Contacts of the strand formed by residues 74 - 83 (chain A) in PDB entry 4FU9
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 MET 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.3 8.7 - - - -
61A LEU 2.9 30.5 + - - +
72A GLY 4.3 2.2 - - - +
73A GLU* 1.3 75.5 - - - +
75A LYS* 1.3 58.1 + - - +
76A PHE* 3.4 34.8 - - + -
105A SER* 5.3 8.7 - - - -
109A ARG* 5.9 2.2 - - + -
110A CYS 4.1 7.9 - - - +
111A ALA* 4.2 0.2 - - - -
112A GLN* 3.4 42.4 - - + +
117A ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 4.9 9.2 - - - +
58A ILE* 3.7 30.6 - - + +
59A VAL 3.6 3.6 - - - -
60A TYR* 3.6 38.9 + - + +
73A GLU* 5.4 0.8 - - - +
74A MET* 1.3 71.0 - - - +
76A PHE* 1.3 73.3 + - - +
105A SER* 4.0 13.5 - - - -
106A LYS* 5.0 1.8 + - - +
306A GOL 3.1 49.8 + - - +
307A GOL 4.9 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.5 9.9 - - - +
59A VAL* 2.7 44.5 + - + +
61A LEU* 3.6 24.0 - - + -
74A MET* 3.4 44.9 - - + -
75A LYS* 1.3 78.2 - - - +
77A GLU* 1.3 71.9 + - - +
103A ILE* 3.8 26.0 - - + -
104A ARG 3.6 8.5 - - - +
105A SER* 3.6 20.2 - - - +
109A ARG 3.8 4.3 - - - -
110A CYS 3.8 8.5 - - - -
111A ALA* 3.7 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.4 38.3 + - - +
55A GLU* 5.1 3.2 - - - +
57A TYR 4.1 5.6 - - - +
76A PHE* 1.3 76.6 - - - +
78A VAL* 1.3 66.0 + - - +
79A GLU 3.9 0.2 - - - -
103A ILE* 3.4 4.9 - - - +
104A ARG* 2.9 49.1 + - + +
105A SER 5.4 0.5 - - - +
106A LYS* 4.4 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 3.4 34.3 + - + +
55A GLU* 5.4 1.1 - - - +
57A TYR* 3.7 31.3 + - + +
59A VAL* 3.9 12.6 - - + -
77A GLU* 1.3 77.7 - - - +
79A GLU* 1.3 62.1 + - - +
80A ASN 3.4 29.2 - - - +
81A LEU* 3.9 15.7 - - + +
101A LEU* 3.9 28.5 - - + -
102A LYS 3.4 5.8 - - - +
103A ILE* 5.1 0.4 - - + -
104A ARG* 4.8 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 2.8 24.9 + - - +
77A GLU 3.8 2.2 + - - -
78A VAL* 1.3 74.4 - - - +
80A ASN* 1.3 58.0 + - + +
102A LYS* 2.7 50.4 + - + +
103A ILE 4.5 1.6 - - - +
104A ARG* 3.7 55.6 + - + +
108A GLY 5.6 0.7 - - - +
110A CYS* 5.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.4 5.2 - - + -
54A LYS* 4.3 3.4 - - - +
78A VAL* 3.4 6.5 - - - +
79A GLU* 1.3 83.3 - - + +
81A LEU* 1.3 65.5 + - - +
82A ILE* 3.5 31.7 - - + +
100A LEU 3.7 1.7 - - - +
101A LEU* 3.5 2.1 - - - -
102A LYS* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 4.1 25.8 - - + -
52A PRO* 3.9 29.6 - - + +
54A LYS* 3.9 23.9 - - + +
57A TYR* 4.3 14.4 - - + -
78A VAL* 3.9 4.4 - - + +
80A ASN* 1.3 77.3 + - - +
82A ILE* 1.3 60.2 + - - +
83A LEU* 3.9 27.8 + - + +
100A LEU 3.7 0.9 - - - +
101A LEU* 3.8 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.8 14.4 - - + -
80A ASN* 3.5 36.1 - - + +
81A LEU* 1.3 70.1 - - - +
83A LEU* 1.3 67.7 + - - +
99A ALA* 3.2 7.1 - - - +
100A LEU* 2.8 46.1 + - + +
240A TRP* 3.9 16.9 - - + -
244A HIS* 3.5 55.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.5 22.0 - - + +
48A PHE* 3.9 25.6 - - + +
49A ILE* 4.0 40.6 - - + +
52A PRO* 4.5 14.4 - - + -
81A LEU* 3.9 20.3 + - + +
82A ILE* 1.3 88.3 - - - +
84A HIS* 1.3 67.4 + - - +
85A LYS* 3.3 4.5 + - - +
99A ALA* 3.9 10.5 - - + -
240A TRP* 4.3 3.1 + - - -
----------------------------------------------------------
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