Contacts of the helix formed by residues 70 - 89 (chain A) in PDB entry 4XWX
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 ASP 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 4.2 0.4 + - - -
69A LEU* 1.3 78.1 - - - +
71A PHE* 1.3 58.5 + - - +
72A ASN* 2.9 17.1 + - - +
73A THR* 2.7 47.4 + - - -
74A ARG* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 1.3 74.0 - - - +
72A ASN* 1.3 68.0 + - + +
74A ARG* 3.1 29.2 + - - +
75A THR* 2.9 44.6 + - + -
152A PHE* 4.0 23.8 - + - -
154A SER* 6.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 2.9 10.5 + - - +
71A PHE* 1.3 84.1 - - + +
73A THR* 1.3 59.6 + - - +
75A THR* 3.4 9.3 + - - +
76A GLN* 2.9 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.0 30.5 - - + -
70A ASP* 2.7 38.5 + - - -
72A ASN* 1.3 73.2 + - - +
74A ARG* 1.3 65.4 + - - +
76A GLN* 3.1 13.8 + - - +
77A VAL* 2.9 29.3 + - + +
106A LEU* 4.6 9.4 - - + -
109A ILE* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 2.9 49.7 + - + +
67A ARG* 4.1 13.3 + - - +
69A LEU* 2.9 26.1 + - + -
70A ASP* 2.9 14.2 + - - +
71A PHE* 3.1 34.1 + - - +
73A THR* 1.3 74.4 - - - +
75A THR* 1.3 62.7 + - - +
77A VAL* 3.3 7.5 + - - +
78A THR* 3.1 26.0 + - - +
151A SER 5.8 0.2 - - - -
152A PHE* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 2.9 36.5 + - + -
72A ASN* 3.5 14.1 - - - +
74A ARG* 1.3 76.8 - - - +
76A GLN* 1.3 57.0 + - + +
78A THR* 2.9 23.1 + - - +
79A ARG* 3.0 18.5 + - + +
152A PHE* 4.1 6.8 - - - -
154A SER* 5.2 4.6 - - - +
155A GLY 5.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 2.9 46.7 + - - +
73A THR* 3.1 14.8 + - - +
75A THR* 1.3 72.6 - - + +
77A VAL* 1.3 61.5 + - - +
79A ARG* 3.3 6.9 + - - +
80A GLU* 3.0 30.8 + - - +
106A LEU* 3.6 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.7 8.5 - - + -
66A MET* 4.7 11.4 - - + -
69A LEU* 4.4 7.2 - - + -
73A THR* 2.9 21.7 + - + +
74A ARG* 3.5 8.3 - - - +
76A GLN* 1.3 73.4 - - - +
78A THR* 1.3 68.4 + - + +
80A GLU 3.2 1.4 + - - -
81A ALA* 2.8 22.4 + - + +
106A LEU* 4.0 14.6 - - + -
109A ILE* 3.8 38.8 - - + -
110A LEU* 3.5 31.4 - - + +
167A VAL* 5.9 0.2 - - + -
177A CYS* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 4.6 5.4 - - + -
74A ARG 3.1 6.5 + - - +
75A THR* 2.9 20.8 + - - +
77A VAL* 1.3 77.2 - - + +
79A ARG* 1.3 61.5 + - - +
81A ALA* 3.3 8.1 + - - +
82A ILE* 2.9 29.6 + - - +
152A PHE* 3.6 25.8 - - + -
154A SER* 2.7 28.3 + - - +
155A GLY 4.4 2.8 + - - -
165A ALA* 3.7 22.3 - - + +
167A VAL* 4.9 2.2 - - + -
177A CYS* 4.1 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.0 19.9 + - + +
76A GLN* 3.7 8.1 - - - +
77A VAL 3.2 0.2 - - - -
78A THR* 1.3 76.6 + - - +
80A GLU* 1.3 58.2 + - - +
82A ILE* 3.3 9.8 + - - +
83A SER* 3.0 35.3 + - - +
94A GLY 5.4 2.6 + - - -
156A GLY* 4.9 3.4 - - - -
157A ASP* 2.9 41.1 + - - +
159A ASP* 4.5 9.5 + - - +
160A THR* 3.6 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN 3.0 16.7 + - - +
79A ARG* 1.3 77.0 - - - +
81A ALA* 1.3 58.6 + - - +
83A SER* 3.1 15.6 + - - -
84A LEU* 2.8 53.0 + - + +
104A ARG* 3.8 7.3 - - - +
105A PRO* 3.6 43.0 - - + +
106A LEU* 4.3 6.7 - - + -
110A LEU* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 4.0 21.0 - - + +
77A VAL 2.8 20.4 + - - +
78A THR 3.6 4.5 - - - +
80A GLU* 1.3 72.8 - - - +
82A ILE* 1.3 62.0 + - - +
84A LEU* 3.4 6.1 + - - +
85A VAL* 3.2 28.4 + - - +
110A LEU* 3.9 8.4 - - + +
177A CYS* 3.7 28.0 - - + -
179A ILE* 4.0 7.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
78A THR 2.9 24.7 + - - +
79A ARG* 3.5 10.8 - - - +
81A ALA* 1.3 76.1 - - - +
83A SER* 1.3 64.3 + - - +
85A VAL* 3.5 4.3 + - - +
86A CYS* 3.1 31.6 + - - -
155A GLY 4.3 5.4 - - - +
156A GLY* 3.9 30.1 - - - +
160A THR* 3.9 27.4 - - + +
163A TYR* 3.9 32.8 - - + -
165A ALA* 4.5 9.0 - - + -
179A ILE* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.0 27.5 + - - +
80A GLU* 3.1 23.7 + - - -
82A ILE* 1.3 76.9 - - - +
84A LEU* 1.3 64.7 + - - +
86A CYS* 3.9 3.9 - - - +
87A GLU* 3.1 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 4.2 29.6 - - + -
80A GLU* 2.8 46.2 + - + +
81A ALA* 3.7 5.4 - - - +
82A ILE 3.3 0.2 - - - -
83A SER* 1.3 79.2 - - - +
85A VAL* 1.3 62.2 + - - +
87A GLU* 3.6 3.8 + - - +
88A ALA* 3.5 18.5 + - - +
104A ARG* 4.1 35.9 - - + +
110A LEU* 4.5 2.7 - - + -
111A GLY 5.2 1.3 - - - +
113A SER* 4.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.3 30.5 - - + +
58A GLY 4.6 7.4 - - - -
59A CYS 4.6 1.3 - - - +
60A VAL* 3.9 19.5 - - + -
81A ALA 3.2 9.7 + - - +
82A ILE 3.5 9.6 - - - +
84A LEU* 1.3 76.2 - - + +
86A CYS* 1.3 63.2 + - - +
88A ALA* 3.2 4.3 + - - -
89A VAL* 2.9 36.4 + - - +
113A SER* 4.9 2.7 - - - +
115A LEU* 4.6 11.9 - - + -
179A ILE* 3.7 38.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
57A MET* 5.0 1.3 - - - -
82A ILE* 3.1 31.4 + - - +
83A SER* 3.9 4.5 - - - +
85A VAL* 1.3 79.0 - - - +
87A GLU* 1.3 62.2 + - + +
88A ALA 3.6 0.2 + - - -
89A VAL 3.6 5.8 - - - +
92A ALA* 3.4 17.7 - - + +
94A GLY* 3.8 27.8 - - - +
95A ALA* 3.3 19.2 - - - +
160A THR* 5.3 0.2 - - - -
163A TYR* 3.3 42.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.1 27.5 + - - +
84A LEU* 4.1 4.3 - - - +
86A CYS* 1.3 77.2 - - + +
88A ALA* 1.3 58.6 + - - +
89A VAL 5.1 0.2 - - - -
94A GLY 4.2 1.7 - - - +
95A ALA* 2.9 36.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.5 10.5 + - - +
85A VAL 3.2 6.5 + - - +
87A GLU* 1.3 80.0 - - - +
89A VAL* 1.3 62.2 + - - +
90A PRO* 3.5 8.3 - - - +
115A LEU* 3.6 31.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
55A ARG* 4.0 2.2 - - - +
57A MET* 3.9 28.3 - - + +
85A VAL 2.9 20.7 + - - +
86A CYS 3.6 4.9 - - - +
87A GLU 5.1 0.4 - - - -
88A ALA* 1.3 77.1 - - - +
90A PRO* 1.3 85.0 - - + +
91A GLY 3.4 0.3 + - - -
92A ALA* 3.4 16.1 + - - +
115A LEU* 4.2 10.1 - - + -
118A ALA* 3.6 28.3 - - + +
119A GLY* 4.0 26.7 - - - +
----------------------------------------------------------
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