Contacts of the helix formed by residues 329 - 344 (chain A) in PDB entry 3C6G
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 TYR 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A PHE* 2.9 50.7 + + - +
326A MET* 3.5 5.5 - - + +
327A ALA 3.3 0.2 - - - -
328A LEU* 1.3 104.9 - - + +
330A PRO* 1.4 59.5 - - - +
331A ASN* 3.2 3.6 - - + -
332A ILE* 2.9 39.2 + - + +
333A GLN 3.2 8.1 + - - -
420A PHE* 4.3 21.8 - + + +
481A LEU* 5.4 2.1 - - - +
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Residues in contact with PRO 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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326A MET 3.6 9.1 - - - +
327A ALA 3.7 9.4 - - - +
328A LEU 3.3 11.0 - - - +
329A TYR* 1.4 86.9 - - - +
331A ASN* 1.3 60.8 + - - +
333A GLN* 3.5 8.6 - - + +
334A GLY* 2.8 28.8 + - - -
470A HIS* 5.2 11.4 - - + -
471A LEU 6.0 0.4 - - - +
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Residues in contact with ASN 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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329A TYR* 3.1 1.9 + - + -
330A PRO* 1.3 81.7 - - - +
332A ILE* 1.3 63.7 + - + +
334A GLY* 3.8 1.3 + - - -
335A GLN* 3.3 26.5 + - - +
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Residues in contact with ILE 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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326A MET* 3.6 21.5 - - + -
329A TYR* 2.9 28.6 + - + +
331A ASN* 1.3 79.5 - - + +
333A GLN* 1.3 64.4 + - - +
335A GLN* 3.2 4.5 + - - +
336A VAL* 3.2 21.0 + - - +
360A TYR* 3.6 23.8 - - - +
364A VAL* 3.9 15.5 - - + -
420A PHE* 3.8 28.9 - - + +
422A PRO* 4.2 12.8 - - + -
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Residues in contact with GLN 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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326A MET* 2.9 46.0 + - + +
329A TYR 3.2 5.9 + - - -
330A PRO* 3.2 12.5 + - - +
332A ILE* 1.3 76.2 - - - +
334A GLY* 1.3 56.3 + - - +
336A VAL* 3.2 6.4 + - - +
337A GLN* 3.0 54.6 + - - +
466A LEU* 4.1 10.8 - - + +
470A HIS* 3.6 10.4 + - - -
471A LEU* 2.8 55.7 + - - +
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Residues in contact with GLY 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 PRO 2.8 19.9 + - - -
331A ASN* 4.1 2.5 - - - -
333A GLN* 1.3 73.2 - - - +
335A GLN* 1.3 58.4 + - - +
337A GLN* 3.4 14.4 + - - +
338A LYS* 2.9 28.1 + - - +
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Residues in contact with GLN 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 ASN 3.3 14.4 + - - +
332A ILE* 3.2 4.9 + - - +
334A GLY* 1.3 73.9 - - - +
336A VAL* 1.3 65.1 + - - +
338A LYS* 3.6 33.7 + - - +
339A GLU* 3.2 21.0 + - - +
360A TYR* 3.6 36.8 - - + +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A MET* 4.4 11.4 - - - -
332A ILE 3.2 14.4 + - - +
333A GLN 3.5 6.7 - - - +
335A GLN* 1.3 74.5 - - - +
337A GLN* 1.3 59.6 + - - +
339A GLU* 3.0 8.3 + - - +
340A ILE* 2.9 36.6 + - + +
360A TYR* 3.9 8.7 - - + -
361A THR* 3.4 23.3 - - + +
364A VAL* 3.7 29.8 - - + -
462A PHE* 4.1 12.6 - - + -
463A THR* 5.9 0.2 - - + -
466A LEU* 3.8 18.6 - - + -
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Residues in contact with GLN 337 (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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333A GLN* 3.0 44.3 + - - +
334A GLY* 3.6 14.0 - - - +
335A GLN 3.3 0.2 - - - -
336A VAL* 1.3 77.1 - - - +
338A LYS* 1.3 60.1 + - - +
340A ILE* 3.3 8.0 + - - +
341A ASP* 3.1 32.9 + - - +
466A LEU* 3.3 28.6 + - + +
469A PHE 2.9 29.1 + - - -
470A HIS* 4.0 7.3 + - - +
501A ARG* 3.5 26.9 + - - +
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Residues in contact with LYS 338 (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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334A GLY 2.9 20.7 + - - +
335A GLN* 3.7 33.3 + - - +
336A VAL 3.3 0.2 - - - -
337A GLN* 1.3 72.7 - - - +
339A GLU* 1.3 62.4 + - - +
341A ASP* 3.5 8.2 + - - +
342A LEU* 3.1 23.9 + - + +
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Residues in contact with GLU 339 (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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335A GLN 3.2 9.4 + - - +
336A VAL* 3.0 9.7 + - - +
338A LYS* 1.3 79.2 - - - +
340A ILE* 1.3 65.5 + - - +
342A LEU* 3.3 7.9 + - + +
343A ILE* 3.0 31.1 + - + +
357A LYS 4.6 4.7 - - - +
358A MET* 3.3 24.0 - - + +
359A PRO* 3.3 13.3 - - - +
360A TYR* 2.8 35.1 + - + +
361A THR* 2.9 31.5 + - - +
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Residues in contact with ILE 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 VAL* 2.9 26.5 + - + +
337A GLN* 3.3 10.5 + - - +
339A GLU* 1.3 74.3 - - - +
341A ASP* 1.3 62.1 + - - +
344A MET* 2.5 53.1 + - + +
345A GLY 3.1 3.0 + - - +
358A MET* 3.8 22.2 - - + -
463A THR* 3.6 29.2 - - + +
466A LEU* 3.7 17.5 - - + -
467A GLN* 3.7 41.5 - - + +
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Residues in contact with ASP 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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337A GLN 3.1 17.0 + - - +
338A LYS* 3.8 7.1 - - - +
340A ILE* 1.3 80.1 - - - +
342A LEU* 1.3 66.5 + - - +
345A GLY* 3.0 32.3 + - - +
346A PRO* 4.7 3.5 - - + +
467A GLN* 5.1 0.3 - - - +
501A ARG* 2.9 35.5 + - - -
502A HIS* 4.5 10.5 - - - -
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Residues in contact with LEU 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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338A LYS* 3.1 18.4 + - + +
339A GLU* 3.3 8.9 + - + +
341A ASP* 1.3 79.0 - - - +
343A ILE* 1.3 77.1 + - + +
345A GLY 4.5 0.3 + - - -
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Residues in contact with ILE 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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339A GLU* 3.0 18.3 + - + +
342A LEU* 1.3 99.1 - - + +
344A MET* 1.3 61.9 + - - +
345A GLY 3.5 0.2 - - - -
354A ASP* 4.1 24.5 - - + +
357A LYS* 3.3 57.0 - - + +
358A MET* 4.1 15.9 - - + -
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Residues in contact with MET 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 ILE* 2.5 34.0 + - + +
343A ILE* 1.3 74.1 - - - +
345A GLY* 1.3 58.1 + - - +
348A GLY* 3.2 27.5 + - - +
349A LYS 4.8 0.9 - - - +
350A PRO* 3.5 39.7 - - + -
351A SER 3.8 3.8 - - - +
354A ASP* 3.5 33.0 - - + +
358A MET* 3.6 27.4 - - - +
459A PHE* 4.1 11.9 - - + -
463A THR* 4.1 11.9 - - - -
467A GLN* 3.9 12.8 - - - +
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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