Contacts of the helix formed by residues 152 - 174 (chain A) in PDB entry 2DXU
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 PRO 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 5.3 1.3 - - + -
150A GLU* 4.3 5.6 - - - +
151A VAL* 1.3 86.9 - - + +
153A LEU* 1.3 67.1 + - - +
154A LEU* 3.2 2.9 - - + +
155A SER* 3.0 33.7 + - - +
156A VAL* 3.2 13.2 + - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 5.2 3.4 - - - +
58A GLY* 4.0 15.3 - - - +
59A GLY 3.6 26.7 - - - +
60A LEU* 4.0 10.3 - - + -
132A VAL* 3.7 32.8 - - + -
133A ASN* 4.5 6.4 - - - +
151A VAL 3.0 7.1 + - - +
152A PRO* 1.3 70.7 - - - +
154A LEU* 1.3 62.1 + - - +
156A VAL* 3.1 9.5 + - + +
157A PHE* 3.0 21.0 + - - +
1B MET* 3.6 36.6 - - + +
3B GLY* 6.5 0.2 - - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.5 9.6 - - + -
152A PRO* 3.2 2.8 - - + -
153A LEU* 1.3 78.9 - - - +
155A SER* 1.3 58.2 + - - +
157A PHE* 3.2 5.6 + - + -
158A ARG* 2.9 61.4 + - + +
1B MET* 3.6 40.1 + - + +
2B LEU* 4.7 1.6 - - + -
154B LEU* 3.2 33.9 - - + -
158B ARG* 4.8 7.9 - - - +
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.0 18.8 - - - -
152A PRO* 3.0 29.2 + - - +
154A LEU* 1.3 78.1 - - - +
156A VAL* 1.3 62.7 + - - +
158A ARG* 3.8 9.7 - - - +
159A SER* 3.0 24.3 + - - -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.0 9.9 - - + -
89A THR* 4.0 10.3 - - + -
93A PHE* 3.9 13.5 - - + -
130A LEU* 3.7 30.1 - - + -
132A VAL* 4.2 12.8 - - + -
143A MET* 3.9 17.5 - - - -
151A VAL* 3.8 22.9 - - + -
152A PRO 3.5 13.0 - - - +
153A LEU* 3.1 8.2 + - + +
155A SER* 1.3 73.9 - - - +
157A PHE* 1.3 65.2 + - - +
159A SER* 3.3 1.6 + - - -
160A LEU* 2.9 23.4 + - + +
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.7 4.5 - - + -
4A LEU* 4.4 19.5 - - + -
13A VAL* 4.0 24.7 - - + -
36A VAL* 4.0 18.2 - - + -
38A VAL* 4.4 9.0 - - + -
60A LEU* 4.0 15.7 - - + +
62A LEU* 4.0 19.5 - - + -
153A LEU 3.0 12.7 + - - +
154A LEU* 3.4 14.1 - - + +
156A VAL* 1.3 77.2 - - - +
158A ARG* 1.3 71.2 + - + +
160A LEU* 3.3 1.3 + - - +
161A ILE* 2.9 51.4 + - + +
1B MET* 3.6 44.4 - - + -
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 5.1 1.2 + - - -
2A LEU* 2.8 41.7 + - - +
3A GLY 4.8 2.6 + - - -
4A LEU* 3.8 20.0 - - + +
154A LEU* 2.9 53.9 + - + +
155A SER* 3.8 7.4 - - - +
157A PHE* 1.3 82.8 - - + +
159A SER* 1.3 64.2 + - - +
161A ILE* 3.5 3.6 + - - +
162A THR* 3.1 29.5 + - - +
154B LEU* 4.9 6.9 - - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 2.9 23.3 + - - +
92A GLU* 2.7 31.0 + - - -
93A PHE* 4.1 8.1 - - - -
155A SER 3.0 17.7 + - - -
156A VAL 3.6 4.3 - - - -
157A PHE 3.3 0.2 - - - -
158A ARG* 1.3 77.4 - - - +
160A LEU* 1.3 62.1 - - - +
162A THR* 3.3 6.7 + - - -
163A ASN* 3.0 26.0 + - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 23.1 - - + -
62A LEU* 4.3 13.9 - - + -
85A GLY* 3.5 33.2 - - - +
86A VAL* 3.7 13.0 - - + +
89A THR* 3.2 12.5 + - + +
128A ILE* 4.4 20.9 - - + -
130A LEU* 5.1 5.2 - - + -
156A VAL 2.9 18.1 + - - +
157A PHE 3.8 2.7 - - - +
159A SER* 1.3 77.0 - - - +
161A ILE* 1.3 58.8 + - + +
163A ASN* 3.2 1.5 + - - +
164A LEU* 2.9 55.2 + - + +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.5 11.4 - - + -
6A THR* 3.9 10.5 - - + +
9A ILE* 3.4 34.0 - - + +
10A GLY* 4.3 5.8 - - - -
36A VAL* 4.0 25.4 - - + -
62A LEU* 4.5 8.7 - - + -
64A ILE* 4.4 9.6 - - + -
157A PHE* 2.9 50.8 + - + +
158A ARG* 4.0 4.3 - - - +
160A LEU* 1.3 76.9 - - + +
162A THR* 1.3 64.6 + - - +
164A LEU* 3.4 5.3 + - + +
165A ASP* 2.9 23.4 + - - +
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 4.0 15.5 - - + +
158A ARG* 3.1 19.1 + - - +
159A SER* 3.6 6.3 - - - +
160A LEU 3.3 0.2 - - - -
161A ILE* 1.3 78.1 - - - +
163A ASN* 1.3 65.1 + - - +
165A ASP* 3.5 2.1 + - - +
166A ARG* 3.2 33.8 + - + +
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY* 4.2 11.2 - - - +
88A GLU* 3.6 15.6 - - - +
89A THR* 3.0 34.1 + - - +
92A GLU* 2.9 28.1 + - - +
159A SER 3.0 13.5 + - - +
160A LEU 3.7 3.6 - - - +
162A THR* 1.3 80.2 - - - +
164A LEU* 1.3 56.8 + - - +
166A ARG* 2.7 36.8 + - - +
167A LEU* 3.0 34.2 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.6 15.2 - - + +
62A LEU* 5.1 0.7 - - + -
64A ILE* 3.4 27.4 - - + -
81A LEU* 3.4 29.3 - - + +
82A GLY* 4.0 12.8 - - - -
85A GLY* 4.0 10.5 - - - -
126A LEU* 4.6 6.3 - - + -
128A ILE* 3.8 12.6 - - + -
160A LEU* 2.9 42.3 + - + +
161A ILE* 3.9 7.6 - - + +
163A ASN* 1.3 72.5 - - - +
165A ASP* 1.3 61.4 + - - +
167A LEU* 3.8 4.1 - - + +
168A TYR* 2.8 32.4 + - - +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 3.5 20.0 - - + +
7A SER* 2.8 30.6 + - - -
8A ILE* 2.9 27.6 + - - +
9A ILE* 2.9 22.1 + - + +
161A ILE 2.9 17.9 + - - +
162A THR 3.8 2.9 - - - +
163A ASN 3.3 0.2 - - - -
164A LEU* 1.3 77.3 - - - +
166A ARG* 1.3 62.2 + - - +
168A TYR* 3.8 1.6 - - - +
169A LEU* 3.0 38.2 + - - +
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU* 3.0 26.9 + - - +
162A THR* 3.2 19.2 + - - +
163A ASN* 2.7 37.9 + - - +
165A ASP* 1.3 81.1 - - - +
167A LEU* 1.3 65.6 + - - +
169A LEU* 3.8 8.5 - - - +
170A ASN* 3.1 25.2 + - + +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.8 25.8 - - + +
84A VAL* 4.0 8.5 - - + -
85A GLY* 3.6 36.1 - - - +
88A GLU* 3.6 16.2 - - - +
163A ASN 3.0 22.6 + - - +
164A LEU* 3.8 6.1 - - - +
166A ARG* 1.3 80.7 - - + +
168A TYR* 1.3 57.3 + - - +
170A ASN* 3.4 5.5 + - - +
171A PHE* 2.9 28.2 + - - +
178A ILE* 4.2 8.3 - - + -
181A LEU* 3.6 31.4 - - + -
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.2 19.7 - - + -
9A ILE* 3.7 19.7 - - + -
33A GLU* 2.6 29.2 + - - -
66A LEU* 3.8 26.7 - - + -
67A SER 3.6 0.5 + - - -
68A PRO* 3.2 39.9 - - + +
78A ILE* 4.6 0.7 - - + -
81A LEU* 4.0 21.3 - - + -
164A LEU 2.8 17.5 + - - +
165A ASP* 3.8 2.7 - - - +
167A LEU* 1.3 75.6 - - - +
169A LEU* 1.3 68.3 + - + +
171A PHE* 3.1 10.3 + + - +
172A LEU* 3.0 51.8 + - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER* 3.9 18.2 - - - +
8A ILE* 3.7 33.0 - - + -
165A ASP* 3.0 41.4 + - - +
166A ARG* 3.8 7.4 - - - +
168A TYR* 1.3 78.0 - - + +
170A ASN* 1.3 62.4 + - - +
172A LEU* 3.4 17.9 + - + +
173A LYS* 3.6 21.6 + - - +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.1 18.1 + - + +
167A LEU* 3.9 4.9 - - - +
169A LEU* 1.3 75.5 - - - +
171A PHE* 1.3 55.9 + - - +
173A LYS* 3.2 12.1 + - - +
174A ASN* 2.7 56.7 + - - +
177A ASP* 3.0 36.8 + - - +
181A LEU* 6.3 1.2 - - - +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PRO* 4.6 2.9 - - + -
70A VAL* 4.0 23.9 - - + +
74A ASP* 3.5 26.0 - - + -
77A LYS* 4.0 19.7 - - + -
78A ILE* 3.4 31.2 - - + -
81A LEU* 3.9 22.9 - - + -
167A LEU 2.9 15.2 + - - +
168A TYR* 3.1 19.0 + + - +
170A ASN* 1.3 79.3 - - - +
172A LEU* 1.3 63.4 + - + +
174A ASN 4.1 4.9 - - - -
175A PRO* 3.1 59.3 - - + +
178A ILE* 4.2 7.2 - - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.2 16.2 - - + -
33A GLU* 5.5 1.3 - - - +
68A PRO* 4.1 3.8 - - + -
69A LYS* 4.0 26.5 - - + +
70A VAL* 4.2 19.9 - - + +
168A TYR* 3.0 58.1 + - + +
169A LEU* 3.6 13.9 - - + +
170A ASN 3.2 0.2 - - - -
171A PHE* 1.3 78.6 - - + +
173A LYS* 1.3 64.6 + - + +
175A PRO* 4.5 2.4 - - - +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.6 19.8 + - - +
170A ASN* 3.2 16.7 + - - +
172A LEU* 1.3 83.5 - - + +
174A ASN* 1.3 76.5 + - - +
175A PRO* 3.7 5.9 - - - +
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASN* 2.7 37.8 + - - +
171A PHE* 4.1 3.1 - - - -
173A LYS* 1.3 92.2 - - - +
175A PRO* 1.3 59.0 - - - +
176A MET* 3.0 12.0 + - - +
177A ASP* 3.1 38.4 + - - +
178A ILE 4.6 0.7 + - - -
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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