Contacts of the helix formed by residues 90 - 109 (chain A) in PDB entry 4WNF
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 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 2.8 35.7 + - - -
55A SER* 5.2 1.2 + - - -
85A ALA* 2.9 16.4 + - - +
88A ILE* 3.8 22.8 - - + +
89A GLY* 1.3 73.8 - - - +
91A GLN* 1.3 64.2 + - - +
92A LEU* 3.5 8.7 + - - +
93A GLY* 3.1 22.6 + - - -
94A GLU* 2.8 21.8 + - - +
1005B LYS* 4.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY* 3.6 8.0 + - - +
90A ASP* 1.3 72.0 + - - +
92A LEU* 1.3 58.5 + - - +
94A GLU* 3.1 17.5 + - - +
95A ALA* 2.7 28.8 + - - +
120A ARG* 5.4 3.4 - - - +
124A ILE* 3.5 30.0 - - + +
127A GLU* 3.9 23.0 + - - +
128A LEU* 3.9 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP* 3.3 7.6 + - - +
91A GLN* 1.3 76.3 - - - +
93A GLY* 1.3 59.2 + - - +
95A ALA* 2.9 11.3 + - + +
96A LYS* 2.8 61.9 + - + +
125A SER* 5.7 2.7 - - - +
128A LEU* 4.0 23.7 - - + +
130A ASP* 4.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 5.0 0.4 - - - -
85A ALA* 3.6 4.7 - - - -
90A ASP* 2.9 23.5 + - - -
92A LEU* 1.3 79.0 - - - +
94A GLU* 1.3 55.3 + - - +
96A LYS* 3.4 2.3 + - - -
97A ALA* 2.9 26.9 + - - +
1005B LYS* 3.1 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.7 19.8 - - + +
85A ALA* 3.4 15.2 - - + +
86A ARG* 3.1 38.6 + - + +
90A ASP 2.8 14.1 + - - +
91A GLN* 3.5 17.9 + - - +
93A GLY* 1.3 70.2 - - - +
95A ALA* 1.3 65.1 + - - +
98A SER* 3.0 26.4 + - - +
120A ARG* 3.2 28.5 + - - -
124A ILE* 3.6 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN 2.7 16.5 + - - +
92A LEU* 3.2 17.7 - - + +
94A GLU* 1.3 73.2 - - - +
96A LYS* 1.3 64.7 + - + +
98A SER* 3.3 4.6 - - - -
99A GLY 3.1 16.6 + - - -
121A HIS* 3.3 30.2 - - + +
124A ILE* 3.6 30.2 - - + +
125A SER* 4.3 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 2.8 51.1 + - + +
93A GLY* 3.7 7.0 - - - +
95A ALA* 1.3 75.6 - - + +
97A ALA* 1.3 65.8 + - - +
99A GLY* 2.9 11.4 + - - -
100A ASN* 3.0 22.0 + - - +
121A HIS* 4.9 1.3 - - - +
136A ARG* 6.1 1.0 - - - +
1003B GLU* 3.4 35.9 - - + +
1004B THR 3.2 28.4 + - - +
1005B LYS* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 4.0 6.2 - - - +
81A ASP* 3.2 27.6 - - + +
82A LEU* 3.4 35.9 - - + +
93A GLY 2.9 15.6 + - - +
94A GLU 4.2 1.3 - - - +
96A LYS* 1.3 76.2 - - - +
98A SER* 1.3 53.6 + - - +
100A ASN* 3.3 7.1 + - - +
101A LEU* 2.8 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.0 16.5 - - - +
86A ARG* 4.8 0.3 + - - -
94A GLU 3.0 21.4 + - - -
95A ALA* 3.3 6.5 - - - -
97A ALA* 1.3 75.6 - - - +
99A GLY* 1.3 53.1 + - - -
101A LEU* 3.2 5.8 + - - +
102A GLY* 2.7 34.5 + - - -
117A CYS* 3.3 27.3 + - - +
120A ARG* 3.6 24.3 - - - +
121A HIS* 4.1 7.4 - - - -
124A ILE* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 3.1 4.2 + - - -
96A LYS 2.9 8.3 + - - -
98A SER* 1.3 78.7 - - - +
100A ASN* 1.3 59.9 + - - +
102A GLY* 3.0 2.9 + - - -
103A ASN* 2.8 39.3 + - - +
117A CYS 4.8 0.7 - - - -
118A CYS* 4.5 4.4 - - - -
121A HIS* 3.5 29.4 - - - +
140A ASN* 4.7 4.0 - - - -
1003B GLU* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.8 12.1 + - - -
63A ASN* 3.7 8.1 + - - -
78A HIS* 3.4 35.9 + - + +
96A LYS* 3.0 17.8 + - - +
97A ALA* 3.7 4.4 - - - +
99A GLY* 1.3 76.0 - - - +
101A LEU* 1.3 63.5 + - - +
103A ASN* 3.3 1.2 + - - -
104A THR* 2.7 30.2 + - - -
1002B MET* 3.4 18.1 - - + +
1003B GLU* 3.0 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.4 44.0 - - + +
78A HIS* 3.7 6.1 - - + +
79A HIS* 3.5 29.2 - - + +
82A LEU* 3.5 33.0 - - + -
97A ALA 2.8 20.0 + - - +
98A SER 3.6 3.8 - - - +
100A ASN* 1.3 74.0 - - - +
102A GLY* 1.3 52.6 - - - +
104A THR* 3.0 5.2 + - - -
105A LEU* 2.7 49.7 + - + +
113A GLU* 5.5 3.1 - - - +
117A CYS* 4.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER 2.7 15.5 + - - -
99A GLY 3.4 3.6 - - - -
101A LEU* 1.3 73.6 - - - +
103A ASN* 1.3 62.5 + - - +
105A LEU 3.2 0.5 + - - -
106A LYS* 2.9 19.6 + - - +
114A ALA* 3.4 16.0 - - - +
117A CYS* 3.5 22.6 - - - +
118A CYS* 3.7 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.5 4.0 - - + -
99A GLY 2.8 23.1 + - - +
100A ASN* 3.8 4.0 + - - +
102A GLY* 1.3 70.6 - - - +
104A THR* 1.3 58.6 + - - +
106A LYS* 2.9 32.7 + - - +
107A VAL* 3.0 17.7 + - - +
118A CYS* 3.9 4.9 - - - -
140A ASN* 3.2 40.8 + - - +
143A ASN* 5.6 0.7 + - - -
144A VAL* 5.3 0.7 - - - +
1000B GLU* 4.7 9.2 - - + +
1001B THR 2.8 29.1 + - - -
1002B MET* 3.7 20.7 - - - +
1003B GLU* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.8 22.5 - - + -
71A TYR* 3.5 34.3 - - + +
74A ALA* 4.1 5.1 - - + +
75A LEU* 3.6 22.7 - - + +
78A HIS* 3.9 11.4 + - - -
100A ASN 2.7 20.8 + - - -
101A LEU* 3.4 9.4 - - - -
103A ASN* 1.3 74.0 - - - +
105A LEU* 1.3 65.3 + - - +
107A VAL* 3.0 13.2 + - - +
108A LEU* 3.0 16.4 + - + +
1002B MET* 4.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.5 29.2 - - + -
101A LEU* 2.7 32.4 + - + +
102A GLY 3.5 4.3 - - - +
104A THR* 1.3 72.5 - - - +
106A LYS* 1.3 62.3 + - - +
108A LEU* 3.3 4.8 + - - +
109A GLY 3.0 17.0 + - - -
110A ASN* 3.0 33.5 + - + +
113A GLU* 4.0 28.5 - - - +
114A ALA* 3.7 18.8 - - + +
117A CYS* 3.9 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 2.9 12.8 + - - +
103A ASN* 2.9 23.2 + - - +
105A LEU* 1.3 76.0 - - - +
107A VAL* 1.3 68.5 + - - +
109A GLY* 3.0 15.2 + - - -
111A PHE* 3.7 13.7 - - + -
114A ALA* 3.8 6.5 - - + +
140A ASN 5.2 0.2 - - - +
143A ASN* 3.8 38.5 - - + +
144A VAL* 4.0 25.1 - - + +
147A ALA* 4.1 15.0 - - + +
1000B GLU* 2.9 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.8 26.0 - - + -
71A TYR* 3.5 49.4 - - + -
103A ASN 3.0 15.1 + - - +
104A THR 3.0 8.5 + - - +
106A LYS* 1.3 85.9 - - - +
108A LEU* 1.3 59.5 + - + +
109A GLY* 3.6 0.3 + - - -
1000B GLU* 4.2 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 4.0 27.1 - - + +
72A ALA* 4.8 8.3 - - + +
75A LEU* 3.4 34.8 - - + -
104A THR* 3.0 20.0 + - + +
105A LEU 3.8 3.1 - - - +
106A LYS 3.1 0.2 - - - -
107A VAL* 1.3 78.2 - - - +
109A GLY* 1.3 58.7 + - - +
110A ASN* 3.5 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 3.0 0.6 + - - -
106A LYS 3.0 16.1 + - - -
107A VAL 3.3 0.8 - - - -
108A LEU* 1.3 79.4 - - - +
110A ASN* 1.3 65.3 + - - +
111A PHE* 3.4 31.1 + - - -
----------------------------------------------------------
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