Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 1X1R
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 GLY 25 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.3 0.8 - - - -
24A VAL* 1.3 79.8 - - - +
26A LYS* 1.3 60.8 + - - +
27A SER 3.3 2.5 - - - -
28A ALA* 3.8 0.5 - - - +
29A LEU* 2.9 38.3 + - - +
126A ASN* 3.6 10.3 - - - -
1179A GDP 3.0 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.7 28.6 - - + +
19A VAL 3.5 26.9 - - - -
20A GLY* 3.1 12.7 + - - +
21A ASP 2.9 23.2 + - - -
22A GLY* 4.0 2.6 - - - -
24A VAL* 3.7 11.6 - - + +
25A GLY* 1.3 76.7 - - - +
27A SER* 1.3 56.7 + - - +
29A LEU* 3.5 5.8 + - - +
30A THR* 2.8 33.8 + - - -
67A ASP* 3.4 11.9 - - - +
68A THR* 3.2 29.4 + - - -
69A ALA* 5.3 1.5 - - - +
91A VAL* 4.3 4.9 - - + -
1179A GDP 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 1.3 72.9 - - - +
28A ALA* 1.3 60.6 + - - +
30A THR* 3.2 0.9 + - - -
31A ILE* 2.8 39.2 + - - +
42A TYR* 3.5 31.8 - - - -
46A ILE 4.7 0.7 + - - -
67A ASP* 2.6 24.9 + - - -
1179A GDP 3.0 12.1 + - - -
1180A MG 2.1 29.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.4 1.1 + - - +
27A SER* 1.3 72.6 - - - +
29A LEU* 1.3 57.6 + - - +
31A ILE* 4.0 4.5 - - - +
32A GLN* 3.0 30.8 + - - +
37A ILE 4.8 1.4 - - - +
38A PHE* 3.8 14.8 - - + -
39A VAL 4.2 13.6 + - - +
42A TYR* 5.4 0.2 - - - +
157A ALA* 3.6 15.1 - - + +
1179A GDP 2.8 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.8 2.5 - - + -
25A GLY 2.9 21.0 + - - +
26A LYS* 3.8 4.0 - - - +
28A ALA* 1.3 77.7 - - - +
30A THR* 1.3 57.5 + - - +
32A GLN* 3.4 2.0 + - - -
33A PHE* 2.9 25.5 + - - +
89A LEU* 6.2 3.1 - - + -
91A VAL* 4.0 25.6 - - + -
124A VAL* 4.2 8.7 - - + -
126A ASN* 3.5 33.7 - - - +
155A THR* 3.7 18.4 - - + +
157A ALA* 3.9 10.5 - - + +
164A VAL* 3.5 35.7 - - + +
167A THR* 6.3 1.1 - - + -
168A PHE* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.8 20.4 - - - +
26A LYS 2.8 19.5 + - - -
27A SER* 3.8 2.5 - - - -
29A LEU* 1.3 75.6 - - - +
31A ILE* 1.3 58.6 + - - +
33A PHE* 3.2 1.9 + - - +
34A PHE* 3.0 41.8 + - + +
50A TYR* 3.7 34.3 - - + -
65A VAL* 4.2 10.1 - - + -
67A ASP* 4.0 15.8 - - + +
168A PHE* 4.0 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 2.8 25.1 + - - +
28A ALA* 4.1 4.0 - - - +
30A THR* 1.3 74.6 - - - +
32A GLN* 1.3 58.0 + - - +
34A PHE* 5.0 2.5 - - - -
35A GLN* 2.6 51.3 + - + +
36A LYS 3.4 0.3 + - - -
37A ILE* 3.9 8.0 - - + +
39A VAL* 3.7 33.0 - - + -
42A TYR* 3.8 41.1 - - + -
50A TYR* 3.5 24.5 - - + +
67A ASP* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 3.0 20.7 + - - +
29A LEU* 3.6 6.1 - - - +
31A ILE* 1.3 74.5 - - - +
33A PHE* 1.3 60.3 + - - +
36A LYS* 2.9 66.3 + - - +
37A ILE 3.5 18.2 + - - +
157A ALA* 3.0 23.9 - - + +
159A ASP* 3.3 16.9 + - - +
161A PRO* 3.7 37.4 - - + +
164A VAL* 3.8 15.0 - - + -
165A ASP* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 2.9 15.4 + - - +
30A THR 3.5 7.4 - - - +
31A ILE 3.2 0.2 - - - -
32A GLN* 1.3 78.2 - - - +
34A PHE* 1.3 86.6 + + - +
36A LYS* 4.6 9.5 + - - +
52A LYS* 3.9 31.9 + - - -
54A THR* 5.3 0.9 - - + -
63A LEU* 3.8 29.4 - - + -
65A VAL* 5.2 0.2 - - + -
164A VAL* 3.7 6.3 - - + +
165A ASP* 3.3 33.2 - - - +
168A PHE* 3.5 51.8 - + + -
169A HIS* 4.0 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.0 30.3 + - + +
31A ILE 4.4 0.7 - - - +
33A PHE* 1.3 98.6 - + - +
35A GLN* 1.3 72.3 + - + +
36A LYS* 3.7 3.1 - - - +
50A TYR* 3.4 57.2 - + + -
51A LEU 4.4 1.3 - - - -
52A LYS* 3.6 49.5 + - + +
63A LEU* 4.8 4.0 - - + -
65A VAL* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 2.6 29.6 + - + +
34A PHE* 1.3 87.1 - - + +
36A LYS* 1.3 70.8 + - - +
37A ILE* 3.2 27.4 + - + +
50A TYR* 5.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE 3.4 0.4 + - - -
32A GLN* 2.9 36.3 + - - +
33A PHE 4.6 8.5 + - - +
34A PHE 4.9 2.7 - - - +
35A GLN* 1.3 80.9 - - - +
37A ILE* 1.3 62.9 + - - +
52A LYS* 6.3 1.1 - - - +
159A ASP* 4.8 2.6 - - - +
165A ASP* 3.9 23.0 + - - -
----------------------------------------------------------
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