Contacts of the helix formed by residues 33 - 55 (chain B) 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 GLU 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.7 0.4 - - - -
30B GLY 5.6 1.4 - - - +
32B ILE* 1.3 85.1 - - - +
34B ALA* 1.3 67.4 + - - +
35B SER* 3.1 18.4 - - - +
36B LEU* 3.0 19.2 + - + +
37B ALA* 3.2 8.3 + - - +
28C ALA* 6.5 0.9 - - + -
30C ILE* 5.2 5.0 - - + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.9 30.5 - - + +
32B ILE 4.1 0.8 + - - -
33B GLU* 1.3 72.9 + - - +
35B SER* 1.3 56.9 + - - +
37B ALA* 3.0 4.2 + - - +
38B MET* 2.9 31.0 + - + +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 3.6 15.3 - - - +
34B ALA* 1.3 78.9 - - - +
36B LEU* 1.3 63.0 + - - +
38B MET* 3.3 8.5 + - - +
39B ARG* 3.0 22.9 + - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.9 18.2 - - + -
33B GLU* 3.0 16.8 + - + +
35B SER* 1.3 82.3 + - - +
37B ALA* 1.3 62.2 + - - +
39B ARG* 3.3 6.9 + - + +
40B VAL* 3.0 29.0 + - + +
24C ASP* 4.0 30.1 - - + +
25C PHE* 4.0 33.9 - - + -
28C ALA* 4.1 12.6 - - + -
30C ILE* 3.5 32.5 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.7 30.1 - - + +
27B ILE* 3.6 30.3 - - + -
32B ILE* 4.3 5.8 - - + +
33B GLU 3.2 6.2 + - - +
34B ALA 3.0 10.8 + - - +
36B LEU* 1.3 77.2 - - - +
38B MET* 1.3 61.0 + - + +
40B VAL* 3.1 7.3 + - - +
41B LEU* 3.0 24.0 + - + +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 3.8 19.5 - - - +
34B ALA* 2.9 14.3 + - + +
35B SER* 3.3 11.6 + - - +
37B ALA* 1.3 76.0 - - - +
39B ARG* 1.3 60.2 + - - +
41B LEU* 3.2 31.1 + - + +
42B GLU* 2.8 44.7 + - - +
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 3.0 13.6 + - - +
36B LEU* 3.5 15.9 - - + +
37B ALA 3.2 0.2 - - - -
38B MET* 1.3 76.2 - - - +
40B VAL* 1.3 61.8 + - - +
42B GLU* 3.4 32.5 + - - +
43B THR* 3.1 31.5 + - - +
21C VAL* 5.4 0.7 - - - -
24C ASP* 2.9 43.1 + - + +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.0 15.7 - - + -
23B LEU* 3.8 28.0 - - + -
36B LEU* 3.0 22.6 + - + +
37B ALA 3.1 7.8 + - - +
39B ARG* 1.3 76.7 - - - +
41B LEU* 1.3 58.2 + - - +
43B THR* 3.2 3.1 + - - -
44B PHE* 2.9 26.7 + - - +
17C VAL* 4.1 16.2 - - + +
21C VAL* 4.0 17.5 - - + -
25C PHE* 3.9 28.0 - - + -
38C LEU* 4.3 6.5 - - + -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 3.7 30.8 + - + +
16B GLY 5.1 0.7 - - - +
19B LEU* 3.5 15.7 - - + -
20B VAL* 4.0 27.6 - - + -
23B LEU* 3.4 27.6 - - + -
37B ALA* 3.0 15.5 + - + +
38B MET* 3.2 38.8 + - + +
40B VAL* 1.3 77.0 - - - +
42B GLU* 1.3 56.0 + - - +
44B PHE* 3.2 7.6 - - + +
45B ASP* 3.0 31.7 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 5.1 3.1 - - - -
8B GLU* 5.8 0.4 - - - +
11B ARG* 3.5 13.5 + - - +
38B MET* 2.8 30.4 + - - +
39B ARG* 3.7 32.6 + - - +
40B VAL 3.3 0.2 - - - -
41B LEU* 1.3 73.3 - - - +
43B THR* 1.3 63.4 + - - +
45B ASP* 3.6 12.5 + - - +
46B LYS* 3.6 16.5 + - - +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 3.1 31.9 + - - +
40B VAL 3.2 7.6 + - - -
42B GLU* 1.3 74.7 - - - +
44B PHE* 1.3 68.2 + - - +
46B LYS* 3.1 10.3 + - + +
47B VAL* 2.9 31.4 + - + +
17C VAL* 4.5 4.0 - - + +
20C GLU* 3.2 42.1 + - + +
21C VAL* 3.8 17.3 - - + +
24C ASP* 4.5 1.4 + - - -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.5 29.8 - - + -
11B ARG* 3.9 8.7 - - + -
15B ILE* 4.1 9.4 - - + -
16B GLY* 3.3 33.9 - - - -
19B LEU* 3.8 24.5 - - + -
40B VAL 2.9 13.3 + - - +
41B LEU* 3.2 11.9 - - + +
43B THR* 1.3 77.1 - - - +
45B ASP* 1.3 75.0 + - - +
46B LYS 3.2 0.2 + - - -
47B VAL* 3.2 0.7 + - - +
48B VAL* 2.8 56.8 + - + +
13C ILE* 4.0 16.8 - - + -
17C VAL* 4.0 13.2 - - + +
42C TRP* 4.1 14.6 - + - -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 3.9 16.6 - - + +
7B TYR 3.5 25.0 - - - +
8B GLU* 3.5 10.3 - - - +
10B TYR* 4.9 4.7 - - - +
11B ARG* 2.8 56.3 + - - +
41B LEU 3.0 9.0 + - - +
42B GLU* 3.7 10.7 - - - +
43B THR 3.2 0.4 - - - -
44B PHE* 1.3 81.3 - - - +
46B LYS* 1.3 62.6 + - - +
48B VAL* 3.7 4.1 + - - +
49B ALA* 3.3 21.1 + - - +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 3.4 51.8 - - + +
42B GLU 3.6 7.0 + - - +
43B THR* 3.1 13.7 + - + +
45B ASP* 1.3 77.1 - - - +
47B VAL* 1.3 69.9 + - + +
49B ALA* 3.1 4.5 + - - +
50B GLU* 2.9 60.4 + - - +
20C GLU* 3.8 20.4 + - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 2.9 19.0 + - + +
44B PHE 3.7 3.1 - - - +
46B LYS* 1.3 78.4 - - + +
48B VAL* 1.3 55.6 + - - +
50B GLU* 3.4 10.1 + - - +
51B THR* 2.5 48.4 + - - +
13C ILE* 3.9 9.4 - - + +
16C SER* 3.7 24.7 - - - -
17C VAL* 3.8 22.7 - - + -
20C GLU* 3.8 32.8 - - + +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.8 24.0 - - + -
15B ILE* 5.6 2.9 - - + -
44B PHE* 2.8 61.1 + - + +
45B ASP 4.0 3.1 - - - +
47B VAL* 1.3 72.8 - - - +
49B ALA* 1.3 58.9 + - - +
51B THR* 4.0 0.2 - - - -
52B LEU* 2.9 52.7 + - + +
13C ILE* 4.1 21.8 - - + -
266C VAL* 5.7 2.0 - - + -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 4.0 21.3 - - + -
10B TYR* 4.7 16.1 - - + -
45B ASP 3.3 11.2 + - - +
46B LYS 3.1 9.5 + - - +
48B VAL* 1.3 80.7 - - - +
50B GLU* 1.3 59.5 + - + +
52B LEU* 4.2 3.5 - - - +
53B LYS* 3.3 27.5 + - - +
247C LEU* 6.4 2.2 - - + -
264C ASP* 4.7 3.8 - - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 4.1 10.2 + - + -
46B LYS* 2.9 56.0 + - + +
47B VAL* 3.9 8.7 - - - +
49B ALA* 1.3 79.4 - - + +
51B THR* 1.3 60.6 + - - +
53B LYS* 3.3 6.4 + - - +
54B ASP* 3.0 41.5 + - - +
20C GLU* 6.0 0.2 - - - -
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Residues in contact with THR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 2.5 35.3 + - - +
48B VAL 4.0 2.0 - - - -
50B GLU* 1.3 78.9 - - - +
52B LEU* 1.3 58.3 + - - +
55B ASN* 2.9 43.6 + - + +
9C VAL* 3.8 22.1 - - + +
12C ILE* 3.8 24.2 - - + +
13C ILE* 3.6 25.4 - - + +
16C SER* 5.2 0.5 + - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR* 3.4 41.3 - - + -
48B VAL* 2.9 32.0 + - + +
49B ALA* 4.3 2.2 - - - +
51B THR* 1.3 76.6 - - - +
53B LYS* 1.3 55.3 + - - +
56B THR* 2.7 40.4 - - - +
9C VAL* 4.2 16.2 - - + -
13C ILE* 5.8 0.2 - - + -
264C ASP* 3.6 24.3 - - + +
265C GLY* 3.7 23.1 - - - +
266C VAL* 4.6 4.9 - - + -
275C THR* 4.2 19.3 - - + -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA 3.3 18.8 + - - +
50B GLU* 3.3 8.0 + - - +
51B THR 3.2 0.6 - - - -
52B LEU* 1.3 81.0 - - - +
54B ASP* 1.3 71.0 + - - +
56B THR* 4.8 0.4 - - - -
247C LEU* 5.7 4.7 - - - +
263C LYS* 6.2 0.7 - - - -
264C ASP* 3.6 25.3 - - - +
277C GLN* 4.0 17.5 + - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLU* 3.0 24.3 + - - +
53B LYS* 1.3 96.4 - - - +
55B ASN* 1.3 71.1 + - - +
56B THR 3.7 2.9 - - - -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 2.9 36.2 + - + +
54B ASP* 1.3 88.7 + - - +
56B THR* 1.3 59.5 + - - +
57B GLN* 5.7 0.4 - - - -
5C GLU* 4.2 7.1 - - - +
8C ARG* 3.6 33.4 + - + +
9C VAL* 3.6 17.1 - - + +
12C ILE* 3.6 23.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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