Contacts of the helix formed by residues 38 - 58 (chain A) in PDB entry 4U7I
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 GLN 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 2.8 30.8 + - - +
36A LEU* 3.9 33.9 - - - +
37A GLY* 1.3 78.1 - - - +
39A LYS* 1.3 58.2 + - - +
40A GLU 3.4 2.7 - - - -
41A GLU* 3.3 29.7 + - + +
42A ALA* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 4.6 8.3 - - - +
37A GLY* 3.1 20.0 + - - +
38A GLN* 1.3 73.7 - - - +
40A GLU* 1.3 68.9 + - + +
42A ALA* 3.6 7.3 - - - +
43A LYS* 3.0 33.5 + - - +
91A ARG* 5.0 4.5 - - - +
95A LEU* 3.8 22.4 - - + +
100A ALA* 3.8 27.4 - - + -
101A THR* 5.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN 3.4 0.4 - - - -
39A LYS* 1.3 79.9 - - + +
41A GLU* 1.3 63.0 + - - +
43A LYS* 2.8 38.0 + - - +
44A ASN* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 3.8 17.3 - - - +
38A GLN* 3.3 35.4 + - + +
40A GLU* 1.3 75.8 - - - +
42A ALA* 1.3 66.7 + - - +
44A ASN* 3.2 9.9 + - - +
45A TYR* 2.8 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 3.6 13.9 - - - +
33A THR* 3.2 18.6 - - - +
34A ASP* 3.9 18.2 - - + +
38A GLN 2.9 15.7 + - - +
39A LYS* 3.6 8.5 - - - +
40A GLU 3.3 0.2 - - - -
41A GLU* 1.3 77.7 - - - +
43A LYS* 1.3 62.8 + - - +
45A TYR* 3.1 2.9 + - - +
46A TYR* 2.9 36.9 + - + -
95A LEU* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.0 20.5 + - - +
40A GLU* 2.8 43.8 + - - +
42A ALA* 1.3 75.3 - - - +
44A ASN* 1.3 63.1 + - - +
46A TYR* 3.4 3.2 + - - +
47A LYS* 3.0 37.7 + - - +
92A LEU* 3.9 16.6 - - + -
95A LEU* 3.9 38.3 + - + -
96A GLU* 3.9 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU 3.3 10.0 + - - +
41A GLU* 3.2 12.6 + - - +
42A ALA 3.1 0.6 - - - -
43A LYS* 1.3 80.4 - - - +
45A TYR* 1.3 79.3 + - - +
47A LYS* 3.4 13.4 + - - +
48A GLN* 3.2 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.4 31.6 - + + +
29A LYS* 3.5 47.4 + - + -
30A GLY* 3.6 6.7 - - - +
33A THR* 3.7 26.0 - - + -
41A GLU* 2.8 51.4 + - + +
44A ASN* 1.3 92.5 + - - +
46A TYR* 1.3 60.5 + - - +
48A GLN* 3.1 17.0 + - - +
49A GLY* 2.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE 5.2 0.2 - - - -
27A VAL* 4.0 10.3 - - - +
30A GLY* 3.4 28.1 + - - -
31A LEU* 3.6 18.0 - - - +
34A ASP* 2.7 39.1 + - - +
42A ALA* 2.9 24.4 + - + +
43A LYS* 3.7 6.1 - - - +
45A TYR* 1.3 77.6 - - - +
47A LYS* 1.3 58.2 + - - +
49A GLY* 3.1 2.5 + - - +
50A ILE* 2.8 33.6 + - - +
88A VAL* 3.7 24.2 - - + +
91A ARG* 3.6 14.5 - - + +
92A LEU* 4.4 15.7 - - + -
95A LEU* 3.8 14.4 - - + -
328B PHE* 3.7 23.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.0 34.1 + - - +
44A ASN* 3.8 10.8 - - - +
46A TYR* 1.3 76.1 - - - +
48A GLN* 1.3 62.6 + - + +
50A ILE* 3.4 9.9 + - + +
51A GLY* 3.3 17.3 + - - -
92A LEU* 3.6 22.9 - - + -
96A GLU* 4.5 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.2 41.8 - - + -
44A ASN* 3.2 41.5 + - - +
45A TYR* 3.1 14.1 + - - +
47A LYS* 1.3 77.6 - - + +
49A GLY* 1.3 63.7 + - - +
51A GLY* 3.2 10.4 + - - -
52A HIS* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.1 3.5 - - - +
26A PHE* 3.8 15.6 - - - +
27A VAL* 4.1 13.9 - - - -
45A TYR 2.8 14.2 + - - -
46A TYR 3.1 4.0 + - - -
48A GLN* 1.3 76.5 - - - +
50A ILE* 1.3 55.8 + - - +
52A HIS* 3.1 7.5 + - - +
53A LEU* 2.8 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR 2.8 16.1 + - - +
47A LYS* 3.6 9.9 - - + +
48A GLN 3.3 0.2 - - - -
49A GLY* 1.3 76.3 - - - +
51A GLY* 1.3 56.5 + - - +
53A LEU* 3.2 7.6 + - - +
54A LEU* 2.9 48.4 + - + +
85A LEU* 4.0 18.6 - - + -
88A VAL* 3.7 18.8 - - + +
89A ARG* 3.8 28.7 - - + +
92A LEU* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 3.3 7.0 + - - -
48A GLN* 3.2 9.2 + - - -
50A ILE* 1.3 78.8 - - - +
52A HIS* 1.3 62.4 + - - +
54A LEU* 3.5 8.8 + - - +
55A ARG* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.4 16.7 - - - +
22A LYS* 3.6 33.3 - - + +
23A ALA* 3.8 17.5 - - - +
26A PHE* 3.6 34.9 - + - -
48A GLN* 3.0 27.2 + - - +
49A GLY* 3.1 5.5 + - - +
51A GLY* 1.3 74.5 - - - +
53A LEU* 1.3 66.5 + - - +
55A ARG* 3.0 34.6 + - - +
56A GLY 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 3.5 21.3 - - + -
27A VAL* 4.3 7.0 - - + -
49A GLY 2.8 27.0 + - - +
50A ILE* 3.7 8.1 - - - +
52A HIS* 1.3 75.6 - - - +
54A LEU* 1.3 65.3 + - - +
56A GLY* 3.3 2.3 + - - -
57A ILE* 3.0 30.7 + - + +
81A MET* 3.7 37.8 - - + +
84A THR* 4.0 12.3 - - + -
85A LEU* 3.7 37.7 - - + +
88A VAL* 4.4 4.9 - - + -
321B PHE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 2.9 38.5 + - + +
51A GLY* 3.8 7.6 - - - +
53A LEU* 1.3 78.1 - - - +
55A ARG* 1.3 61.9 + - - +
57A ILE* 3.4 6.8 + - + +
58A SER* 3.0 24.8 + - - -
85A LEU* 3.8 20.6 - - + -
89A ARG* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.4 20.1 + - + +
18A GLU* 5.0 2.6 - - - +
19A ALA* 4.0 23.8 - - - +
22A LYS* 4.4 7.3 - - - +
51A GLY 3.2 15.4 + - - +
52A HIS* 3.0 38.0 + - - +
53A LEU 3.2 0.8 - - - -
54A LEU* 1.3 80.0 - - - +
56A GLY* 1.3 61.0 + - - +
58A SER* 2.6 26.9 + - - +
59A ILE* 3.6 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.9 0.7 - - - -
16A ILE* 3.7 13.0 - - - +
19A ALA* 3.5 21.7 - - - +
52A HIS 3.1 8.7 + - - -
53A LEU 3.8 2.2 - - - -
55A ARG* 1.3 79.8 - - - +
57A ILE* 1.3 58.5 + - - +
58A SER 3.4 0.5 + - - -
59A ILE* 3.6 3.9 + - - -
78A GLN* 2.9 24.8 + - - +
81A MET* 3.9 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.0 22.9 + - - +
54A LEU* 3.8 5.6 - - + +
56A GLY* 1.3 75.7 - - - +
58A SER* 1.3 63.2 + - - +
59A ILE 3.2 2.8 + - - +
78A GLN* 3.6 17.2 + - + +
81A MET* 3.7 20.9 - - + +
82A LYS* 3.6 54.5 - - + +
85A LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.0 15.4 + - - -
55A ARG* 2.6 24.3 + - - +
57A ILE* 1.3 78.3 - - - +
59A ILE* 1.3 68.3 + - - +
60A SER* 3.4 3.6 + - - -
----------------------------------------------------------
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