Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 5ELI
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 ARG 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 3.9 2.4 + - - -
46A ARG* 1.3 75.4 - - - +
48A LYS* 1.3 70.4 + - - +
62A ARG* 6.0 1.2 - - - +
65A SER* 3.1 23.8 + - - -
66A THR* 2.7 27.7 + - - +
67A HIS 3.7 9.2 - - - +
68A ASN* 3.5 39.1 + - - +
70A TRP* 4.4 4.4 - - - +
73A SER* 6.4 0.7 - - - -
77A ARG* 3.2 24.2 - - - +
113A LEU* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.5 40.7 + - - -
43A HIS* 3.8 11.6 + - - -
46A ARG 2.5 25.5 + - - -
47A ARG* 1.3 79.9 - - - +
49A ALA* 1.3 62.2 + - - +
65A SER* 3.1 7.2 - - - -
66A THR* 2.8 34.8 + - + +
70A TRP* 4.1 5.3 - - - +
84A ILE* 4.4 1.3 - - - -
86A ASP* 3.3 24.5 + - - +
88A THR* 4.4 0.4 - - - +
93A LEU* 3.7 29.2 - - + -
111A GLN 3.2 7.4 - - - +
112A SER* 4.0 23.3 - - - +
113A LEU* 4.4 2.5 - - - -
121A LEU* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 1.3 77.1 - - - +
50A TRP* 1.3 59.7 + - - +
51A CYS* 4.2 0.4 - - + -
62A ARG* 3.6 36.1 - - + +
64A VAL 3.3 7.0 - - - +
65A SER* 4.0 3.4 - - - +
84A ILE* 4.3 4.7 - - - -
93A LEU* 4.5 2.2 - - - +
109A GLN 4.1 0.3 - - - +
110A CYS* 3.6 4.0 - - - +
111A GLN* 2.9 38.3 + - + +
113A LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.7 28.9 - - + -
36A CYS* 5.2 0.4 - - - -
49A ALA* 1.3 74.4 - - - +
51A CYS* 1.3 54.4 + - - +
62A ARG* 3.9 0.5 - - - +
63A VAL* 2.8 48.6 + - + +
64A VAL* 2.8 23.1 + - + +
82A THR* 3.9 22.2 + - + +
84A ILE* 4.2 0.8 - - + +
95A ILE* 3.3 40.4 - - + -
97A LEU* 4.5 16.7 - - + +
108A TYR* 3.3 55.3 - + + -
109A GLN 3.7 11.7 - - - -
110A CYS* 3.8 19.1 - - - -
124A VAL* 3.8 17.7 - - + -
126A VAL* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 4.2 0.4 - - + -
50A TRP* 1.3 73.9 - - - +
52A ARG* 1.3 59.3 + - - +
60A CYS* 2.1 44.0 - - - -
61A GLN 3.1 24.9 - - - +
62A ARG* 3.9 6.1 - - + +
63A VAL* 4.0 2.9 - - - +
108A TYR* 3.4 10.2 - - - +
109A GLN* 2.9 48.7 + - - +
111A GLN* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS* 1.3 73.9 - - - +
53A GLN* 1.3 72.4 + - - +
54A LEU* 5.2 7.0 - - - +
59A PRO 3.7 1.4 - - - +
60A CYS* 3.3 5.4 - - - -
61A GLN* 3.0 34.1 + - + +
63A VAL* 4.3 9.8 - - + +
103A HIS* 3.1 23.4 + - - -
104A ASP* 4.0 3.8 + - - +
105A ALA 2.3 31.8 + - - -
106A GLY* 3.9 5.7 - - - -
107A LEU 3.7 6.5 - - - +
108A TYR* 3.1 46.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 1.3 85.6 + - - +
54A LEU* 1.3 66.2 + - - +
55A GLY 3.6 16.7 + - - +
56A GLU 3.2 13.4 + - - +
57A LYS 3.8 3.2 + - - -
58A GLY* 3.0 35.6 - - - +
59A PRO 3.5 7.2 + - - -
60A CYS* 3.4 23.8 - - - +
107A LEU* 2.9 43.4 + - + +
108A TYR* 4.7 1.8 - - - +
109A GLN* 3.6 13.4 + - - +
----------------------------------------------------------
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