Contacts of the helix formed by residues 241 - 249 (chain B) in PDB entry 4DVQ
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 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.6 9.9 - - + -
114B GLU* 6.5 0.9 - - + -
240B MET* 1.4 89.3 - - + +
242B ARG* 1.3 65.0 + - - +
243B SER* 3.9 17.9 - - - -
244B LEU* 3.0 25.3 + - + +
245B SER* 3.1 9.5 + - - -
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Residues in contact with ARG 242 (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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114B GLU* 5.5 22.2 + - + +
118B ALA* 3.3 33.2 + - - +
121B GLN* 3.4 19.6 - - - +
240B MET 3.6 1.2 + - - -
241B PRO* 1.3 68.9 - - - +
243B SER* 1.3 66.7 + - - +
245B SER* 3.3 9.4 - - - -
246B ARG* 3.0 67.7 + - + +
253B TRP* 3.9 29.5 - - + -
257B PHE* 5.9 1.8 - - - -
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Residues in contact with SER 243 (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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241B PRO* 3.9 17.3 - - - -
242B ARG* 1.3 77.9 - - - +
244B LEU* 1.3 69.8 + - - +
246B ARG* 3.6 17.9 + - - +
247B TRP* 3.5 17.7 + - - -
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Residues in contact with LEU 244 (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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50A LEU* 4.7 14.6 - - + -
53A LEU* 4.0 14.4 - - + -
49B TRP* 3.9 30.3 - - + -
52B LEU* 4.3 15.7 - - + -
240B MET* 3.6 16.8 - - + -
241B PRO* 3.0 19.3 + - + +
243B SER* 1.3 83.8 - - - +
245B SER* 1.3 56.2 + - - +
246B ARG 3.2 2.0 - - - -
247B TRP* 3.1 26.5 + - + +
248B ILE* 2.7 40.5 + - + +
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Residues in contact with SER 245 (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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237B LEU* 4.0 15.8 + - - -
240B MET* 3.9 29.2 + - - +
241B PRO 3.1 10.0 + - - -
242B ARG* 3.3 18.2 - - - -
244B LEU* 1.3 77.1 - - - +
246B ARG* 1.3 64.7 + - - +
248B ILE 4.3 0.9 - - - +
249B SER* 2.9 31.2 + - - +
253B TRP* 3.0 25.8 + - - -
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Residues in contact with ARG 246 (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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57A ARG* 5.5 3.1 - - - +
242B ARG* 3.0 67.1 + - + +
243B SER* 3.6 18.4 + - - +
245B SER* 1.3 77.5 + - - +
247B TRP* 1.3 68.3 + - + +
250B PRO* 3.5 21.1 - - - +
253B TRP* 3.9 13.9 - - + +
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Residues in contact with TRP 247 (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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53A LEU* 3.6 41.1 - - + -
54A GLN* 5.2 1.3 - - - -
56A TRP* 3.5 33.4 - + - -
57A ARG* 3.2 64.8 - - + +
243B SER 3.5 25.2 + - - -
244B LEU* 3.1 24.7 + - + +
246B ARG* 1.3 84.5 - - + +
248B ILE* 1.3 86.7 + - + +
249B SER 3.5 1.1 - - - -
250B PRO* 3.3 12.4 - - - +
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Residues in contact with ILE 248 (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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53A LEU* 4.4 17.3 - - + -
56A TRP* 4.8 13.8 - - + -
53B LEU* 6.1 3.6 - - + -
56B TRP* 3.1 43.3 + - + +
240B MET* 3.3 28.5 - - + -
244B LEU* 2.7 29.6 + - + +
247B TRP* 1.3 107.0 - - + +
249B SER* 1.3 61.9 + - - +
250B PRO* 3.4 3.6 - - - +
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Residues in contact with SER 249 (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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56B TRP* 3.4 14.3 + - - -
236B GLN* 6.4 0.2 - - - -
237B LEU* 4.9 6.5 - - - -
240B MET* 4.8 6.3 - - - -
245B SER* 2.9 14.7 + - - -
248B ILE* 1.3 91.7 + - - +
250B PRO* 1.3 59.0 - - - +
251B LYS* 3.1 4.3 - - - -
252B VAL* 2.9 44.7 + - - +
253B TRP* 3.3 7.4 + - - -
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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