Contacts of the strand formed by residues 229 - 247 (chain A) in PDB entry 3DPR
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 VAL 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 2.8 39.8 - - + +
129A ILE* 4.5 14.6 - - + -
130A SER 3.8 7.9 - - - +
131A ALA* 4.1 6.1 - - - -
132A LEU* 3.6 17.5 - - - +
135A ASP 4.3 12.8 - - - +
136A ILE* 4.7 12.3 - - - +
139A ILE* 5.3 9.2 - - + -
220A ILE* 6.1 0.9 - - + -
225A HIS* 5.0 5.2 - - + +
227A HIS* 3.6 15.0 - - + +
228A LYS* 1.3 88.9 - - - +
230A HIS* 1.3 77.5 + - - +
231A ILE* 4.8 5.2 - - + -
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.8 25.8 + - - -
82A LEU 3.7 2.2 - - - +
83A GLU* 3.3 46.9 + - + +
84A VAL* 4.0 3.8 + - - -
128A CYS 3.3 3.6 - - - +
129A ILE* 3.4 0.5 - - - -
130A SER* 3.0 47.2 + - - +
132A LEU* 3.8 25.1 - - + +
228A LYS* 5.6 1.8 - - - +
229A VAL* 1.3 96.2 - - - +
231A ILE* 1.3 69.8 + - - +
232A MET* 5.6 0.7 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.4 5.8 - - - +
82A LEU* 2.8 58.9 + - + +
84A VAL* 5.0 4.0 - - + -
127A PRO* 5.9 1.6 - - + -
128A CYS 3.6 2.9 - - - +
129A ILE* 4.0 28.0 - - + -
139A ILE* 4.4 15.3 - - + -
141A MET* 4.0 39.0 - - + -
143A TYR* 4.3 3.4 - - - +
171A TRP* 5.8 2.9 - - + -
218A SER* 5.6 0.4 - - - +
220A ILE* 6.0 0.4 - - + -
229A VAL* 4.8 7.2 - - + -
230A HIS* 1.3 81.7 - - - +
232A MET* 1.3 60.0 + - - +
233A THR* 3.2 26.2 - - + +
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.4 18.2 - - + +
80A SER 3.1 24.9 - - - +
81A LYS* 3.7 28.7 - - + -
126A VAL 3.1 12.5 - - - +
128A CYS* 2.8 37.1 + - + +
130A SER* 5.0 7.2 - - - +
230A HIS* 5.6 0.7 - - + -
231A ILE* 1.3 72.0 - - - +
233A THR* 1.3 82.3 + - - +
234A ARG* 3.4 27.1 + - - +
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.6 0.2 - - - -
80A SER* 3.0 38.4 + - - -
125A LEU* 4.7 9.4 - - + -
126A VAL 3.3 2.5 - - - -
127A PRO* 3.4 31.4 - - + -
143A TYR* 2.6 48.1 + - + +
218A SER* 4.8 2.6 + - - -
231A ILE* 3.2 15.4 + - + +
232A MET* 1.3 73.5 - - - +
234A ARG* 1.3 62.9 + - - +
235A ILE* 3.9 6.3 + - - +
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Residues in contact with ARG 234 (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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76A CYS* 4.5 1.1 - - - -
78A HIS 3.5 4.0 - - - +
79A GLU* 3.2 46.0 + - + +
124A THR 3.8 0.5 - - - +
125A LEU* 3.5 5.0 - - - +
126A VAL* 2.7 44.8 + - + +
128A CYS* 4.9 11.7 - - - +
232A MET* 3.5 29.2 + - + +
233A THR* 1.3 75.7 - - - +
235A ILE* 1.3 62.7 + - - +
236A TYR* 3.6 33.2 + - + -
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Residues in contact with ILE 235 (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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76A CYS* 3.3 7.1 - - - -
77A ILE* 3.0 51.3 + - + -
78A HIS* 2.6 44.2 + - + +
80A SER* 5.0 4.5 - - - -
97A TRP* 4.8 3.1 - - + -
123A ILE* 4.3 16.6 - - + -
124A THR 3.6 4.7 - - - +
125A LEU* 3.9 18.6 - - + -
143A TYR* 6.5 0.2 - - + -
216A LEU* 3.5 30.1 - - + -
233A THR* 4.3 9.6 - - - +
234A ARG* 1.3 78.2 - - - +
236A TYR* 1.3 67.9 + - - +
290A DAO 5.7 2.7 - - + -
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Residues in contact with TYR 236 (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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74A SER* 3.7 14.8 - - - +
75A GLY* 3.1 25.6 - - - -
76A CYS* 3.2 28.6 - - + +
122A GLU 3.5 0.2 - - - +
123A ILE* 3.3 5.4 - - - +
124A THR* 2.5 50.3 + - - +
126A VAL* 3.8 24.9 - - + -
234A ARG* 3.6 39.6 + - + -
235A ILE* 1.3 79.3 - - - +
237A HIS* 1.3 60.9 + - - +
13C PHE* 4.2 12.1 - + + -
15C THR* 4.9 9.9 - - + -
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Residues in contact with HIS 237 (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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73A ARG 3.4 3.6 - - - +
74A SER* 3.4 6.1 + - - -
75A GLY* 2.8 31.6 + - - +
77A ILE* 4.3 20.7 - - + +
101A LEU* 4.3 12.4 - - + +
107A ILE* 4.4 7.0 - - + +
111A PHE* 4.2 15.4 - + - -
119A PHE* 3.4 25.0 - + - -
121A SER* 3.4 24.3 + - - -
122A GLU 3.4 3.6 - - - -
123A ILE* 3.7 13.7 - - + -
236A TYR* 1.3 75.3 - - - +
238A LYS* 1.3 58.4 + - - +
239A ALA* 3.3 34.1 - - + -
290A DAO 4.1 12.0 - - + +
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Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 3.4 32.1 - - - +
73A ARG* 3.8 5.6 - - - +
74A SER* 3.8 16.7 + - - +
121A SER* 3.5 3.8 - - - -
122A GLU* 2.8 67.0 + - + +
237A HIS* 1.3 75.9 - - - +
239A ALA* 1.3 69.0 + - - +
240A LYS* 3.8 15.8 + - + +
15C THR 4.7 1.8 - - - +
16C THR 5.6 0.2 - - - -
17C ASP* 2.6 44.6 + - - +
18C ASP* 3.3 17.8 + - - +
19C PHE 4.2 1.2 + - - +
40D ALA* 5.6 3.1 - - - +
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Residues in contact with ALA 239 (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 GLU* 4.4 2.3 - - - +
71A LEU* 3.2 26.8 + - + +
72A GLY* 3.3 22.7 + - - -
111A PHE* 4.0 6.7 - - + -
119A PHE* 3.9 15.5 - - + -
120A ASP 3.7 3.6 - - - -
237A HIS* 3.3 19.2 - - + -
238A LYS* 1.3 73.1 - - - +
240A LYS* 1.4 60.7 + - - +
242A VAL* 3.9 18.0 - - + +
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Residues in contact with LYS 240 (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 GLU* 3.5 4.7 - - - +
119A PHE* 3.2 3.1 - - - +
120A ASP* 2.9 38.1 + - + +
121A SER 5.1 1.8 - - - -
122A GLU* 4.1 17.4 + - + +
181A SER* 3.9 5.6 + - - -
238A LYS* 4.4 29.4 - - - +
239A ALA* 1.4 77.7 - - - +
241A HIS* 1.3 86.7 + - + +
242A VAL* 3.5 1.8 - - - -
18C ASP* 5.5 0.2 - - - +
19C PHE 4.2 7.8 + - - +
21C SER* 3.4 22.6 + - - -
36D ALA 3.1 22.0 + - - -
37D SER 3.5 5.5 + - - -
38D ASN 3.0 25.1 + - - +
39D GLY* 4.4 9.6 - - - +
40D ALA* 4.7 3.1 - - + +
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Residues in contact with HIS 241 (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 GLU* 2.4 28.0 + - - -
118A ARG* 3.6 4.0 - - - +
119A PHE* 3.5 10.9 - - - -
120A ASP* 2.8 24.2 + - - +
240A LYS* 1.3 81.8 - - + +
242A VAL* 1.3 57.9 + - - +
243A LYS* 4.1 2.8 + - - +
35D ALA 3.7 15.8 + - - -
36D ALA 3.6 14.8 - - - -
38D ASN* 3.2 18.2 + - + +
39D GLY 2.6 29.6 + - - -
41D SER* 3.7 23.1 - - - +
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Residues in contact with VAL 242 (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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67A LEU* 4.2 22.9 - - + +
68A GLU* 2.5 29.1 + - - +
71A LEU* 4.0 26.7 - - + -
117A THR* 6.0 0.9 - - - -
118A ARG 3.5 3.6 - - - +
119A PHE* 3.6 23.6 - - + -
239A ALA* 3.9 22.7 - - + +
240A LYS 3.8 7.4 - - - -
241A HIS* 1.3 71.2 - - - +
243A LYS* 1.3 82.9 + - - +
244A ALA* 5.3 0.2 - - + -
39C GLU* 5.1 0.2 - - - +
41C LYS* 5.7 2.1 + - - +
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Residues in contact with LYS 243 (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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67A LEU* 4.0 4.9 - - - -
117A THR* 3.4 1.4 - - - -
118A ARG* 3.0 38.9 + - + +
241A HIS 5.2 2.9 - - - +
242A VAL* 1.3 84.4 - - - +
244A ALA* 1.3 64.9 + - - +
245A TRP* 3.5 21.3 - - + -
33C GLU* 3.5 37.5 + - - +
39C GLU* 3.7 22.1 + - - +
41C LYS* 4.2 19.3 - - - +
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Residues in contact with ALA 244 (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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67A LEU* 3.6 17.2 - - + +
71A LEU* 5.7 1.6 - - + -
114A PHE* 3.8 27.6 - - + -
116A TYR 3.2 11.9 - - - +
117A THR* 4.1 5.4 - - + -
242A VAL* 5.3 1.8 - - + -
243A LYS* 1.3 78.3 - - - +
245A TRP* 1.3 72.8 + - - +
39C GLU* 3.3 2.1 + - - +
40C VAL* 2.8 32.7 + - - +
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Residues in contact with TRP 245 (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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114A PHE* 3.3 6.3 - - - +
115A THR 3.2 10.9 + - - -
116A TYR* 3.0 28.3 + - + -
117A THR* 4.1 2.2 - - - -
118A ARG* 3.9 25.8 - - + -
189A SER* 5.5 1.8 - - - -
190A ALA* 4.4 7.6 - - + -
243A LYS* 3.3 50.7 - - + -
244A ALA* 1.3 81.0 - - - +
246A CYS* 1.3 82.8 + - - +
247A PRO* 3.7 1.3 - - - -
33C GLU* 4.7 9.4 - - + -
36C ILE* 2.6 63.9 + - + +
37C PRO 3.2 10.1 - - - +
38C GLY 3.4 6.5 - - - +
39C GLU* 3.3 24.9 - - + +
40C VAL* 4.6 0.7 - - - -
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Residues in contact with CYS 246 (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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115A THR* 2.4 45.6 + - - +
116A TYR* 4.3 8.1 - - - -
245A TRP* 1.3 88.1 - - - +
247A PRO* 1.3 71.9 - - - +
35B TYR* 3.3 37.9 - - - +
128B PRO* 4.4 6.5 - - + -
207B VAL* 3.9 25.6 - - - -
37C PRO 4.3 4.3 - - - -
38C GLY 3.1 9.9 + - - -
40C VAL* 4.6 0.4 - - - +
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Residues in contact with PRO 247 (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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113A LEU* 3.2 10.5 - - + +
114A PHE* 3.8 11.0 - - + -
245A TRP 3.7 0.4 - - - -
246A CYS* 1.3 90.8 - - - +
248A ARG* 1.3 62.2 + - - +
35B TYR* 3.8 18.7 + - + +
186B ILE* 3.4 39.0 - - + +
187B PHE* 4.2 3.8 - - - -
38C GLY 5.1 0.2 - - - +
40C VAL* 4.2 15.3 - - + -
46C ILE* 3.4 29.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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