Contacts of the helix formed by residues 75 - 89 (chain A) in PDB entry 5E0F
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 ASN 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 3.1 10.8 - - - -
70A CYS* 4.3 13.0 - - - +
74A GLY* 1.3 74.1 - - - -
76A GLU* 1.3 59.6 + - - +
77A ASP* 3.1 16.2 + - - +
78A GLU* 2.9 41.9 + - - +
79A PHE* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 2.9 31.3 + - + +
70A CYS* 5.5 0.4 - - - +
75A ASN* 1.3 77.5 - - - +
77A ASP* 1.3 60.5 + - - +
79A PHE* 3.2 2.3 + - - +
80A ARG* 2.7 63.4 + - + +
185A HIS* 2.7 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.1 15.1 + - - +
76A GLU* 1.3 80.8 - - - +
78A GLU* 1.3 60.4 + - + +
80A ARG* 3.4 10.8 + - - +
81A ASN* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.6 18.3 - - + +
22A VAL* 3.9 25.5 - - + +
73A SER 5.2 0.9 - - - -
74A GLY* 3.1 10.6 - - - -
75A ASN* 2.9 49.2 + - - +
77A ASP* 1.3 75.9 - - + +
79A PHE* 1.3 64.4 + - - +
81A ASN* 3.4 8.2 + - - +
82A MET* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.4 29.7 - + + +
42A VAL* 4.4 10.1 - - + -
45A PRO* 3.7 20.2 - - + -
69A LEU* 4.1 10.8 - - + -
75A ASN 2.9 17.0 + - - +
76A GLU* 3.6 7.9 - - - +
78A GLU* 1.3 76.9 - - - +
80A ARG* 1.3 62.1 + - - +
82A MET* 3.2 27.0 + - + +
83A VAL* 3.0 45.6 + - + +
93A ILE* 4.6 0.9 - - + -
95A VAL* 4.0 5.4 - - + -
186A LEU* 3.5 28.3 - - + -
189A ILE* 4.0 22.4 - - + -
191A VAL* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 2.7 51.3 + - + +
77A ASP* 3.7 9.9 - - - +
79A PHE* 1.3 73.1 - - - +
81A ASN* 1.3 63.0 + - - +
83A VAL* 3.3 1.2 + - - +
84A THR* 3.0 31.1 + - - +
185A HIS* 3.8 13.7 + - - -
188A ASP 5.6 0.8 + - - -
189A ILE* 3.6 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 5.5 6.2 - - - +
25A ALA* 4.1 3.3 - - - +
77A ASP 2.9 17.7 + - - +
78A GLU* 3.5 9.5 - - - +
79A PHE 3.3 0.2 - - - -
80A ARG* 1.3 75.3 - - - +
82A MET* 1.3 58.7 + - - +
84A THR* 3.8 4.2 - - - -
85A ARG* 2.8 78.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.6 42.8 - - + +
24A ILE* 3.6 35.4 - - + -
25A ALA* 3.8 15.3 - - + +
42A VAL* 4.1 12.3 - - + -
78A GLU 3.0 13.7 + - - +
79A PHE* 3.2 44.8 + - + +
81A ASN* 1.3 75.3 + - - +
83A VAL* 1.3 70.3 + - + +
85A ARG* 3.4 0.5 + - - +
86A CYS* 2.9 38.5 + - - -
93A ILE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.0 44.8 + - + +
80A ARG 3.3 0.6 + - - +
82A MET* 1.3 84.0 - - + +
84A THR* 1.3 57.0 + - - +
86A CYS* 3.9 0.7 - - - +
87A ASN* 2.9 36.5 + - - +
93A ILE* 4.1 21.1 - - + -
189A ILE* 3.5 24.5 - - + +
190A GLY* 3.5 34.1 - - - +
191A VAL* 3.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.0 19.0 + - - +
81A ASN* 3.8 5.2 - - - -
83A VAL* 1.3 78.9 - - - +
85A ARG* 1.3 62.3 + - + +
87A ASN* 3.8 0.9 - - - +
88A ASN* 2.9 52.9 + - - +
189A ILE* 4.7 4.0 + - - +
221A TRP* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.9 6.9 + - - +
25A ALA* 3.6 19.5 - - + +
26A LEU* 3.4 29.1 - - - +
28A CYS* 5.0 1.6 - - - -
29A GLU* 2.9 46.5 + - - +
81A ASN* 2.8 52.3 + - - +
82A MET 4.0 2.2 - - - +
84A THR* 1.3 81.1 - - + +
86A CYS* 1.3 65.3 + - - +
88A ASN* 3.5 8.6 + - - +
89A VAL* 3.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.9 7.2 - - - -
25A ALA* 4.1 3.4 - - - -
28A CYS* 2.0 52.3 - - - -
82A MET* 2.9 30.0 + - - +
83A VAL 3.9 2.2 - - - +
85A ARG* 1.3 74.9 - - - +
87A ASN* 1.3 65.8 + - - +
89A VAL* 3.0 11.3 + - - +
91A VAL 2.9 32.6 + - - +
93A ILE* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 2.9 28.9 + - - +
86A CYS* 1.3 72.7 - - - +
88A ASN* 1.3 57.7 + - - +
90A GLY* 2.9 19.1 + - - +
91A VAL 3.3 5.7 + - - +
92A ARG* 3.1 39.8 + - - +
93A ILE* 4.8 1.5 + - - -
190A GLY 2.9 26.8 + - - +
221A TRP* 3.3 55.3 - - + +
222A PHE* 4.1 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 2.9 39.1 + - - +
85A ARG* 3.8 8.7 - - - +
86A CYS 3.1 0.4 - - - -
87A ASN* 1.3 76.2 - - - +
89A VAL* 1.3 62.0 + - + +
90A GLY 3.5 0.4 + - - -
221A TRP* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 4.8 1.0 - - - +
10A ARG* 4.2 7.6 + - - -
28A CYS* 3.7 33.7 - - + +
29A GLU* 4.3 17.9 - - + +
33A ALA* 3.5 24.2 - - + +
85A ARG 3.4 12.8 + - - +
86A CYS 3.0 10.5 + - - +
88A ASN* 1.3 80.4 - - + +
90A GLY* 1.3 60.5 + - - +
91A VAL* 4.0 2.6 - - + +
----------------------------------------------------------
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