Contacts of the helix formed by residues 200 - 207 (chain F) in PDB entry 3DBL
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 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151F ARG* 3.9 44.9 - - + +
152F ARG* 4.3 16.4 - - + +
155F ASN* 3.3 26.4 + - + +
177F LEU* 4.7 4.0 - - + -
179F ASP* 4.5 12.6 - - + +
190F ARG* 4.3 10.8 - - - +
192F ILE* 3.4 23.5 - - + +
199F CYS* 1.3 75.0 - - - +
201F GLU* 1.3 62.9 + - - +
203F THR* 3.3 16.8 + - - -
204F LEU* 3.6 11.7 + - + +
207F TYR* 5.0 10.9 - - + +
172K GLN* 5.2 3.0 - - - +
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Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ARG* 2.8 61.9 + - - +
155F ASN* 3.9 7.9 - - - +
199F CYS* 3.0 4.4 - - - -
200F ILE* 1.3 74.6 - - - +
202F CYS* 1.3 56.4 + - - +
203F THR 2.8 11.8 + - - -
204F LEU* 3.1 26.8 + - - +
340F LYS* 5.0 6.6 + - - +
343F CYS* 3.3 22.5 - - - -
344F PRO* 4.8 11.9 - - + +
345F ALA* 3.3 22.7 - - + -
373F SER 5.0 5.2 - - - +
374F LEU* 4.9 2.4 - - - -
429F THR* 4.0 4.2 - - - +
430F THR* 5.8 2.6 - - - -
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Residues in contact with CYS 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ZN 2.4 38.6 - - - -
198F ALA* 4.0 16.8 - - + -
199F CYS 3.3 25.3 + - - +
201F GLU* 1.3 75.5 - - - +
203F THR* 1.3 57.4 + - - +
204F LEU 3.7 0.4 - - - -
205F GLU* 5.4 0.2 - - - +
338F GLU 4.2 2.0 - - - +
339F ARG* 4.2 1.8 - - - -
340F LYS* 3.8 45.5 - - - +
343F CYS* 3.5 7.4 - - - -
346F CYS* 3.9 3.4 - - - -
149K GLN* 3.1 19.6 + - - -
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Residues in contact with THR 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ARG* 2.5 46.0 + - - +
200F ILE 3.3 9.4 + - - -
201F GLU 2.9 0.4 - - - -
202F CYS* 1.3 86.1 - - + +
204F LEU* 1.3 51.8 + - - +
205F GLU 2.8 17.9 + - - +
206F LEU* 2.9 38.0 + - + -
337F ALA* 4.1 13.2 - - + -
338F GLU 5.1 0.7 - - - +
149K GLN* 3.8 13.7 - - - +
172K GLN* 3.2 15.3 + - - -
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Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ILE* 4.6 2.9 - - + -
152F ARG* 3.7 48.9 - - + +
200F ILE* 3.6 9.6 + - + +
201F GLU* 3.1 22.4 + - - +
203F THR* 1.3 76.6 - - - +
205F GLU* 1.3 62.9 + - + +
207F TYR* 3.3 39.6 - - + +
340F LYS* 6.2 0.7 - - - +
372F ALA 4.0 8.7 - - - +
373F SER 4.6 2.7 - - - +
374F LEU* 4.2 4.5 - - - -
375F GLN* 3.5 48.5 - - + +
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Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F THR* 2.8 2.3 + - - -
204F LEU* 1.3 77.0 - - + +
206F LEU* 1.3 52.7 + - - +
207F TYR* 2.4 23.6 + - - +
340F LYS* 3.6 27.5 + - - +
372F ALA* 3.0 40.6 - - - +
373F SER* 4.1 6.6 - - - -
375F GLN* 5.1 0.8 - - - +
142K ARG* 3.2 18.5 + - - -
149K GLN* 3.5 20.9 - - + +
151K ASN* 5.3 6.8 + - - -
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Residues in contact with LEU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F THR* 2.9 31.2 + - + +
205F GLU* 1.3 74.4 - - - +
207F TYR* 1.3 58.9 + - - +
321F TYR* 3.6 27.1 - - + +
335F PHE* 4.7 8.5 - - + -
337F ALA* 5.3 0.7 - - + -
142K ARG* 3.8 25.5 - - + +
144K ILE* 3.8 17.7 - - + -
149K GLN* 3.7 20.6 - - + +
170K VAL* 3.6 26.7 - - + -
171K LEU* 4.3 1.7 - - - +
172K GLN* 3.3 36.4 + - + +
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Residues in contact with TYR 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ILE* 3.7 48.0 - - + +
151F ARG* 4.0 24.1 - - - +
200F ILE* 5.0 11.3 - - + +
203F THR 5.4 0.2 - - - -
204F LEU* 3.3 37.5 - - + +
205F GLU 2.4 15.4 + - - +
206F LEU* 1.3 71.4 - - - +
208F PRO* 1.3 69.2 - - + +
375F GLN* 5.9 0.7 - - - +
142K ARG* 2.5 35.4 + - - -
171K LEU* 5.5 0.4 - - - -
172K GLN* 3.3 56.6 + - + +
173K LEU 4.2 8.8 + - - -
174K ARG* 4.3 4.2 - - + -
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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