Contacts of the helix formed by residues 4 - 19 (chain A) in PDB entry 5U5S
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 SER 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 5.0 3.5 + - - -
3A LEU* 1.3 74.3 - - - +
5A GLU* 1.3 61.6 + - - +
6A GLN* 3.2 8.1 - - - -
7A LEU* 2.9 22.4 + - - +
8A LYS* 2.8 25.9 + - - +
66A ARG* 4.8 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU 4.8 3.3 - - - +
4A SER* 1.3 75.1 - - - +
6A GLN* 1.3 79.9 + - - +
8A LYS* 3.3 11.4 + - - +
9A HIS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.2 6.4 - - - -
5A GLU* 1.3 92.3 + - - +
7A LEU* 1.3 61.4 + - + +
9A HIS* 3.3 5.9 + - - +
10A CYS* 3.0 27.8 + - - -
66A ARG 5.7 0.2 - - - +
67A ASP* 4.6 7.6 - - + -
68A ALA* 3.4 22.0 - - + +
110A MET* 3.7 9.8 - - + +
111A PRO 3.5 19.0 + - - -
112A ASP* 3.5 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.6 29.3 - - + +
4A SER* 2.9 27.1 + - - +
6A GLN* 1.3 74.3 - - + +
8A LYS* 1.3 64.9 + - - +
10A CYS* 3.2 13.1 - - + +
11A ASN* 3.0 19.9 + - - +
60A MET* 4.2 4.1 - - + +
63A ARG* 5.8 3.6 - - + -
65A TYR* 3.2 42.8 - - + +
66A ARG 3.5 17.0 - - - +
67A ASP* 3.4 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS 4.4 9.8 + - - -
3A LEU* 3.9 29.0 + - - +
4A SER 2.8 11.3 + - - +
5A GLU* 3.3 16.8 + - - +
7A LEU* 1.3 74.4 - - - +
9A HIS* 1.3 67.2 + - - +
11A ASN* 3.1 26.2 + - + +
12A GLY* 3.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU 3.1 12.7 + - - +
6A GLN* 3.5 10.8 - - - +
7A LEU 3.2 0.2 - - - -
8A LYS* 1.3 77.1 - - - +
10A CYS* 1.3 56.9 + - - +
12A GLY* 3.2 2.7 + - - +
13A ILE* 3.0 47.8 + - + +
106A ARG 4.5 2.6 + - - -
109A LYS* 4.9 3.1 - - - +
110A MET* 3.6 47.8 + - + +
111A PRO* 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN 3.0 22.4 + - - -
7A LEU* 3.2 17.0 - - + +
9A HIS* 1.3 75.1 - - - +
11A ASN* 1.3 59.6 + - - +
13A ILE* 3.2 4.1 + - - +
14A LEU* 2.9 33.8 + - - +
60A MET* 4.0 8.3 - - + -
68A ALA* 3.2 33.2 - - - -
71A PHE* 3.3 41.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.5 12.7 - - + +
7A LEU 3.0 9.6 + - - +
8A LYS* 3.1 23.5 + - + +
10A CYS* 1.3 75.7 - - - +
12A GLY* 1.3 58.1 + - - +
14A LEU* 4.0 1.6 - - - +
15A LYS* 3.1 32.1 + - - +
57A LYS* 4.4 17.3 + - - +
60A MET* 3.6 29.5 - - - +
61A GLU* 6.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS 3.2 8.3 + - - -
9A HIS* 3.2 4.2 + - - -
10A CYS 3.1 0.8 - - - -
11A ASN* 1.3 80.8 + - - +
13A ILE* 1.3 63.4 + - - +
15A LYS* 3.4 10.3 - - - +
16A GLU* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 3.0 35.1 + - + +
10A CYS* 3.8 4.0 - - - +
12A GLY* 1.3 73.9 - - - +
14A LEU* 1.3 66.7 + - - +
16A GLU* 3.0 17.4 + - - +
17A LEU* 3.2 19.2 + - + +
71A PHE* 4.2 18.2 - - + -
103A PHE* 4.0 20.9 - - + -
106A ARG* 3.6 52.7 - - + +
107A TYR* 4.0 12.8 - - + +
110A MET* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS 2.9 15.9 + - - +
11A ASN 4.0 3.1 - - - +
13A ILE* 1.3 75.5 - - - +
15A LYS* 1.3 62.4 + - - +
17A LEU* 3.3 10.7 + - - +
18A LEU* 3.0 63.2 + - + +
53A LEU* 3.4 31.6 - - + +
56A VAL* 3.5 16.6 - - + -
57A LYS* 3.4 28.9 - - + +
60A MET* 3.3 26.7 - - + -
71A PHE* 3.8 7.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.1 20.4 + - - +
12A GLY* 3.4 10.3 - - - +
14A LEU* 1.3 78.3 - - - +
16A GLU* 1.3 54.5 + - - +
18A LEU* 3.2 8.8 + - + +
19A SER* 2.6 52.0 + - - +
57A LYS* 4.4 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.1 11.6 + - - +
13A ILE* 3.0 10.5 + - - +
15A LYS* 1.3 75.3 - - - +
17A LEU* 1.3 68.3 + - - +
18A LEU 3.0 4.7 - - - -
19A SER* 2.9 27.9 + - - +
21A LYS* 4.9 6.3 - - + +
22A HIS* 2.6 45.8 + - + +
102A VAL* 3.1 20.9 - - - +
106A ARG* 2.6 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.2 23.4 + - + +
14A LEU* 3.8 5.6 - - - +
16A GLU* 1.3 84.3 - - - +
18A LEU* 1.3 58.2 + - - +
22A HIS* 3.9 8.7 - - + +
26A ALA* 3.2 27.7 - - - +
30A TYR* 3.3 5.8 + - - -
53A LEU* 3.7 33.8 - - + +
71A PHE* 5.3 1.1 - - + -
75A VAL* 4.5 9.6 - - + -
79A PHE* 4.9 2.9 - - + -
99A LEU* 4.0 17.7 - - + +
102A VAL* 3.7 30.1 - - + -
103A PHE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.0 39.9 + - + +
15A LYS* 3.5 7.0 - - + +
16A GLU 3.0 0.8 - - - -
17A LEU* 1.3 75.8 - - - +
19A SER* 1.3 55.5 + - - +
20A LYS 3.7 0.7 + - - -
30A TYR* 2.7 56.2 + - + -
53A LEU* 3.7 28.0 - - + +
54A SER* 4.9 6.7 - - - +
57A LYS* 3.9 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 2.6 40.3 + - - +
16A GLU* 2.9 19.9 + - - +
18A LEU* 1.3 78.2 - - - +
20A LYS* 1.3 55.2 + - - +
21A LYS* 2.9 15.0 - - - -
22A HIS* 2.8 26.9 + - - +
23A ALA 3.1 6.9 + - - -
30A TYR* 3.2 2.5 + - - -
----------------------------------------------------------
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