Contacts of the helix formed by residues 93 - 104 (chain D) in PDB entry 2P2N
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 THR 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B PRO* 4.3 11.9 - - + -
242B TYR* 3.3 42.0 - - + +
60D SER* 2.8 39.6 + - - +
61D SER 5.0 0.2 - - - -
63D MET* 3.9 7.2 - - - +
68D TRP* 5.8 0.6 + - - -
89D HIS* 3.6 8.1 - - - -
92D ASP* 1.3 79.1 - - - +
94D MET* 1.3 65.8 + - - +
95D ALA 3.2 3.8 - - - +
96D TYR* 3.1 16.6 + - + -
97D THR* 3.1 19.8 + - - -
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Residues in contact with MET 94 (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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89D HIS* 3.5 29.4 - - - +
90D GLY 3.4 11.4 + - - +
91D THR* 3.2 19.4 + - + -
93D THR* 1.3 77.1 - - - +
95D ALA* 1.3 58.0 + - - +
97D THR* 3.3 2.9 + - - -
98D ALA* 2.9 27.5 + - - +
114D VAL* 3.3 22.3 - - + +
115D THR* 3.4 39.7 - - - +
116D GLY* 3.5 6.5 - - - +
149D LEU* 3.7 31.9 - - + -
151D PHE* 4.1 3.4 - - + -
172D PHE* 3.6 16.2 - - + -
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Residues in contact with ALA 95 (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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93D THR 3.2 0.6 - - - -
94D MET* 1.3 76.3 - - - +
96D TYR* 1.3 61.7 + - + +
98D ALA* 3.9 1.2 - - - +
99D SER* 2.7 34.8 + - - -
149D LEU* 4.3 2.9 - - - -
158D GLY 4.2 0.5 - - - +
161D THR* 3.4 43.1 - - - +
162D THR* 3.9 10.5 - - - -
163D LYS* 4.4 5.4 - - + +
172D PHE* 4.2 6.8 - - + -
303D GLU* 4.0 11.4 - - + +
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Residues in contact with TYR 96 (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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217B ILE 3.7 6.6 + - - -
218B TYR* 3.9 12.7 - - + +
219B PRO* 3.6 26.5 - - + -
242B TYR* 4.0 12.6 - + - -
272B GLN* 2.7 30.8 + - - -
9009B EDO 3.4 15.1 - - - -
68D TRP* 4.0 18.6 - - + +
92D ASP 4.5 5.6 - - - -
93D THR* 3.1 23.8 + - - +
95D ALA* 1.3 77.0 - - + +
97D THR* 1.3 58.1 + - - +
99D SER* 3.3 1.6 + - - -
100D ALA* 2.8 31.0 + - - +
302D VAL* 4.8 6.9 - - + +
303D GLU* 3.7 43.3 - - + -
306D LEU* 4.4 13.0 - - + -
307D THR* 3.5 5.0 - - + +
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Residues in contact with THR 97 (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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63D MET* 4.1 4.5 - - - -
68D TRP* 3.4 26.8 + - + +
71D ILE* 3.8 26.4 - - + +
87D ILE* 5.1 3.1 - - + -
89D HIS* 2.9 34.8 + - + +
93D THR* 3.1 7.5 + - - -
94D MET 3.7 4.5 - - - -
96D TYR* 1.3 77.4 - - - +
98D ALA* 1.3 61.9 + - - +
100D ALA* 3.3 0.9 + - - +
101D LEU* 3.0 39.9 + - + +
114D VAL* 5.2 3.1 - - + -
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Residues in contact with ALA 98 (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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94D MET 2.9 20.7 + - - +
95D ALA 4.0 3.4 - - - +
97D THR* 1.3 74.0 - - - +
99D SER* 1.3 62.6 + - - +
101D LEU 3.4 0.5 + - - -
102D SER* 3.3 19.8 + - - -
114D VAL* 3.9 24.8 - - + +
147D VAL* 3.5 18.4 - - + +
148D THR 4.7 0.2 - - - +
149D LEU* 4.4 11.2 - - + -
158D GLY* 3.9 25.6 - - - +
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Residues in contact with SER 99 (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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95D ALA 2.7 23.2 + - - -
96D TYR 3.7 2.0 - - - -
98D ALA* 1.3 73.0 - - - +
100D ALA* 1.3 65.4 + - - +
102D SER* 2.9 19.4 + - - -
103D PHE* 3.2 10.2 - - - -
158D GLY 3.5 2.8 + - - -
159D ASN* 3.4 30.1 - - - -
161D THR 4.8 1.2 + - - -
301D THR* 4.9 0.2 + - - -
303D GLU* 3.6 22.7 - - - +
304D ALA* 3.9 4.7 + - - -
307D THR* 3.3 16.8 - - - -
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Residues in contact with ALA 100 (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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68D TRP* 3.5 46.0 - - + -
96D TYR 2.8 20.1 + - - +
97D THR 3.3 2.2 + - - +
99D SER* 1.3 72.6 - - - +
101D LEU* 1.3 64.7 + - - +
103D PHE* 3.3 6.8 + - - +
104D MET* 3.2 29.5 + - - +
307D THR* 3.6 15.6 + - + +
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Residues in contact with LEU 101 (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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68D TRP* 3.7 26.7 - - + +
71D ILE* 3.9 22.4 - - + -
72D ALA* 3.9 26.5 - - + +
75D ILE* 4.2 12.8 - - + -
87D ILE* 4.4 11.2 - - + -
97D THR* 3.0 32.8 + - + +
98D ALA 3.4 2.7 + - - +
99D SER 3.3 0.2 - - - -
100D ALA* 1.3 77.0 - - - +
102D SER* 1.3 63.5 + - - +
104D MET* 4.5 4.0 - - - +
105D LEU* 2.9 34.3 + - + +
112D VAL* 4.6 5.2 - - + -
114D VAL* 4.7 2.7 - - + -
147D VAL* 3.7 19.7 - - + -
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Residues in contact with SER 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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98D ALA 3.3 12.4 + - - -
99D SER 2.9 16.7 + - - -
100D ALA 3.2 0.4 - - - -
101D LEU* 1.3 76.2 - - - +
103D PHE* 1.3 58.0 + - - +
105D LEU* 3.4 7.5 - - - +
147D VAL* 3.6 20.1 - - - +
159D ASN* 2.8 36.0 + - - +
331D ARG* 2.7 38.0 + - - +
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Residues in contact with PHE 103 (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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99D SER 3.2 21.5 - - - -
100D ALA 3.3 5.0 + - - +
101D LEU 3.2 0.4 - - - -
102D SER* 1.3 82.3 + - - +
104D MET* 1.3 62.7 + - - +
159D ASN* 4.5 2.0 - - + -
205D HIS* 3.9 0.5 - - - -
304D ALA* 3.5 24.7 - - - -
307D THR* 3.5 14.8 - - - +
308D LYS* 3.7 33.7 - - + -
311D TYR* 3.6 38.6 - + + -
330D LEU* 4.4 5.8 - - + -
331D ARG* 2.8 41.5 + - + +
333D GLU* 3.6 47.8 - - + -
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Residues in contact with MET 104 (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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68D TRP* 4.2 24.0 - - - +
69D GLN* 3.2 35.2 - - - +
72D ALA* 3.7 27.6 - - + -
100D ALA* 3.2 22.4 + - - +
101D LEU* 4.1 6.7 - - - +
103D PHE* 1.3 79.7 - - + +
105D LEU* 1.3 60.8 + - - +
106D GLU 3.7 0.2 + - - -
203D ILE 3.2 5.4 - - - +
204D VAL* 3.3 4.8 - - + -
205D HIS* 2.7 52.3 + - - +
206D PRO* 4.3 0.2 - - + -
207D ILE* 3.9 22.7 - - + -
311D TYR* 5.1 4.7 - - + -
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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
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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