Contacts of the helix formed by residues 20 - 31 (chain A) in PDB entry 1RFU
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 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.7 16.9 - - - +
12A SER* 3.0 25.3 + - - -
19A VAL* 1.3 73.4 - - - +
21A ASN* 1.3 67.4 + - - -
23A ALA* 3.0 11.8 + - - +
24A ALA* 3.2 12.0 + - - +
84A TYR* 5.5 0.2 - - - -
235A ASP* 3.8 17.5 + - - +
401A PLP 3.9 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 2.6 40.7 + - - +
11A GLN* 3.1 18.0 + - - +
12A SER 2.6 12.9 + - - +
13A HIS* 5.1 2.7 - - + +
20A GLY* 1.3 71.4 - - - -
22A ARG* 1.3 55.1 + - - +
24A ALA* 4.3 4.5 - - - +
25A THR* 2.6 48.3 + - - +
37A ALA* 4.3 9.4 - - + +
38A VAL 2.8 27.7 - - - +
39A ASN* 3.1 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 4.1 0.4 + - - -
13A HIS* 3.8 23.3 + - - +
14A VAL* 3.3 27.3 + - + +
15A VAL 3.6 15.4 + - - -
17A GLY 2.8 44.5 + - - +
18A TYR* 3.4 43.2 - - - -
19A VAL 3.2 13.5 - - - +
21A ASN* 1.3 79.9 - - - +
23A ALA* 1.3 56.8 + - - +
25A THR* 4.5 3.1 + - - -
26A PHE* 4.6 10.2 + - - +
25E THR* 4.9 7.7 - - - +
29E GLN* 5.4 1.6 + - - +
34E GLU* 4.7 0.2 + - - -
35E VAL* 3.0 35.0 + - - +
37E ALA* 3.6 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.6 11.4 - - + +
19A VAL* 3.5 24.6 + - - +
20A GLY 3.0 7.6 + - - +
22A ARG* 1.3 79.6 - - - +
24A ALA* 1.3 59.2 + - - +
27A PRO* 3.0 24.6 - - - +
232A GLY 4.1 15.9 - - - +
235A ASP* 4.4 3.8 - - + -
236A LEU* 3.5 15.2 - - + +
291A LEU* 5.0 0.9 - - + -
293A MET* 3.7 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 4.6 2.9 - - - +
11A GLN* 3.4 29.8 - - - +
20A GLY 3.2 8.7 + - - +
21A ASN* 3.1 3.9 + - - +
23A ALA* 1.3 76.9 - - - +
25A THR* 1.3 65.5 + - - +
27A PRO* 3.0 12.4 - - - +
28A LEU* 3.4 22.5 + - + +
81A LEU* 4.5 3.8 - - + -
235A ASP 4.2 6.1 - - - +
239A ALA* 3.7 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.6 41.0 + - - +
22A ARG* 5.2 1.6 - - - -
24A ALA* 1.3 72.4 - - - +
26A PHE* 1.3 67.3 + - - +
28A LEU* 3.5 1.0 + - - +
29A GLN* 2.9 55.4 + - + +
35A VAL* 4.3 23.5 - - + +
37A ALA* 4.8 4.4 - - + +
22E ARG* 4.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG 4.6 8.9 + - - +
25A THR* 1.3 73.8 - - - +
27A PRO* 1.3 63.8 - - + +
29A GLN* 2.9 9.1 + - - +
30A VAL* 2.7 60.5 + - + +
293A MET* 3.4 33.7 - - + -
294A VAL* 4.2 15.5 - - + -
297A LYS* 3.9 37.0 - - + -
300A ILE* 4.4 5.2 - - + -
26E PHE* 4.4 7.0 - + - -
29E GLN* 3.2 48.7 - - + +
30E VAL* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 25.1 - - - +
24A ALA* 3.0 14.8 - - - +
26A PHE* 1.3 93.9 - - + +
28A LEU* 1.3 62.6 + - - +
30A VAL* 3.3 2.5 + - + +
31A LEU* 2.9 32.1 + - + +
236A LEU* 3.2 24.5 - - + -
239A ALA* 4.6 5.2 - - + -
240A MET* 4.1 16.6 - - + +
293A MET* 4.1 8.1 - - - -
300A ILE* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.2 19.5 - - + -
9A SER* 5.3 2.2 - - - -
24A ALA* 3.4 19.7 + - + +
27A PRO* 1.3 80.3 - - - +
29A GLN* 1.3 59.3 + - - +
31A LEU* 3.3 6.5 + - - +
32A GLY 3.1 4.7 + - - -
33A PHE* 2.8 36.5 + - + +
35A VAL* 3.8 27.8 - - + -
81A LEU* 4.2 22.2 - - + -
239A ALA* 2.7 32.1 - - + +
242A LEU* 3.9 19.1 - - + -
243A ALA* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.9 49.9 + - + +
26A PHE* 2.9 9.3 + - - +
28A LEU* 1.3 72.7 - - - +
30A VAL* 1.3 64.1 + - - +
31A LEU 2.8 5.6 + - - -
32A GLY 2.9 3.3 + - - -
33A PHE 3.8 9.2 - - - +
35A VAL* 4.1 10.9 - - + +
18E TYR* 3.5 32.9 + - - +
22E ARG* 5.0 6.3 + - - +
26E PHE* 3.3 38.2 - - + +
29E GLN* 5.0 2.4 - - - +
294E VAL* 2.8 33.1 - - + +
297E LYS* 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 2.7 61.1 + - + +
27A PRO* 3.5 9.9 - - + +
29A GLN* 1.3 71.9 - - - +
31A LEU* 1.3 62.4 + - + +
32A GLY 3.4 0.2 - - - -
297A LYS* 4.3 7.0 - - + +
300A ILE* 3.9 21.5 - - + -
301A GLU* 3.8 33.2 - - + +
26E PHE* 4.1 8.5 - - + -
297E LYS* 3.7 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 2.6 33.0 + - - +
27A PRO 2.9 25.8 + - - +
28A LEU* 3.5 8.3 - - - +
29A GLN 2.8 1.0 - - - -
30A VAL* 1.3 86.5 - - + +
32A GLY* 1.3 50.7 + - - +
33A PHE* 3.6 11.0 - - + -
240A MET* 4.6 14.4 - - + -
243A ALA* 3.6 24.0 - - + -
244A TRP* 4.3 21.1 - - + -
300A ILE* 3.9 28.0 - - + +
301A GLU* 4.2 15.5 - - - +
----------------------------------------------------------
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