Contacts of the helix formed by residues 144 - 160 (chain D) in PDB entry 2P1N
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP 4.2 1.3 - - - +
143D PHE* 1.3 74.7 - - - +
145D PRO* 1.3 93.8 - - - +
146D GLU* 2.3 31.8 + - - +
147D GLU* 3.0 26.8 + - - +
148D GLU* 2.9 23.4 + - - +
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Residues in contact with PRO 145 (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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143D PHE 3.8 1.4 - - - -
144D THR* 1.3 115.7 - - - +
146D GLU* 1.3 81.9 + - + +
148D GLU* 3.6 7.1 + - + +
149D GLU* 3.5 22.1 + - - +
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Residues in contact with GLU 146 (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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144D THR* 2.3 31.4 + - - +
145D PRO* 1.3 97.9 - - + +
147D GLU* 1.3 76.4 + - + +
149D GLU* 3.5 13.8 + - - +
150D GLU* 3.1 20.8 + - - +
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Residues in contact with GLU 147 (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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142D ASP 4.9 1.9 - - - +
143D PHE* 4.1 14.8 - - + -
144D THR* 3.0 47.4 + - - +
146D GLU* 1.3 82.2 - - + +
148D GLU* 1.3 56.3 + - - +
149D GLU 2.6 16.8 + - - -
150D GLU* 2.6 18.2 + - - +
151D VAL* 2.9 16.9 + - + +
35E LYS* 5.1 15.2 + - - +
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Residues in contact with GLU 148 (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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130D PRO* 5.4 0.5 - - - +
131D GLU* 4.0 3.5 - - - +
134D ARG* 3.8 21.5 + - - -
141D ASN* 3.6 20.5 + - - -
143D PHE* 3.7 23.0 - - + +
144D THR 2.9 21.5 + - - +
145D PRO* 3.9 6.3 - - - +
147D GLU* 1.3 72.2 - - - +
149D GLU* 1.3 57.0 + - - +
151D VAL* 4.0 1.3 - - - +
152D ARG* 3.1 59.1 + - - +
32E LEU* 3.5 16.8 - - + +
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Residues in contact with GLU 149 (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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145D PRO 3.5 15.9 + - - +
146D GLU* 3.6 11.7 - - - +
147D GLU 2.6 5.7 + - - -
148D GLU* 1.3 76.9 - - + +
150D GLU* 1.3 64.9 + - - +
152D ARG* 3.9 11.9 - - - +
153D ARG* 3.1 40.7 + - - +
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Residues in contact with GLU 150 (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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146D GLU 3.1 12.8 + - - +
147D GLU* 2.6 17.6 + - - +
149D GLU* 1.3 72.9 - - - +
151D VAL* 1.3 62.3 + - + +
153D ARG* 3.3 29.2 + - - +
154D GLU* 3.2 33.5 + - - +
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Residues in contact with VAL 151 (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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143D PHE* 4.6 12.8 - - + -
147D GLU* 2.9 15.1 + - + +
148D GLU* 4.9 0.2 - - - -
150D GLU* 1.3 74.5 - - + +
152D ARG* 1.3 59.9 + - - +
153D ARG 3.2 0.2 + - - -
154D GLU* 3.3 7.5 + - - +
155D ASN* 2.8 43.6 + - - +
31E SER* 4.4 0.9 - - - +
32E LEU* 3.4 28.5 - - + -
38E TYR* 4.0 39.9 - - + +
64E ARG* 4.1 4.9 - - - +
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Residues in contact with ARG 152 (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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130D PRO* 4.8 8.7 - - - +
131D GLU* 4.7 8.1 + - - -
148D GLU* 3.1 59.8 + - - +
149D GLU* 3.9 11.9 - - - +
151D VAL* 1.3 78.3 - - - +
153D ARG* 1.3 57.7 + - + +
155D ASN* 3.3 4.7 + - - +
156D GLN* 3.0 57.7 + - + +
32E LEU* 3.6 30.7 - - + +
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Residues in contact with ARG 153 (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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149D GLU* 3.1 40.5 + - + +
150D GLU* 3.3 34.0 + - - +
151D VAL 3.1 0.6 - - - -
152D ARG* 1.3 76.4 - - - +
154D GLU* 1.3 58.2 + - - +
156D GLN* 4.8 2.0 - - - -
157D TRP* 2.8 89.4 + - + +
532E LYS* 3.5 28.2 - - - +
562E VAL* 4.1 14.3 - - + +
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Residues in contact with GLU 154 (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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150D GLU* 3.2 25.6 + - - +
151D VAL* 3.7 6.6 - - - +
153D ARG* 1.3 76.3 - - - +
155D ASN* 1.3 69.8 + - - +
158D ALA* 3.1 18.9 + - + +
159D PHE* 3.0 34.9 - - + -
38E TYR* 4.8 1.7 + - - -
56E VAL* 5.4 0.4 - - + -
60E THR* 4.4 16.1 + - - +
64E ARG* 2.9 34.7 + - - +
562E VAL* 4.5 24.4 - - + +
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Residues in contact with ASN 155 (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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151D VAL* 2.8 19.9 + - - +
152D ARG* 3.5 10.1 - - + +
154D GLU* 1.3 70.8 - - - +
156D GLN* 1.3 58.2 + - + +
159D PHE* 2.8 33.5 + - - -
160D GLU 3.2 1.6 + - - -
28E ASN* 2.8 52.5 + - + +
31E SER* 2.8 25.6 + - - -
32E LEU* 4.0 12.7 - - + +
45E ARG* 4.9 0.2 + - - -
64E ARG* 3.0 30.5 + - - -
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Residues in contact with GLN 156 (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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152D ARG* 3.0 46.9 + - + +
153D ARG* 4.8 0.9 - - - -
155D ASN* 1.3 77.6 - - + +
157D TRP* 1.3 79.0 + - + +
160D GLU* 3.4 44.3 + - - +
560E ARG* 3.6 16.3 + - - +
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Residues in contact with TRP 157 (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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153D ARG* 2.8 55.3 + - + +
156D GLN* 1.3 92.0 + - + +
158D ALA* 1.3 58.8 + - - +
160D GLU* 5.0 1.8 - - - +
52E ASN* 5.7 0.2 - - - +
55E ALA* 3.4 22.5 - - + +
506E GLU* 3.5 50.9 + - + -
532E LYS* 3.7 17.5 - - + -
560E ARG* 3.4 53.9 + - + +
561E THR* 3.5 36.6 - - - -
562E VAL* 4.0 7.9 - - + +
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Residues in contact with ALA 158 (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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154D GLU* 3.1 21.7 + - + +
157D TRP* 1.3 80.7 - - - +
159D PHE* 1.3 81.0 + - + +
160D GLU* 3.8 2.2 - - - -
49E PHE 3.3 12.1 - - - +
50E ILE* 3.7 15.6 - - - +
51E GLY 4.7 1.9 + - - -
55E ALA* 4.5 4.7 - - - +
56E VAL* 3.7 33.2 - - + -
562E VAL* 5.0 3.1 - - + -
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Residues in contact with PHE 159 (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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154D GLU* 3.0 52.3 - - + -
155D ASN* 2.8 22.9 + - - +
158D ALA* 1.3 90.1 - - + +
160D GLU* 1.3 59.2 + - - +
24E ASP* 3.6 23.0 - - - +
28E ASN* 4.4 3.1 + - - +
45E ARG* 4.3 14.9 + - - +
48E VAL* 3.7 22.0 - - + -
49E PHE* 3.6 13.3 + - - +
50E ILE* 4.6 7.0 - - + -
56E VAL* 4.8 2.7 - - + -
60E THR 5.3 1.3 - - - -
61E VAL* 4.0 31.9 - - + -
64E ARG* 3.8 14.1 - - - -
65E PHE* 3.5 29.4 - + - -
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Residues in contact with GLU 160 (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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155D ASN 3.2 3.0 + - - -
156D GLN* 3.4 42.6 + - - +
157D TRP 5.0 1.7 - - - +
158D ALA 4.8 2.3 - - - -
159D PHE* 1.3 81.8 + - - +
24E ASP* 4.4 5.3 - - + +
25E LYS* 3.5 63.5 + - + +
28E ASN* 3.0 32.9 + - - +
49E PHE* 3.0 34.2 - - - -
51E GLY* 5.4 3.5 + - - -
484E ARG* 6.0 0.2 + - - -
509E ARG* 5.2 3.2 + - - -
560E ARG* 5.4 1.6 + - - -
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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