Contacts of the helix formed by residues 241 - 247 (chain B) in PDB entry 5FQD
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A ARG* 5.7 0.2 - - - +
812A TYR* 3.2 39.5 - - + +
814A LEU* 4.3 7.9 - - + -
235B ALA* 4.2 0.9 - - + -
239B SER 4.7 0.4 - - - +
240B TRP* 1.4 97.4 - - + +
242B ARG* 1.3 64.4 + - - +
243B TRP* 3.2 43.1 - - + +
244B LEU* 3.1 19.0 + - + +
245B TYR* 3.3 16.5 + - - -
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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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740A ILE* 5.8 1.8 - - - +
787A GLU* 3.7 21.5 + - - -
228B GLN* 3.4 49.4 - - + +
229B LYS* 3.5 51.2 + - - +
232B PHE* 3.1 39.5 - - + +
233B HIS* 4.6 5.9 + - - +
235B ALA* 4.1 5.9 - - + +
241B PRO* 1.3 72.1 - - - +
243B TRP* 1.4 63.7 + - + +
245B TYR* 3.1 6.5 + - - +
246B SER* 3.1 22.7 + - - -
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Residues in contact with TRP 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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812A TYR* 3.6 14.4 - + - -
814A LEU* 4.2 10.8 - - + -
834A ALA* 3.9 17.0 - - + -
836A VAL* 3.3 42.0 - - + +
840A GLU 6.2 0.2 - - - +
841A ALA 4.5 8.2 - - - +
843A PRO* 3.4 33.2 - - + -
869A ALA* 4.0 6.1 - - + -
871A TYR* 3.4 36.6 - + - -
228B GLN* 3.7 20.5 + - - +
241B PRO* 3.3 30.7 - - + +
242B ARG* 1.4 78.9 - - + +
244B LEU* 1.3 69.1 + - + +
246B SER* 3.6 13.5 - - - -
247B LEU* 3.7 13.9 - - + +
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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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871A TYR* 3.5 33.4 - - + +
910A MET* 3.6 24.2 - - + -
912A LEU* 3.7 18.2 - - + -
926A LEU* 4.1 13.7 - - + -
240B TRP* 3.5 33.9 - - + -
241B PRO* 3.1 22.3 + - + +
243B TRP* 1.3 84.4 - - + +
245B TYR* 1.3 68.2 + - + +
247B LEU* 3.1 21.2 + - + +
248B TYR* 3.5 9.9 - - + -
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Residues in contact with TYR 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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926A LEU* 3.8 24.7 - - + +
1003A PHE* 5.3 2.9 - - - -
193B THR* 3.3 33.7 - - + +
194B MET* 3.7 16.2 - - + -
232B PHE* 3.5 26.4 - - + -
235B ALA* 3.5 30.1 - - + -
238B THR* 2.7 29.2 + - - +
240B TRP* 3.6 33.3 - + + -
241B PRO 3.3 17.7 + - - -
242B ARG* 3.1 5.1 + - - +
244B LEU* 1.3 76.4 - - + +
246B SER* 1.4 56.6 + - - +
248B TYR* 3.0 21.5 + - - +
249B ASP* 3.3 10.4 + - - +
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Residues in contact with SER 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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841A ALA 6.1 0.2 - - - -
227B TYR* 5.9 0.3 - - - -
228B GLN* 3.2 37.8 + - - +
232B PHE* 3.6 15.2 - - - -
242B ARG 3.1 5.2 + - - -
243B TRP 3.6 11.9 - - - -
244B LEU 3.2 0.2 - - - -
245B TYR* 1.4 76.4 - - - +
247B LEU* 1.3 61.1 + - - +
248B TYR 3.1 0.7 - - - -
249B ASP* 3.2 17.9 + - - +
252B THR* 3.8 27.7 + - - +
253B LEU* 4.5 3.3 - - - +
256B ARG* 5.3 1.0 + - - -
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Residues in contact with LEU 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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841A ALA* 3.4 29.6 - - + +
842A GLU* 3.9 28.5 - - + +
843A PRO* 4.6 0.4 - - + -
871A TYR* 4.1 18.8 - - - +
910A MET* 4.6 8.3 - - - -
243B TRP* 3.7 20.9 - - + +
244B LEU* 3.1 16.9 + - + +
246B SER* 1.3 77.0 - - - +
248B TYR* 1.3 61.6 + - + +
249B ASP 3.6 0.7 - - - -
253B LEU* 3.4 13.0 - - - +
256B ARG* 3.5 24.0 - - - +
309B ARG* 2.8 36.3 + - - +
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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