Contacts of the helix formed by residues 93 - 113 (chain D) in PDB entry 4B86
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 93 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLN* 4.1 12.6 + - - -
1D MET 3.6 22.0 + - - -
3D PRO* 3.7 15.6 - - - +
54D PRO* 3.4 11.0 + - - +
56D ALA* 4.1 16.0 - - + +
65D TYR* 5.2 0.6 - - - -
91D GLU 3.4 1.7 + - - +
92D GLU* 1.3 71.8 - - - +
94D LYS* 1.3 66.7 + - - +
95D GLN* 3.3 12.5 + - - +
96D LEU* 3.3 49.3 + - + +
97D SER* 3.4 14.8 + - - -
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Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN* 3.4 44.6 + - + +
238A GLN* 5.2 9.1 + - - +
92D GLU* 3.9 14.1 + - + +
93D ASN* 1.3 71.0 + - - +
95D GLN* 1.3 66.9 + - - +
97D SER* 3.1 9.6 + - - -
98D ILE* 2.9 31.0 + - + +
78L LYS* 6.3 2.2 - - - +
79L PRO* 5.9 2.4 - - - +
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.8 20.8 - - + +
235A GLN* 4.6 11.6 + - + +
236A GLN* 3.6 22.6 + - + +
239A GLN* 2.7 41.2 + - - +
237B GLN* 3.4 20.6 - - - +
240B LEU* 4.2 1.0 - - - +
2D ASN* 3.2 22.1 - - - +
3D PRO* 3.9 14.2 - - + +
7D THR* 4.4 4.2 - - - +
93D ASN* 3.3 9.4 + - - +
94D LYS* 1.3 78.5 - - - +
96D LEU* 1.3 56.5 + - - +
98D ILE* 3.5 3.8 + - - +
99D LEU* 2.9 37.0 + - + +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PRO* 3.8 12.3 - - + -
6D ALA* 5.0 0.2 - - + -
41D SER 5.1 0.7 - - - +
42D LEU* 4.1 18.3 - - + +
51D LEU* 3.8 13.5 - - + -
54D PRO* 3.5 28.9 - - + -
55D ILE 4.9 0.4 - - - +
56D ALA* 4.2 2.5 - - + -
65D TYR* 3.5 55.0 - - + -
93D ASN* 3.3 30.3 + - + +
94D LYS 3.3 0.6 - - - -
95D GLN* 1.3 78.0 - - - +
97D SER* 1.3 57.3 + - - +
99D LEU* 3.4 5.9 + - - +
100D VAL* 2.9 33.4 + - - +
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Residues in contact with SER 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASP* 5.0 3.2 + - - -
54D PRO* 3.4 26.1 + - - +
93D ASN 3.4 8.6 + - - -
94D LYS* 3.1 12.9 + - - -
96D LEU* 1.3 73.6 - - - +
98D ILE* 1.3 68.0 + - - +
100D VAL* 3.0 7.9 + - - +
101D ASN* 3.0 30.2 + - - -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.4 33.4 - - + +
231A ASP* 3.8 25.4 - - + +
232A LEU* 3.6 20.9 - - + +
235A GLN* 3.8 28.9 - - + -
94D LYS* 2.9 23.5 + - + +
95D GLN* 3.9 5.4 - - - +
97D SER* 1.3 75.9 - - - +
99D LEU* 1.3 57.5 + - - +
101D ASN* 3.4 11.2 + - - +
102D CYS* 2.9 30.1 + - - -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.2 14.1 - - + -
3D PRO* 4.4 8.3 - - + -
6D ALA* 3.8 22.2 - - + +
7D THR* 3.5 33.7 - - + -
10D TYR* 3.8 41.3 - - + -
38D PHE* 4.6 2.4 - - + -
42D LEU* 3.7 16.5 - - + +
95D GLN* 2.9 26.2 + - + +
96D LEU* 3.6 6.1 - - - +
97D SER 3.1 0.2 - - - -
98D ILE* 1.3 74.3 - - - +
100D VAL* 1.3 59.9 + - - +
102D CYS* 3.3 5.2 - - + +
103D TYR* 2.9 28.1 + - - +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 4.5 11.7 - - + +
50D LEU* 3.8 32.1 - - + -
51D LEU* 3.7 39.5 - - + +
52D GLN 5.6 1.6 - - - +
54D PRO* 4.6 2.9 - - + -
96D LEU 2.9 20.9 + - - +
97D SER* 3.0 8.9 + - - +
99D LEU* 1.3 75.0 - - - +
101D ASN* 1.3 64.3 + - - +
103D TYR* 3.1 9.4 + - - +
104D LYS* 3.0 36.4 + - - +
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.5 33.6 - - + +
97D SER* 3.0 21.4 + - - +
98D ILE* 3.5 11.4 - - - +
100D VAL* 1.3 80.7 - - - +
102D CYS* 1.3 55.6 + - - +
104D LYS* 3.2 14.7 + - - +
105D LYS* 2.9 29.2 + - + +
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Residues in contact with CYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.3 2.9 - - - +
228A LEU* 3.7 26.4 - - - +
229A GLN 4.7 1.1 - - - -
232A LEU* 4.7 5.8 - - - -
10D TYR* 3.5 49.1 - - + -
98D ILE* 2.9 29.9 + - - +
99D LEU* 3.3 13.7 - - - +
101D ASN* 1.3 72.0 - - - +
103D TYR* 1.3 60.3 + - - +
105D LYS* 3.4 2.2 + - - +
106D LEU* 2.9 31.7 + - - +
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 4.6 9.7 + - + +
38D PHE* 3.2 46.4 - + + -
39D ARG* 3.0 47.9 + - + +
42D LEU* 4.0 9.9 - - + -
50D LEU* 3.9 31.0 - - + -
99D LEU 2.9 14.1 + - - +
100D VAL* 3.1 8.0 + - - +
102D CYS* 1.3 76.4 - - - +
104D LYS* 1.3 59.8 + - + +
106D LEU* 3.3 1.9 + - + +
107D CYS* 2.9 59.9 + - - -
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 3.8 27.4 - - + -
100D VAL* 3.0 21.8 + - + +
101D ASN* 3.2 19.4 + - - +
103D TYR* 1.3 80.6 - - + +
105D LYS* 1.3 65.0 + - + +
107D CYS* 3.4 6.1 + - - +
108D GLU* 2.9 27.8 + - - +
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A CYS* 4.0 11.1 - - - -
224A GLN* 2.8 48.6 + - + +
225A ILE* 4.3 21.2 - - + +
228A LEU* 4.0 16.8 - - + -
101D ASN* 2.9 22.7 + - + +
102D CYS 4.1 2.2 - - - +
104D LYS* 1.3 79.9 - - + +
106D LEU* 1.3 60.5 + - - +
108D GLU* 3.2 31.4 + - - +
109D TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.1 14.9 - - + +
10D TYR* 4.7 2.7 - - + -
13D ALA* 4.0 28.5 - - + -
14D SER* 3.4 33.7 - - - +
17D VAL* 4.3 17.7 - - + -
18D LEU* 5.1 5.8 - - + -
35D LEU* 5.1 4.0 - - + -
38D PHE* 4.1 18.4 - - + -
102D CYS 2.9 18.3 + - - +
103D TYR* 3.7 3.8 - - + +
105D LYS* 1.3 75.4 - - - +
107D CYS* 1.3 57.5 + - - +
109D TYR* 3.4 9.4 + - + +
110D ILE* 2.9 47.7 + - + +
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Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 4.8 11.9 - - - -
103D TYR* 2.9 62.3 + - - +
104D LYS* 3.5 6.7 - - - +
105D LYS 3.3 0.2 - - - -
106D LEU* 1.3 77.2 - - - +
108D GLU* 1.3 55.7 + - - +
110D ILE* 3.3 9.9 + - - +
111D THR* 2.9 34.4 + - - +
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A CYS* 4.4 6.1 - - - -
104D LYS 2.9 13.1 + - - +
105D LYS* 3.2 45.2 + - - +
107D CYS* 1.3 76.9 - - - +
109D TYR* 1.3 58.1 + - - +
111D THR* 3.3 7.6 + - - -
112D GLN* 2.9 53.6 + - + +
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLN* 4.0 24.3 + - + -
221A CYS* 4.0 17.2 - - + -
222A LEU* 3.7 38.5 - - + +
225A ILE* 6.0 3.8 - - + -
223B LYS* 4.1 21.8 + - - +
17D VAL* 3.8 31.5 + - + -
18D LEU* 4.4 12.4 - - + +
105D LYS 2.9 16.1 + - - +
106D LEU* 3.8 9.9 - - + +
108D GLU* 1.3 72.6 - - - +
110D ILE* 1.3 67.4 + - - +
112D GLN* 3.7 4.7 - - + -
113D THR* 3.0 50.5 + - + +
115D LEU* 5.6 1.1 - - + -
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.7 40.6 - - + -
31D ILE* 4.9 3.6 - - + -
35D LEU* 4.1 28.3 - - + -
106D LEU* 2.9 31.9 + - + +
107D CYS* 3.6 8.3 - - - +
109D TYR* 1.3 77.0 - - - +
111D THR* 1.3 59.3 + - - +
113D THR* 2.8 25.4 + - - +
115D LEU* 4.8 14.6 - - + +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D CYS* 2.9 18.5 + - - +
108D GLU* 3.6 7.6 - - - -
109D TYR 3.3 0.2 - - - -
110D ILE* 1.3 79.8 - - - +
112D GLN* 1.3 61.5 + - + +
113D THR 4.0 2.9 - - - +
114D THR* 5.9 0.7 - - - +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.1 41.5 + - - +
218A GLN* 3.6 9.8 + - + +
221A CYS* 3.9 16.9 - - - +
108D GLU* 2.9 42.0 + - + +
109D TYR* 3.3 7.3 + - + +
111D THR* 1.3 79.4 - - + +
113D THR* 1.3 62.9 + - + +
114D THR* 5.2 2.6 - - - +
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Residues in contact with THR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLN* 3.4 41.5 - - + +
109D TYR* 3.0 44.1 + - + +
110D ILE* 2.8 21.5 + - - +
111D THR 4.0 2.3 - - - +
112D GLN* 1.3 78.4 - - + +
114D THR* 1.3 66.0 + - - +
115D LEU* 4.0 18.0 + - - +
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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) + - + + + + + -
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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