Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 5MQI
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 ASP 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.7 10.7 - - + +
28A GLU* 2.9 3.9 + - + +
29A PRO* 1.3 83.0 - - - +
31A CYS* 1.3 57.5 + - - +
32A LEU 3.6 1.3 - - - -
33A GLU* 3.2 30.0 - - - +
34A SER* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 4.2 6.7 - - - -
17A LEU* 3.5 22.9 - - - +
27A LYS* 4.3 11.2 - - + -
28A GLU 2.9 18.6 + - - +
29A PRO 3.2 2.8 + - - +
30A ASP* 1.3 73.6 - - - +
32A LEU* 1.3 67.5 - - - +
33A GLU 3.0 1.1 - - - -
34A SER* 2.9 4.2 + - - -
35A VAL* 2.9 29.1 + - - +
68A ILE* 3.7 27.4 - - - -
78A LEU* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO 5.0 1.7 + - - +
30A ASP* 4.7 0.2 - - - +
31A CYS* 1.3 77.8 - - - +
33A GLU* 1.3 62.7 + - - +
35A VAL* 3.6 1.1 + - - +
36A LYS* 3.2 51.4 + - + +
75A ASP* 5.5 2.0 - - - +
77A PRO* 3.5 46.7 - - + +
78A LEU* 3.7 22.2 - - + +
81A ALA* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.2 41.4 + - - +
31A CYS 3.0 0.4 - - - -
32A LEU* 1.3 81.2 - - - +
34A SER* 1.3 63.1 + - - +
36A LYS* 3.4 9.3 + - - +
37A ASP* 3.0 39.7 + - - +
40A ARG* 4.4 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.3 25.1 + - - +
16A ALA* 3.3 22.8 + - - +
17A LEU* 3.2 26.2 - - - -
30A ASP* 2.9 22.8 + - - +
31A CYS 2.9 2.3 + - - -
33A GLU* 1.3 74.2 - - - +
35A VAL* 1.3 66.2 + - - +
37A ASP* 2.9 14.9 + - - -
38A LEU* 3.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 14.6 - - + -
31A CYS* 2.9 24.2 + - - +
32A LEU 3.8 5.4 - - - +
34A SER* 1.3 74.6 - - - +
36A LYS* 1.3 63.2 + - - +
38A LEU* 3.2 14.3 + - - +
39A ILE* 3.2 20.2 + - + +
65A LEU* 4.6 8.1 - - + -
68A ILE* 4.7 1.1 - - + -
78A LEU* 4.0 16.4 - - + -
81A ALA* 3.7 40.2 - - + +
82A VAL* 3.8 13.7 - - + +
85A LEU* 4.1 12.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
32A LEU* 3.2 51.2 + - + +
33A GLU* 3.7 5.8 - - - +
34A SER 3.2 0.2 - - - -
35A VAL* 1.3 76.7 - - - +
37A ASP* 1.3 62.4 + - - +
39A ILE* 3.2 14.3 + - + +
40A ARG* 3.1 43.3 + - - +
77A PRO* 5.6 2.3 - - - +
81A ALA* 4.4 10.3 - - + -
84A ARG* 5.6 1.1 - - - +
1603A SO4 3.7 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.9 15.8 + - + +
33A GLU* 3.0 30.9 + - - +
34A SER* 2.9 11.7 + - - +
36A LYS* 1.3 76.8 - - - +
38A LEU* 1.3 62.6 + - - +
40A ARG* 2.9 33.2 + - - +
41A TYR* 3.0 40.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.5 29.6 - - + -
13A THR* 3.7 19.7 - - + -
14A CYS* 4.1 8.1 - - - -
17A LEU* 4.1 28.7 - - + -
34A SER 3.0 18.1 + - - +
35A VAL* 3.2 8.0 + - - +
37A ASP* 1.3 74.5 - - - +
39A ILE* 1.3 64.5 + - - +
41A TYR* 3.2 7.5 + - + +
42A LEU* 3.1 25.3 + - - +
51A VAL* 4.9 0.7 - - - +
55A LEU* 3.9 21.1 - - + -
60A ILE* 4.5 4.5 - - + -
85A LEU* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.2 15.4 + - + +
36A LYS* 3.4 14.4 - - + +
37A ASP 3.2 0.4 - - - -
38A LEU* 1.3 76.1 - - - +
40A ARG* 1.3 63.1 + - + +
42A LEU* 3.2 7.9 + - + +
43A ARG* 3.2 33.4 + - + +
81A ALA* 3.7 27.8 - - + +
84A ARG* 3.5 53.4 - - + +
85A LEU* 3.9 22.9 - - + +
88A ASN* 5.5 7.0 - - + +
1603A SO4 5.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 4.4 1.2 + - - +
36A LYS* 3.1 35.8 + - - +
37A ASP* 2.9 35.3 + - - +
39A ILE* 1.3 76.7 - - + +
41A TYR* 1.3 65.1 + - + +
43A ARG* 3.2 39.7 + - - +
44A HIS* 3.3 23.6 + - + +
1603A SO4 3.5 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN 5.6 2.5 - - - -
9A GLU* 3.1 45.7 + - + +
10A LEU* 3.6 26.7 - - + -
13A THR* 3.5 25.0 + - - -
37A ASP* 3.0 41.0 + - + +
38A LEU* 3.2 8.3 + - - +
40A ARG* 1.3 78.2 - - + +
42A LEU* 1.3 56.3 + - - +
44A HIS* 2.9 23.0 + + + +
45A GLU 3.2 9.7 + - - -
51A VAL* 3.6 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 3.1 13.6 + - - +
39A ILE* 3.2 8.0 + - - +
41A TYR* 1.3 76.3 - - - +
43A ARG* 1.3 61.2 + - - +
45A GLU* 3.3 24.9 - - - +
51A VAL* 3.7 12.8 - - + -
52A ARG* 3.5 53.5 + - + +
55A LEU* 4.0 5.8 - - + -
85A LEU* 3.4 33.4 - - + -
88A ASN* 3.7 29.5 + - + +
89A LEU* 3.6 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.2 28.3 + - + +
40A ARG* 3.2 36.1 + - - +
41A TYR 3.1 1.0 - - - -
42A LEU* 1.3 78.6 - - - +
44A HIS* 1.3 80.7 + - - +
45A GLU* 3.6 1.4 + - - +
84A ARG* 4.6 8.8 - - - +
88A ASN* 4.9 10.1 - - - +
1603A SO4 4.9 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.3 16.2 + - + +
41A TYR* 2.9 12.2 + + + +
43A ARG* 1.3 111.5 + - - +
45A GLU* 1.3 64.9 + - - +
46A ASP* 3.9 0.5 + - - -
51A VAL* 5.2 0.4 - - - -
----------------------------------------------------------
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