Contacts of the helix formed by residues 43 - 54 (chain A) in PDB entry 2G5W
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 ASN 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 3.1 23.3 + - - +
37A ALA* 3.8 1.6 - - - +
38A LEU* 3.8 11.5 - - - +
41A VAL 3.7 13.7 + - - +
42A PRO* 1.3 75.8 - - - +
44A ALA* 1.3 67.6 + - - +
45A ALA* 3.3 18.8 + - - +
46A LEU* 3.1 31.8 + - - +
47A ALA* 3.2 10.4 + - - +
91A GLN* 3.4 15.6 + - - +
92A VAL* 4.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 1.3 74.3 - - - +
45A ALA* 1.3 51.8 + - - +
47A ALA* 3.2 6.2 + - - +
48A GLU* 2.7 36.8 + - - +
91A GLN* 3.6 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 5.2 2.2 - - + -
43A ASN* 3.2 13.9 + - - +
44A ALA* 1.3 78.1 - - - +
46A LEU* 1.3 57.0 + - + +
48A GLU* 3.3 8.4 + - - +
49A TYR* 2.8 31.2 + - - +
375A PRO* 3.9 40.2 - - + +
379A TYR* 3.6 10.0 - - + -
380A THR* 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.8 20.4 - - + -
37A ALA* 3.8 17.5 - - + +
42A PRO* 4.1 20.2 - - + -
43A ASN* 3.1 32.7 + - - +
45A ALA* 1.3 73.6 - - - +
47A ALA* 1.3 67.7 + - - +
49A TYR 3.1 0.7 + - - -
50A TYR* 2.9 37.0 + - + -
63A GLU* 3.5 28.9 - - - +
78A PRO* 4.7 0.7 - - + -
89A TRP* 4.2 14.1 - - + -
92A VAL* 4.0 8.1 - - + -
379A TYR* 3.4 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN 3.2 8.4 + - - +
44A ALA* 3.2 11.8 + - - +
46A LEU* 1.3 77.7 - - - +
48A GLU* 1.3 57.9 + - - +
50A TYR* 4.0 0.9 - - - +
51A ALA* 2.9 33.9 + - - +
91A GLN* 4.0 16.6 - - + +
92A VAL* 3.6 33.0 - - + +
95A ALA* 4.2 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 2.7 20.7 + - - +
45A ALA* 3.4 8.5 - - - +
47A ALA* 1.3 73.0 - - - +
49A TYR* 1.3 57.1 - - - +
51A ALA* 3.6 5.0 - - - +
52A GLN* 3.0 67.1 + - - +
380A THR* 3.7 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.8 3.6 - - + +
32A MET* 4.3 19.8 + - - +
34A ARG* 3.3 42.3 + - + +
45A ALA 2.8 20.4 + - - +
46A LEU 3.1 0.8 + - - +
48A GLU* 1.3 73.5 - - - +
50A TYR* 1.3 99.6 + + - +
52A GLN* 3.6 1.2 - - - +
53A ARG* 2.7 76.2 + - - +
63A GLU* 4.7 0.4 - - - -
347A ILE* 4.8 1.6 - - - +
379A TYR* 3.1 48.2 - + + -
380A THR* 3.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 30.1 - - + -
32A MET 4.8 0.5 + - - -
46A LEU* 2.9 35.3 + - + +
47A ALA 4.0 1.8 - - - +
49A TYR* 1.3 93.9 + + - +
51A ALA* 1.3 60.7 + - - +
53A ARG* 3.0 14.9 + - - +
54A THR* 2.7 23.5 + - - -
60A LEU* 3.8 5.0 - - + +
61A ILE 4.2 0.7 - - - -
62A SER* 3.4 17.3 - - - -
63A GLU* 2.7 55.8 + - - +
89A TRP* 4.8 4.5 - + - -
92A VAL* 3.6 20.6 - - + -
96A VAL* 3.9 16.2 - - + -
103A ILE* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 2.9 20.8 + - - +
48A GLU* 3.6 6.5 - - - +
50A TYR* 1.3 73.1 - - - +
52A GLN* 1.3 66.8 + - - +
54A THR* 2.9 26.4 + - - +
95A ALA* 4.3 18.8 - - + +
96A VAL* 4.5 2.1 - - - +
99A LYS* 3.7 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.0 45.3 + - - +
49A TYR* 3.6 5.8 - - - +
51A ALA* 1.3 74.9 - - - +
53A ARG* 1.3 85.9 + - - +
54A THR 3.6 4.0 + - - +
99A LYS* 5.7 2.5 - - - +
350A PRO* 3.3 16.9 - - + +
351A ASP* 5.1 0.2 - - - -
380A THR* 2.9 43.0 + - - +
382A TYR 5.1 0.2 + - - -
384A PHE* 3.4 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.4 18.2 - - + -
49A TYR* 2.7 64.9 + - - +
50A TYR* 3.0 11.1 + - - +
51A ALA 3.0 0.8 - - - -
52A GLN* 1.3 104.9 - - - +
54A THR* 1.3 62.8 + - - +
55A THR* 3.7 6.8 + - - +
60A LEU* 3.9 10.9 - - + +
346A PHE* 3.0 52.2 + - + -
347A ILE 2.9 25.1 + - - -
350A PRO* 3.2 29.9 - - + +
353A VAL* 5.4 0.2 - - - +
379A TYR 3.6 14.6 + - - -
382A TYR* 4.4 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR 2.7 21.0 + - - -
51A ALA* 2.9 20.0 + - - +
52A GLN 4.2 3.6 - - - +
53A ARG* 1.3 78.0 - - - +
55A THR* 1.3 67.2 + - - +
58A GLY 5.4 0.2 - - - +
60A LEU* 3.5 15.4 - - + +
96A VAL* 3.4 33.7 - - + +
99A LYS* 3.8 22.7 + - + +
101A GLY* 3.4 24.5 - - - +
----------------------------------------------------------
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