Contacts of the helix formed by residues 339 - 344 (chain A) in PDB entry 1FQV
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 CYS 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A LYS* 4.1 17.7 - - - +
314A LEU* 3.6 16.6 - - + -
335A LEU* 3.4 34.3 - - + -
336A LYS 3.1 29.8 + - - +
337A ASN 2.8 0.6 + - - -
338A ASP* 1.3 82.9 - - - +
340A PHE* 1.3 61.9 + - + +
341A GLN* 3.0 3.1 - - - -
342A GLU* 2.6 36.2 + - - +
343A PHE* 3.5 11.6 + - + -
360A ILE* 6.2 0.2 - - + -
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LYS 4.0 5.2 - - - -
337A ASN* 3.0 42.8 + - + +
339A CYS* 1.3 79.7 - - + +
341A GLN* 1.3 55.3 + - - +
342A GLU 3.0 4.7 + - - -
343A PHE* 3.1 17.2 + + - +
344A PHE* 3.0 46.6 + - + -
354A LEU* 4.5 6.3 - - + -
360A ILE* 3.6 35.7 - - + -
364A THR 3.1 30.1 - - - -
365A LEU* 4.2 9.2 - - + -
367A GLU* 3.9 17.9 - - + +
368A LEU* 3.8 24.9 - - + -
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 4.1 1.5 - - - +
337A ASN 4.5 0.2 + - - -
338A ASP* 3.3 31.3 + - - +
340A PHE* 1.3 76.8 - - - +
342A GLU* 1.3 67.8 + - - +
344A PHE* 3.5 15.9 - - + +
345A GLN* 3.2 19.2 + - - +
187M ALA* 3.3 8.6 - - - +
188M GLU 2.5 26.5 - - - +
189M HIS* 3.1 20.5 + - - +
211M HIS* 3.4 13.0 + - + +
212M GLY* 4.5 1.4 - - - -
215M SER* 3.5 21.0 + - - +
216M GLN* 3.1 24.9 - - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 4.9 9.2 - - - -
314A LEU* 4.0 13.5 - - + +
315A SER* 2.6 44.3 + - - +
318A VAL* 3.2 52.3 - - + +
339A CYS* 2.6 21.7 + - - +
341A GLN* 1.3 88.3 - - - +
343A PHE* 1.3 61.2 + - - +
344A PHE 3.1 2.0 - - - -
345A GLN* 3.2 24.0 + - - +
346A LEU* 4.0 1.0 - - - +
187M ALA* 4.3 15.6 + - - +
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Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A LEU* 3.7 23.6 - - + -
327A LEU* 3.7 31.0 - - + -
329A LEU* 3.6 22.9 - - + -
335A LEU* 4.9 1.6 - - + -
339A CYS* 4.0 9.2 - - + -
340A PHE* 3.1 34.5 + + - +
342A GLU* 1.3 74.9 - - - +
344A PHE* 1.3 63.1 + - - +
346A LEU* 3.2 29.0 + - + +
349A LEU* 4.1 7.2 - - + +
352A LEU* 3.7 26.7 - - + -
354A LEU* 4.1 22.7 - - + -
360A ILE* 6.0 0.2 - - + -
368A LEU* 4.3 2.5 - - + -
371A ILE* 3.5 28.3 - - + +
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Residues in contact with PHE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PHE* 3.0 38.3 + - + +
341A GLN* 3.5 14.4 - - + +
343A PHE* 1.3 77.6 - - - +
345A GLN* 1.3 56.9 + - - +
346A LEU 3.1 10.6 + - - +
347A ASN* 3.8 1.7 - - - +
367A GLU* 3.5 20.2 - - + -
368A LEU* 4.5 1.1 - - + -
370A GLU* 3.2 44.2 - - + -
371A ILE* 3.3 29.6 - - + +
372A PRO* 6.0 1.6 - - - +
211M HIS* 3.9 22.0 - + + +
215M SER* 6.0 2.0 - - - -
233M PRO* 3.3 20.6 - - + +
237M THR* 5.7 2.0 - - + -
240M LYS* 6.4 2.0 - - - -
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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