Contacts of the strand formed by residues 340 - 345 (chain D) in PDB entry 1F9Q
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 GLN 340 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310D CYS* 3.7 1.2 - - - +
311D LEU* 3.0 32.3 + - - +
312D CYS* 3.1 32.4 + - + +
328D GLU 3.4 3.2 - - - +
330D ILE* 2.9 55.7 + - + +
335D HIS* 4.0 13.3 + - - -
336D CYS* 3.6 35.7 - - - +
338D THR* 4.4 3.6 + - + -
339D ALA* 1.3 82.0 - - - +
341D LEU* 1.3 70.0 + - - +
342D ILE* 3.9 5.6 - - + -
353D LEU 5.8 0.2 - - - -
355D LEU* 4.7 1.3 - - - -
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Residues in contact with LEU 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C LEU* 4.8 10.1 - - + -
312D CYS* 4.9 1.6 - - - -
327D LEU* 4.4 13.2 - - + -
328D GLU 3.5 4.3 - - - -
329D VAL* 4.3 22.7 - - + -
339D ALA* 5.0 1.6 - - + -
340D GLN* 1.3 83.0 - - - +
342D ILE* 1.3 62.3 + - - +
343D ALA 3.8 0.9 + - - -
351D ILE 3.6 0.2 - - - +
352D CYS* 3.2 6.0 - - - +
353D LEU* 2.9 45.2 + - + +
354D ASP 4.2 12.6 - - - +
355D LEU* 3.3 28.5 - - + +
360D TYR* 3.6 37.9 - - + -
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.3 10.3 - - + -
311D LEU* 3.2 37.7 - - + -
312D CYS* 3.7 23.1 - - - -
326D SER 3.7 1.0 - - - +
327D LEU* 3.3 2.9 - - - -
328D GLU* 2.7 51.6 + - + +
330D ILE* 3.7 23.8 - - + -
340D GLN* 4.6 2.5 - - + +
341D LEU* 1.3 75.5 - - - +
343D ALA* 1.3 61.3 + - - +
344D THR* 4.2 1.5 + - - +
350D LYS* 3.7 34.3 - - + +
351D ILE 3.4 7.6 - - - +
352D CYS* 4.1 0.2 - - - -
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ILE* 3.9 29.2 - - + -
326D SER 3.2 4.3 - - - -
327D LEU* 3.9 13.5 - - + -
341D LEU 3.8 0.8 + - - -
342D ILE* 1.3 74.6 - - - +
344D THR* 1.3 62.5 + - - +
345D LEU* 4.3 0.7 - - + -
349D ARG 3.8 0.5 - - - +
350D LYS* 3.2 4.9 - - - +
351D ILE* 2.8 54.5 + - + +
353D LEU* 4.4 6.5 - - + -
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Residues in contact with THR 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LYS 4.0 18.6 - - - +
148B GLY* 4.1 11.6 - - - +
324D ILE* 3.2 7.6 - - - +
325D THR* 2.9 30.1 + - - +
326D SER* 2.6 31.5 + - - -
342D ILE* 5.0 1.4 + - - +
343D ALA* 1.3 74.7 - - - +
345D LEU* 1.3 74.2 + - - +
348D GLY* 4.4 1.8 - - - -
349D ARG 3.5 7.4 - - - +
350D LYS* 3.6 30.3 - - + +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASN 4.5 1.0 - - - +
319D VAL* 5.3 5.8 - - + -
323D HIS* 3.3 21.8 - - + +
324D ILE* 4.5 12.6 - - + -
325D THR* 3.5 8.6 + - - -
343D ALA 4.0 2.9 - - - +
344D THR* 1.3 83.1 - - - +
346D LYS* 1.3 69.1 + - - +
347D ASN* 3.1 24.7 - - - +
348D GLY* 2.8 14.7 + - - -
349D ARG* 2.7 61.7 + - + +
351D ILE* 4.0 24.9 - - + -
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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