Contacts of the helix formed by residues 21 - 30 (chain A) in PDB entry 1RRM
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 ALA 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.5 48.5 - - + +
17A GLY 4.4 0.6 + - - -
18A ALA 3.0 13.3 + - - +
19A VAL 3.0 1.2 - - - -
20A GLY* 1.3 78.9 - - - +
22A LEU* 1.3 63.5 + - - +
23A THR 3.5 0.4 - - - -
24A ASP* 3.4 11.0 + - + +
25A GLU* 3.1 22.2 + - - +
176A PHE* 3.8 2.5 - - + -
3B ALA* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.0 17.6 + - + +
21A ALA* 1.3 78.1 - - - +
23A THR* 1.3 69.8 + - + +
25A GLU* 3.1 4.2 + - - +
26A VAL* 3.0 37.2 + - + +
51A VAL* 4.6 7.9 - - + +
54A LYS* 6.2 0.7 - - + -
55A MSE 4.0 32.5 - - + -
93A ILE* 4.4 13.0 - - + -
136A LEU* 4.2 9.4 - - + -
138A ILE* 3.6 31.2 - - + -
176A PHE* 3.5 33.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 4.7 0.6 + - - +
20A GLY 4.3 9.1 + - - -
21A ALA 3.5 0.2 - - - -
22A LEU* 1.3 82.2 - - + +
24A ASP* 1.3 63.7 + - - +
26A VAL* 3.3 2.4 + - - +
27A LYS* 3.0 32.9 + - - +
54A LYS* 3.6 28.0 - - + +
55A MSE 4.0 4.0 - - - +
58A ALA* 3.6 33.7 - - + +
60A LEU* 3.7 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 5.9 2.1 - - - -
20A GLY 5.5 0.9 - - - +
21A ALA* 3.4 11.8 + - - +
22A LEU 3.2 0.6 - - - -
23A THR* 1.3 81.5 + - - +
25A GLU* 1.3 62.0 + - - +
27A LYS* 3.3 10.7 + - - +
28A ARG* 2.9 75.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 4.2 9.8 - - - +
13A TRP* 2.9 35.8 + - - +
21A ALA 3.1 14.4 + - - +
22A LEU 3.1 7.9 + - - +
24A ASP* 1.3 77.3 - - - +
26A VAL* 1.3 63.4 + - - +
28A ARG* 3.5 23.7 + - - +
29A ARG* 3.1 64.3 + - - +
136A LEU* 4.9 3.4 - - + -
174A VAL* 4.4 4.3 - - + -
176A PHE* 3.9 19.5 - - + -
5B ARG* 4.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.0 30.4 + - + +
23A THR 3.6 6.7 - - - +
25A GLU* 1.3 76.4 - - - +
27A LYS* 1.3 63.0 + - - +
29A ARG* 3.1 3.7 + - - +
30A GLY 3.1 17.3 + - - -
31A TYR* 3.5 30.1 + - + +
60A LEU* 3.9 21.8 - - + -
91A TYR* 3.4 35.7 - - + +
136A LEU* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.0 19.3 + - - +
24A ASP* 3.3 10.1 + - - +
26A VAL* 1.3 77.1 - - - +
28A ARG* 1.3 61.2 + - + +
30A GLY* 3.2 13.8 + - - +
31A TYR 5.8 0.7 - - - -
58A ALA* 3.3 44.6 + - - +
60A LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 5.6 2.0 - - - -
24A ASP* 2.9 49.1 + - - +
25A GLU* 3.8 23.4 + - - +
26A VAL 3.3 0.2 - - - -
27A LYS* 1.3 76.3 - - + +
29A ARG* 1.3 63.2 + - + +
5B ARG* 3.9 22.0 - - - +
129B ASN 4.5 11.4 - - - +
168B PRO* 5.2 5.5 - - - +
169B HIS* 5.1 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 5.3 7.1 + - - -
11A THR* 3.5 19.2 + - - -
25A GLU* 3.1 39.7 + - - +
26A VAL* 3.1 3.2 + - - +
27A LYS 3.1 0.6 - - - -
28A ARG* 1.3 80.3 - - + +
30A GLY* 1.3 63.4 + - - +
31A TYR* 3.3 49.5 + - + +
136A LEU* 5.0 2.9 - - - -
173A GLN* 4.6 8.9 + - - +
174A VAL* 3.4 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 3.1 5.1 + - - -
27A LYS* 3.2 12.0 + - - -
28A ARG 3.4 0.8 + - - -
29A ARG* 1.3 78.7 - - - +
31A TYR* 1.3 67.4 + - - +
32A GLN* 3.1 19.9 + - - +
90A ASP* 4.6 0.5 - - - +
----------------------------------------------------------
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