - - +
38C LEU* 1.3 57.4 + - - +
40C ASN* 3.1 10.5 + - - +
41C ILE* 2.9 39.4 + - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.0 10.8 - - + -
22B ALA* 3.6 22.7 - - + -
23B LEU* 3.5 36.3 - - + +
26B LEU* 3.8 14.7 - - + +
40B VAL* 4.3 15.7 - - + -
17C VAL* 6.1 0.7 - - + -
18C VAL* 5.7 2.7 - - + -
21C VAL* 5.4 1.3 - - + -
25C PHE* 4.0 20.4 - - + -
34C THR 3.0 12.4 + - - +
35C LEU* 3.2 17.7 - - + +
37C ASP* 1.3 76.3 - - - +
39C LYS* 1.3 59.2 + - - +
41C ILE* 3.8 2.5 - - - -
42C TRP* 2.8 41.0 + - + +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.4 11.2 - - + -
15C GLU* 3.2 31.3 + - - +
18C VAL* 3.9 37.3 - - + +
22C ARG* 5.9 0.4 - - - +
35C LEU 3.1 7.7 + - - +
36C GLN* 3.0 33.6 + - - +
38C LEU* 1.3 76.6 - - - +
40C ASN* 1.3 62.2 + - - +
42C TRP* 3.3 7.5 + - - +
43C GLN* 2.8 58.9 + - - +
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Residues in contact with ASN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 4.9 2.6 + - - -
36C GLN* 2.9 29.6 + - - +
37C ASP* 3.4 16.0 - - - +
39C LYS* 1.3 82.1 - - - +
41C ILE* 1.3 62.9 + - + +
43C GLN* 3.2 19.0 + - - +
44C LYS* 2.9 29.5 + - - +
60C PHE* 3.8 9.8 - - + -
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 3.6 25.4 - - + +
25B THR* 3.6 15.7 - - + +
26B LEU* 3.5 34.3 - - + -
31B ARG* 4.2 9.9 - - - +
37C ASP* 2.9 26.0 + - + +
38C LEU 4.0 0.9 - - - +
40C ASN* 1.3 73.1 - - + +
42C TRP* 1.3 61.3 + - - +
44C LYS* 3.7 17.2 - - - +
45C LYS* 2.9 47.8 + - - +
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Residues in contact with TRP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.1 44.4 + - + +
18B SER* 4.0 6.3 - - - -
19B LEU* 3.4 50.1 - - + +
22B ALA* 3.6 10.5 - - + +
44B PHE* 4.1 8.5 - + - -
13C ILE* 4.2 0.9 - - + -
14C VAL* 3.6 36.8 - - + -
17C VAL* 3.6 41.3 - - + -
18C VAL* 4.8 4.0 - - + -
38C LEU* 2.8 30.4 + - + +
39C LYS* 3.4 10.1 - - - +
41C ILE* 1.3 78.2 - - - +
43C GLN* 1.3 62.7 + - + +
45C LYS* 3.5 3.6 + - - +
46C LEU* 3.1 25.2 + - + +
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Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.5 5.5 - - + +
15C GLU* 4.0 8.0 - - - +
39C LYS* 2.8 46.0 + - + +
40C ASN* 3.5 20.9 - - - +
42C TRP* 1.3 74.9 - - + +
44C LYS* 1.3 64.4 + - - +
46C LEU* 3.3 3.0 + - - +
47C THR* 3.0 18.4 + - - -
56C TRP* 3.1 68.9 + - + +
59C GLN* 4.9 5.7 - - - +
60C PHE* 4.0 15.2 - - + -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASN 2.9 16.8 + - - +
41C ILE* 3.7 16.9 - - - +
43C GLN* 1.3 73.8 - - - +
45C LYS* 1.3 84.5 + - - +
47C THR* 3.1 4.9 + - - -
48C GLU* 2.9 50.2 + - + +
60C PHE* 3.6 35.4 - - + -
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.8 28.5 - - - +
21B ASP* 3.7 31.6 + - + +
22B ALA 4.3 1.8 - - - +
25B THR* 4.5 11.2 - - - +
41C ILE* 2.9 41.2 + - + +
42C TRP 3.6 4.7 - - - +
44C LYS* 1.3 87.1 - - - +
46C LEU* 1.3 64.3 + - - +
48C GLU* 3.1 30.8 + - - +
49C THR* 3.2 17.0 + - + +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 4.2 7.0 - - + +
15B ILE* 3.7 35.2 - - + +
18B SER* 3.8 14.4 - - - +
10C TYR* 4.1 17.5 - - + -
14C VAL* 4.1 17.7 - - + -
42C TRP* 3.1 20.0 + - + +
43C GLN* 3.5 8.3 - - - +
44C LYS 3.2 0.2 - - - -
45C LYS* 1.3 79.3 - - - +
47C THR* 1.3 59.7 + - - +
49C THR* 2.6 24.7 + - - -
50C LYS 3.5 2.4 + - - -
54C PHE* 3.5 25.5 - - + -
56C TRP* 3.6 26.5 - - + -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLN 3.0 6.0 + - - -
44C LYS 3.1 8.5 + - - -
46C LEU* 1.3 74.4 - - - +
48C GLU* 1.3 63.9 + - + +
50C LYS* 3.2 24.9 + - + +
52C THR 5.7 0.2 - - - -
54C PHE* 4.0 5.4 - - - -
56C TRP* 3.0 20.8 + - - -
57C ASP* 2.6 35.1 + - + +
60C PHE* 4.0 30.4 - - + +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS* 2.9 48.6 + - + +
45C LYS* 3.1 28.3 + - - +
47C THR* 1.3 77.5 - - + +
49C THR* 1.3 61.6 + - + +
50C LYS* 3.6 16.1 + - - +
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.7 20.5 - - + +
18B SER* 4.0 15.5 - - - +
45C LYS 3.2 16.4 - - - +
46C LEU* 2.6 16.6 + - - +
48C GLU* 1.3 75.4 - - + +
50C LYS* 1.3 72.2 + - - +
51C VAL* 3.4 23.2 + - - +
239C PRO* 6.3 3.1 - - - -
271C ARG* 4.6 16.8 + - - +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU 3.5 1.6 + - - -
47C THR* 3.2 19.7 + - + +
48C GLU* 3.7 15.9 - - - +
49C THR* 1.3 83.0 + - - +
51C VAL* 1.3 61.8 + - - +
52C THR 3.2 11.1 + - - +
271C ARG* 3.4 9.8 - - - +
272C ASN* 3.9 5.9 + - - -
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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