Contacts of the helix formed by residues 13 - 29 (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 SER 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 2.6 23.6 + - - +
12B ARG* 1.3 79.5 - - - +
14B THR* 1.3 60.0 + - - +
15B ILE* 3.5 12.1 - - - +
16B GLY 3.2 10.7 + - - -
17B ASN* 2.8 30.8 + - - +
44B PHE* 4.4 0.2 - - - -
48B VAL* 6.0 0.3 - - - +
243C LEU* 5.8 0.2 - - - -
245C LEU* 3.3 18.6 - - - +
266C VAL* 4.1 24.2 - - - +
268C THR* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 1.3 74.7 - - - +
15B ILE* 1.3 62.3 + - - +
17B ASN* 3.9 4.2 - - - +
18B SER* 3.1 27.5 + - - -
10C TYR* 3.9 1.1 + - - -
46C LEU* 4.5 5.8 - - + -
49C THR* 3.7 33.9 - - + +
51C VAL* 3.8 18.0 - - + +
266C VAL* 5.7 0.4 - - - +
268C THR* 3.0 19.2 + - - +
273C ASP* 2.7 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.5 12.1 - - - +
14B THR* 1.3 78.4 - - - +
16B GLY* 1.3 65.7 + - - +
18B SER* 3.5 0.9 + - - -
19B LEU* 3.2 8.0 + - - +
44B PHE* 4.1 11.9 - - + -
48B VAL* 5.5 2.5 - - + -
10C TYR* 3.5 58.1 + - + +
13C ILE* 3.5 37.9 - - + -
14C VAL* 4.1 7.2 - - + -
42C TRP* 3.1 32.0 + - + +
46C LEU* 3.7 14.1 - - + +
266C VAL* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR 3.8 7.6 - - - -
11B ARG* 3.4 7.4 - - - +
13B SER* 3.2 5.7 + - - -
15B ILE* 1.3 80.8 - - - +
17B ASN* 1.3 65.0 + - - +
19B LEU* 3.4 5.7 + - - +
20B VAL* 3.1 26.0 + - - +
41B LEU* 5.1 0.3 - - - +
44B PHE* 3.3 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG 3.3 13.4 + - - -
12B ARG* 4.1 14.5 + - - +
13B SER 2.8 16.4 + - - +
14B THR* 3.9 4.7 - - - +
16B GLY* 1.3 77.6 - - - +
18B SER* 1.3 57.4 + - - +
20B VAL* 3.2 10.1 + - - +
21B ASP* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.1 18.9 + - - -
15B ILE 3.7 5.2 - - - -
17B ASN* 1.3 75.2 - - - +
19B LEU* 1.3 58.7 + - - +
21B ASP* 3.2 11.5 + - - +
22B ALA* 3.0 28.4 + - - +
42C TRP* 4.0 11.8 - - - -
45C LYS* 3.8 27.9 - - - +
46C LEU* 3.8 16.8 + - - +
49C THR* 4.0 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE 3.2 8.1 + - - +
16B GLY* 3.5 9.9 - - - +
17B ASN 3.2 0.2 - - - -
18B SER* 1.3 72.7 - - - +
20B VAL* 1.3 61.6 + - - +
22B ALA* 3.3 1.0 + - - +
23B LEU* 2.8 43.3 + - + +
40B VAL* 4.0 12.8 - - + -
41B LEU* 3.5 27.4 - - + -
44B PHE* 3.8 29.6 - - + -
38C LEU* 4.0 21.1 - - + -
42C TRP* 3.4 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 4.6 11.9 - - + +
16B GLY 3.1 16.4 + - - +
17B ASN* 3.5 15.3 - - - +
18B SER 3.2 0.4 - - - -
19B LEU* 1.3 76.9 - - - +
21B ASP* 1.3 59.5 + - - +
23B LEU* 3.4 6.7 + - - +
24B ASP* 2.9 49.4 + - - +
41B LEU* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 3.0 26.0 + - - +
18B SER* 3.3 14.3 + - - +
19B LEU 3.2 0.2 - - - -
20B VAL* 1.3 77.6 - - - +
22B ALA* 1.3 65.8 + - - +
24B ASP* 3.1 15.1 + - - +
25B THR* 2.9 21.8 + - - +
45C LYS* 3.7 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER 3.0 16.5 + - - +
19B LEU 3.7 2.2 - - - +
21B ASP* 1.3 76.4 - - - +
23B LEU* 1.3 63.1 + - - +
25B THR* 3.0 18.2 + - - -
26B LEU* 3.3 12.1 + - - +
38C LEU* 3.6 22.9 - - + -
41C ILE* 3.6 30.4 - - + +
42C TRP* 3.6 17.0 - - + +
45C LYS* 4.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.8 26.1 + - + +
20B VAL* 3.6 5.6 - - - +
22B ALA* 1.3 77.7 - - - +
24B ASP* 1.3 60.4 + - - +
26B LEU* 3.5 4.7 + - + +
27B ILE* 3.1 29.6 + - + +
32B ILE* 3.9 16.1 - - + +
37B ALA* 3.7 29.8 - - + +
40B VAL* 3.8 13.9 - - + -
41B LEU* 3.4 34.5 - - + -
38C LEU* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 2.9 38.4 + - - +
21B ASP* 3.1 8.4 + - - +
23B LEU* 1.3 76.0 - - - +
25B THR* 1.3 60.6 + - + +
27B ILE* 3.2 19.9 + - - +
28B SER* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP 2.9 21.5 + - - +
22B ALA* 3.0 11.0 + - - +
24B ASP* 1.3 76.2 - - + +
26B LEU* 1.3 62.1 + - - +
28B SER* 3.0 7.0 + - - -
29B ASP* 2.9 38.6 + - - +
31B ARG* 5.0 1.2 + - - -
41C ILE* 3.6 23.7 - - + +
45C LYS* 4.5 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.3 12.5 + - - +
23B LEU* 3.8 2.2 - - + +
24B ASP 3.3 0.6 - - - -
25B THR* 1.3 81.6 + - - +
27B ILE* 1.3 58.3 + - - +
29B ASP* 3.5 3.0 + - - -
30B GLY 3.1 2.1 + - - -
31B ARG* 2.7 76.0 + - + +
32B ILE* 3.5 28.7 + - + -
25C PHE* 5.5 0.9 - - + -
34C THR* 4.1 20.0 - - + +
37C ASP* 4.6 1.3 - - + -
38C LEU* 3.8 34.3 - - + -
41C ILE* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.1 16.4 + - + +
24B ASP* 3.5 22.4 - - - +
25B THR 3.2 0.2 - - - -
26B LEU* 1.3 77.8 - - - +
28B SER* 1.3 58.9 + - - +
30B GLY* 2.9 19.4 + - - -
32B ILE* 3.9 26.0 - - + +
34B ALA* 3.9 26.9 - - + +
37B ALA* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP 2.9 13.8 + - - -
25B THR* 3.0 18.5 + - - -
27B ILE* 1.3 78.6 - - - +
29B ASP* 1.3 64.8 + - - +
30B GLY* 3.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 2.9 28.1 + - - +
26B LEU 3.8 5.2 - - - +
27B ILE 3.2 0.2 - - - -
28B SER* 1.3 84.6 + - - +
30B GLY* 1.3 61.6 + - - +
31B ARG* 3.5 37.1 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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