Contacts of the helix formed by residues 144 - 155 (chain D) in PDB entry 4GOM
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.6 39.7 - - + +
81D PHE* 4.6 2.0 - - + -
112D LEU* 4.2 16.4 - - + -
116D ARG* 4.1 15.7 - - + +
142D TYR* 3.3 17.5 - - + +
143D PHE* 1.4 87.9 - - + +
145D GLU* 1.3 52.4 + - - +
147D GLU* 3.3 17.4 + - + +
148D LEU* 2.7 43.0 + - + +
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Residues in contact with GLU 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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74D VAL* 4.3 3.4 - - + -
78D ARG* 2.8 44.3 + - - -
142D TYR* 4.9 0.4 + - - -
143D PHE* 3.0 30.7 + - + +
144D PRO* 1.3 74.0 - - - +
146D ALA* 1.3 64.0 + - - +
147D GLU* 4.0 0.2 + - - -
148D LEU* 3.1 9.0 + - - +
149D TYR* 3.0 45.1 + - + -
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Residues in contact with ALA 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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142D TYR* 4.8 5.6 + - - +
144D PRO 3.4 0.4 - - - -
145D GLU* 1.3 77.2 - - - +
147D GLU* 1.3 74.0 + - + +
149D TYR* 3.2 7.9 + - - +
150D HIS* 3.1 23.5 + - - +
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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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5D ARG* 3.5 44.8 - - + +
6D ALA 4.5 2.9 - - - +
7D PHE* 3.7 23.5 + - + +
116D ARG* 6.1 0.4 - - - -
142D TYR* 3.0 39.9 + - - -
144D PRO* 3.3 14.3 - - - +
146D ALA* 1.3 77.3 + - - +
148D LEU* 1.3 63.5 + - - +
150D HIS* 3.3 6.1 + - - +
151D PHE* 2.8 25.6 + - - +
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Residues in contact with LEU 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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7D PHE* 3.5 40.8 - - + +
66D VAL* 3.8 28.7 - - + +
70D THR* 5.4 1.8 - - - -
73D TYR* 3.8 16.2 - - + -
74D VAL* 4.4 18.2 - - + -
112D LEU* 4.1 20.6 - - + -
143D PHE* 4.2 20.4 - - + -
144D PRO* 2.7 23.7 + - + +
145D GLU* 3.1 9.4 + - - +
147D GLU* 1.3 73.9 - - - +
149D TYR* 1.3 63.0 + - - +
151D PHE* 3.2 4.1 + - - +
152D ALA* 3.0 22.4 + - - +
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Residues in contact with TYR 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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70D THR* 3.8 22.0 - - + -
71D ASP* 2.8 30.9 + - - +
74D VAL* 3.9 27.0 - - + +
78D ARG* 5.0 2.3 + - - -
145D GLU* 3.0 49.2 + - + -
146D ALA* 3.2 7.4 + - - +
148D LEU* 1.3 76.1 - - - +
150D HIS* 1.3 57.3 + - - +
152D ALA* 3.3 6.0 + - + +
153D GLU* 2.9 27.3 + - - +
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Residues in contact with HIS 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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4D ASN* 3.4 45.8 + - + +
5D ARG 4.9 5.9 + - - -
43D LEU* 3.8 20.9 - - + +
146D ALA 3.1 17.0 + - - +
147D GLU* 3.9 5.3 + - - +
149D TYR* 1.3 73.1 - - - +
151D PHE* 1.3 67.8 + - - +
153D GLU* 3.1 8.0 + - + +
154D LYS* 3.0 41.6 + - + +
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Residues in contact with PHE 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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7D PHE* 3.6 29.6 - + + +
36D VAL* 6.2 0.4 - - + -
38D ALA 4.1 12.8 - - - -
39D GLY* 4.9 0.7 - - - -
42D PHE* 4.0 23.5 - + - -
43D LEU* 3.6 29.2 - - + -
63D TYR* 3.6 53.4 - + + -
66D VAL* 4.0 11.0 - - + -
147D GLU 2.8 18.3 + - - +
148D LEU 3.5 4.7 - - - +
150D HIS* 1.3 78.7 + - - +
152D ALA* 1.3 50.9 + - - +
154D LYS* 3.3 2.6 + - - +
155D ALA* 2.7 39.3 + - + +
160D PHE* 3.8 23.3 - + - -
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Residues in contact with ALA 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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66D VAL* 3.6 17.0 - - + +
70D THR* 3.6 36.1 - - + +
148D LEU 3.0 9.4 + - - +
149D TYR* 3.6 7.4 - - + +
151D PHE* 1.3 74.4 - - - +
153D GLU* 1.3 68.3 + - - +
155D ALA* 3.3 11.6 + - - -
156D GLN* 3.1 25.6 + - - +
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Residues in contact with GLU 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 TYR 2.9 18.5 + - - +
150D HIS* 3.1 10.0 + - + +
152D ALA* 1.3 73.5 - - - +
154D LYS* 1.3 63.1 + - - +
156D GLN* 3.2 23.0 + - - +
157D ASN* 5.6 1.4 - - - +
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Residues in contact with LYS 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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42D PHE* 2.8 48.9 + - + +
43D LEU* 4.0 18.2 - - + -
45D THR 2.8 23.7 + - - -
46D ASP* 4.6 2.9 - - - +
47D PHE 5.3 0.4 + - - -
50D TYR* 2.9 22.5 + - + -
150D HIS* 3.0 37.6 + - + +
151D PHE 3.7 3.4 - - - +
153D GLU* 1.3 74.9 - - - +
155D ALA* 1.3 56.7 + - - +
156D GLN 2.8 12.3 + - - -
157D ASN* 3.2 16.3 + - - +
158D ALA 4.2 0.2 + - - -
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Residues in contact with ALA 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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42D PHE* 3.7 9.2 - - - -
67D LYS* 3.3 43.3 - - + +
151D PHE* 2.7 24.7 + - + +
152D ALA* 3.3 10.5 + - - +
154D LYS* 1.3 68.0 - - - +
156D GLN* 1.3 60.4 + - - +
157D ASN 2.9 6.5 + - - -
158D ALA* 3.1 15.4 + - - +
160D PHE* 4.0 16.8 - - + -
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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