Contacts of the helix formed by residues 148 - 154 (chain B) in PDB entry 3DGR
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 ILE 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.5 9.2 - - + -
14B ALA 5.9 0.7 - - - -
70B LEU* 4.3 22.2 - - + -
112B LEU* 4.4 6.7 - - + -
114B ILE* 3.3 32.5 - - + -
116B ILE* 4.8 3.4 - - + -
134B VAL* 3.8 18.4 - - + -
144B LEU* 3.4 22.4 - - + +
145B THR 3.2 15.3 - - - +
147B TRP* 1.3 84.3 - - + +
149B GLU* 1.3 65.3 + - - +
150B THR 3.2 1.3 - - - -
151B ILE* 3.3 13.8 - - + +
152B LEU* 3.2 37.1 + - + +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 3.4 25.9 + - - +
246A GLU* 3.9 4.3 - - - +
501A A12 4.1 4.7 + - - -
19B LYS* 2.8 27.5 + - - +
145B THR 3.7 3.6 + - - -
146B ASN* 3.2 26.8 + - - +
148B ILE* 1.3 77.4 - - - +
150B THR* 1.3 61.2 + - - +
152B LEU 3.2 0.9 + - - -
153B VAL* 2.8 37.7 + - + +
399B PHE* 3.3 63.5 + - + +
400B LYS* 4.9 0.3 + - - -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR* 3.6 39.9 - - + -
196A ARG* 3.7 20.8 - - + +
14B ALA 4.2 1.8 - - - +
15B THR* 3.6 14.7 + - - -
16B ASP* 2.6 43.0 + - - +
19B LYS* 3.6 5.5 - - - +
147B TRP 4.2 1.0 + - - -
148B ILE 3.2 0.8 - - - -
149B GLU* 1.3 79.2 - - - +
151B ILE* 1.3 63.2 + - - +
153B VAL 3.4 4.2 + - - -
154B GLN* 3.4 17.7 + - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 3.4 29.2 - - - +
9B PHE* 3.7 18.2 - - + -
11B ILE* 4.4 7.2 - - + -
14B ALA* 4.3 13.4 + - + +
65B ILE* 3.7 23.7 - - + +
69B TYR* 3.7 33.4 - - + -
70B LEU* 4.2 14.8 - - + -
148B ILE* 3.3 28.0 - - + +
150B THR* 1.3 78.6 - - - +
152B LEU* 1.3 70.9 + - + +
154B GLN* 3.4 18.9 + - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.9 25.7 - - + +
65B ILE* 4.2 8.6 - - + +
70B LEU* 3.5 26.7 - - + -
116B ILE* 4.1 8.5 - - + -
132B PHE* 4.0 18.1 - - + -
134B VAL* 3.6 30.7 - - + -
148B ILE* 3.2 36.4 + - + +
149B GLU 3.9 2.2 - - - +
151B ILE* 1.3 84.7 - - + +
153B VAL* 1.3 57.7 + - - +
155B SER* 2.9 31.5 + - - -
399B PHE* 4.2 8.5 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 3.7 24.0 - - + +
501A A12 6.1 0.2 - - - +
37B PHE* 4.1 16.2 - - + -
149B GLU* 2.8 29.5 + - + +
150B THR 3.9 4.7 - - - +
151B ILE 3.3 0.4 - - - -
152B LEU* 1.3 71.0 - - - +
154B GLN* 1.3 55.2 + - - +
155B SER* 2.9 5.1 + - - -
156B TRP* 2.8 27.4 + - - +
392B ARG* 3.7 32.5 - - - +
397B CYS 5.1 1.1 - - - +
399B PHE* 3.3 37.0 - - + +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR* 2.6 40.8 + - - +
196A ARG 3.9 9.6 - - - +
198A VAL* 3.8 16.9 - - - +
199A SER 4.7 6.0 - - - +
200A SER* 3.6 13.7 + - - -
201A GLN* 2.9 38.5 + - - +
65B ILE* 4.3 6.7 - - + -
69B TYR* 5.7 0.7 - - - -
150B THR 3.4 14.1 - - - +
151B ILE* 3.5 10.3 - - - +
152B LEU 3.2 1.2 - - - -
153B VAL* 1.3 75.4 - - - +
155B SER* 1.3 59.9 + - - +
156B TRP* 3.0 10.1 + - - -
157B TYR* 3.2 16.9 + - - +
158B PRO* 3.4 8.1 - - - +
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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