Contacts of the helix formed by residues 323 - 335 (chain A) in PDB entry 6FD3
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 GLU 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A SER* 2.8 31.8 + - - -
261A MET* 3.3 30.8 + - - +
266A ILE* 3.6 29.3 - - + +
321A LYS* 4.0 26.9 - - + -
322A LYS* 1.3 78.6 - - - +
324A LEU* 1.3 68.8 + - + +
325A ILE 3.2 0.2 - - - -
326A ILE* 3.2 23.7 + - - +
327A ASN* 4.3 1.4 + - - -
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Residues in contact with LEU 324 (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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321A LYS* 3.3 36.5 + - + +
322A LYS 3.1 1.6 + - - -
323A GLU* 1.3 84.6 - - + +
325A ILE* 1.3 64.1 + - - +
326A ILE 3.1 0.2 - - - -
327A ASN* 3.1 28.2 + - - +
328A GLU* 3.2 8.3 + - - +
401A ARG* 3.7 17.7 - - - +
422A GLY 3.2 21.4 - - - +
423A PHE* 4.0 17.5 - - + -
424A CYS 3.9 15.0 - - - +
434A ARG* 4.4 3.4 - - - +
436A T8L 3.9 19.5 - - - -
438A VAL* 4.3 11.4 - - + -
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Residues in contact with ILE 325 (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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270A LEU* 4.4 11.0 - - + -
294A SER* 4.8 1.1 - - - +
314A MET* 4.0 13.0 - - + -
316A LEU* 3.7 17.7 - - + -
319A GLN* 3.4 42.4 - - + +
321A LYS 4.7 3.4 - - - +
322A LYS 3.6 14.4 - - - +
323A GLU 3.2 1.0 - - - -
324A LEU* 1.3 77.9 - - - +
326A ILE* 1.3 62.3 + - - +
328A GLU* 3.2 33.8 + - + +
329A ILE* 3.3 8.9 + - + +
353A LEU* 3.4 30.1 - - + -
422A GLY* 4.9 3.6 - - - +
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Residues in contact with ILE 326 (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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261A MET* 3.7 35.9 - - + -
266A ILE* 4.0 14.6 - - + -
269A LYS* 3.8 33.2 - - + -
270A LEU* 3.9 23.1 - - + +
273A ILE* 4.3 3.7 - - + +
323A GLU 3.2 16.6 + - - +
324A LEU 3.1 0.2 - - - -
325A ILE* 1.3 79.7 - - - +
327A ASN* 1.3 65.5 + - - +
328A GLU 3.2 0.5 + - - -
329A ILE* 3.4 2.8 + - - +
330A LEU* 3.1 47.5 + - + +
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Residues in contact with ASN 327 (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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323A GLU 4.3 1.1 + - - -
324A LEU* 3.1 24.0 + - - +
326A ILE* 1.3 81.6 - - - +
328A GLU* 1.3 54.7 + - - +
330A LEU* 4.3 7.6 - - - +
331A VAL* 2.7 38.8 + - - +
424A CYS* 3.2 35.2 + - - +
425A ALA* 4.2 1.2 - - - +
426A GLN* 3.2 40.1 + - - +
434A ARG* 4.9 4.0 - - - +
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Residues in contact with GLU 328 (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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294A SER* 4.9 1.7 + - - -
312A LYS* 2.8 34.0 + - - +
314A MET* 3.7 26.1 - - - +
324A LEU 3.2 2.8 + - - -
325A ILE* 3.2 20.2 + - + +
326A ILE 3.1 0.4 - - - -
327A ASN* 1.3 78.6 - - - +
329A ILE* 1.3 67.5 + - + +
331A VAL* 4.0 0.9 - - - +
332A MET* 3.0 43.0 + - - +
355A VAL* 5.6 3.3 - - + +
420A ASP* 4.4 0.9 - - - -
421A PHE* 3.6 27.3 + - + +
422A GLY* 3.3 29.1 + - - +
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Residues in contact with ILE 329 (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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270A LEU* 4.2 12.3 - - + -
273A ILE* 4.0 22.2 - - + -
274A VAL* 4.0 13.9 - - + -
325A ILE* 3.3 7.0 + - + +
326A ILE 4.0 0.9 - - - +
328A GLU* 1.3 80.0 - - + +
330A LEU* 1.3 64.9 + - - +
332A MET* 3.3 4.9 + - - +
333A ARG* 3.1 35.2 + - - +
343A TYR* 4.1 15.2 - - + +
346A SER* 3.8 29.6 - - - +
353A LEU* 3.8 25.6 - - + -
355A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 330 (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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269A LYS* 4.4 11.2 - - - +
273A ILE* 3.9 29.4 - - + -
326A ILE* 3.1 41.3 + - + +
327A ASN* 3.9 4.0 - - - +
329A ILE* 1.3 77.0 - - - +
331A VAL* 1.3 57.6 + - - +
333A ARG* 3.8 17.0 - - - +
334A GLU* 2.8 61.1 + - - +
426A GLN* 4.2 17.3 - - - +
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Residues in contact with VAL 331 (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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327A ASN 2.7 24.9 + - - +
328A GLU 4.2 1.6 - - - +
330A LEU* 1.3 71.9 - - - +
332A MET* 1.3 62.7 + - - +
335A ASN* 2.9 44.2 + - + +
340A ILE* 5.7 0.8 - - + +
393A LEU* 4.3 3.6 - - + -
398A VAL* 4.1 15.5 - - + -
421A PHE* 3.6 33.9 - - + -
424A CYS* 3.5 19.7 - - - -
426A GLN* 3.8 28.5 - - + +
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Residues in contact with MET 332 (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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328A GLU* 3.0 35.5 + - - +
329A ILE* 3.8 3.8 - - - +
331A VAL* 1.3 79.6 - - - +
333A ARG* 1.3 58.9 + - - +
335A ASN 4.2 2.6 + - - +
336A LYS* 3.8 18.4 + - - +
340A ILE* 5.1 7.0 - - - +
341A VAL* 4.0 29.5 - - + +
343A TYR* 3.8 43.7 + - + +
355A VAL* 4.2 20.0 - - + -
357A MET* 4.3 12.1 - - + +
419A THR* 5.1 3.8 - - - -
420A ASP 5.4 0.7 - - - -
421A PHE* 3.7 29.8 - - + -
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Residues in contact with ARG 333 (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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272A SER 5.3 0.2 + - - -
273A ILE* 2.6 56.4 + - - +
329A ILE* 3.1 22.5 + - - +
330A LEU* 3.8 18.4 - - - +
332A MET* 1.3 79.0 - - - +
334A GLU* 1.3 69.9 + - + +
335A ASN 3.5 0.4 + - - -
336A LYS* 3.9 16.8 - - - +
343A TYR* 3.5 45.4 + - + -
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Residues in contact with GLU 334 (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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330A LEU* 2.8 56.2 + - - +
333A ARG* 1.3 84.7 + - + +
335A ASN* 1.3 71.7 + - - +
336A LYS 3.7 1.9 + - - -
426A GLN* 4.5 12.1 + - - +
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Residues in contact with ASN 335 (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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331A VAL* 2.9 51.3 + - + +
332A MET 4.3 1.1 - - - -
334A GLU* 1.3 87.5 + - - +
336A LYS* 1.3 64.7 + - - +
337A ASN 3.7 1.0 + - - -
340A ILE* 4.1 14.6 - - - +
392A PHE* 3.4 26.6 - - + -
393A LEU* 4.5 5.5 - - + +
396A ASN* 3.8 31.1 + - - +
398A VAL* 4.2 9.7 - - - +
426A GLN* 4.8 3.5 + - - +
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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