Contacts of the helix formed by residues 316 - 328 (chain A) in PDB entry 4GDF
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.4 39.0 - + + -
279A GLU* 3.1 56.0 + - + +
280A THR* 3.9 18.0 - - + +
295A PHE* 4.1 4.5 - - + -
312A SER* 4.1 17.5 - - - -
313A HIS 2.9 2.0 + - - -
315A LYS* 1.3 112.6 + - + +
317A HIS* 1.3 57.8 + - - +
318A GLU 3.6 1.1 - - - -
319A LYS* 3.4 7.6 + - + +
320A HIS* 2.8 41.9 + - + +
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Residues in contact with HIS 317 (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 GLU 4.0 7.0 - - - -
295A PHE* 3.0 45.2 + + + -
297A TYR* 2.6 31.4 + - + -
298A SER 3.9 11.4 - - - -
299A PHE* 4.0 8.5 - + + -
302A CYS* 3.9 4.5 - - - -
305A CYS* 3.8 7.3 - - - -
313A HIS* 2.9 17.1 + - - +
314A TYR* 4.6 1.0 + - - -
315A LYS 3.9 0.6 - - - -
316A TYR* 1.3 72.5 - - - +
318A GLU* 1.3 61.1 + - - +
319A LYS 2.9 0.5 + - - -
320A HIS 2.9 1.9 + - - -
321A TYR* 2.6 43.3 + - + -
700A ZN 2.4 36.7 - - - -
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Residues in contact with GLU 318 (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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299A PHE* 3.2 54.6 - - + -
314A TYR 5.6 0.6 + - - -
315A LYS 5.8 0.2 - - - -
316A TYR 3.6 0.2 - - - -
317A HIS* 1.3 78.3 - - - +
319A LYS* 1.3 67.1 + - - +
321A TYR* 3.5 14.5 + - - +
322A ALA 4.8 0.5 + - - -
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Residues in contact with LYS 319 (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 LEU* 4.5 14.5 - - + +
275A GLU* 5.7 2.5 - - - +
315A LYS 5.3 2.0 - - - +
316A TYR* 3.4 12.4 + - + +
317A HIS 2.9 1.2 + - - -
318A GLU* 1.3 83.7 - - - +
320A HIS* 1.3 74.1 + - + +
321A TYR 3.4 0.3 + - - -
322A ALA* 4.6 4.7 + - - +
323A ASN 5.3 0.7 + - - -
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 3.0 42.2 + - + +
275A GLU* 3.7 21.3 + - - -
276A TYR* 3.5 21.8 - + + +
279A GLU* 4.7 0.2 + - - -
292A TYR* 3.1 34.5 + + + +
295A PHE* 3.9 10.1 - - + -
316A TYR* 2.8 52.7 + + + +
317A HIS 3.3 0.9 - - - -
319A LYS* 1.3 81.1 - - + +
321A TYR* 1.4 55.8 + - - +
322A ALA 3.5 1.1 - - - -
323A ASN* 3.4 3.3 + - - +
324A ALA* 2.9 30.7 + - - +
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE 3.3 13.7 - - - -
296A GLN 3.4 10.7 + - - -
297A TYR 3.1 36.1 - - - -
298A SER* 3.4 20.2 + - - -
299A PHE* 4.4 10.3 - - + -
317A HIS* 2.6 27.7 + - + +
318A GLU* 3.6 13.2 - - - +
319A LYS 3.3 2.2 - - - -
320A HIS* 1.4 67.8 - - - +
322A ALA* 1.3 69.8 + - + +
324A ALA* 3.3 1.4 + - - +
325A ALA* 3.0 27.3 + - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU 4.8 0.8 + - - -
319A LYS 4.6 4.9 + - - +
320A HIS 3.5 0.2 - - - -
321A TYR* 1.3 88.1 - - + +
323A ASN* 1.3 64.9 + - - +
325A ALA* 3.4 5.9 + - - +
326A ILE* 3.2 26.2 + - + +
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Residues in contact with ASN 323 (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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267A GLN 4.4 2.3 - - - +
268A VAL* 3.8 5.9 - - - +
269A SER* 2.8 54.4 + - - +
272A LEU* 3.4 29.8 - - + +
273A VAL* 3.9 3.2 - - - +
292A TYR* 2.9 28.6 + - - +
319A LYS 5.3 0.2 + - - -
320A HIS* 3.4 3.6 + - - +
321A TYR 3.3 0.2 - - - -
322A ALA* 1.3 78.1 - - - +
324A ALA* 1.3 51.7 + - - +
326A ILE* 3.1 10.9 + - - +
327A PHE* 2.7 32.8 + - - +
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Residues in contact with ALA 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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292A TYR* 3.7 16.7 - - + +
295A PHE* 3.4 37.2 - - + -
296A GLN* 3.6 6.0 - - - +
320A HIS 2.9 18.7 + - - +
321A TYR 3.5 1.3 - - - +
323A ASN* 1.3 74.2 - - - +
325A ALA* 1.3 59.4 + - - +
327A PHE* 2.6 31.9 + - - +
328A ALA* 2.7 13.5 + - - +
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Residues in contact with ALA 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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296A GLN* 3.9 23.0 - - - +
321A TYR* 3.0 22.0 + - + +
322A ALA* 3.7 7.0 - - - +
324A ALA* 1.3 79.0 - - - +
326A ILE* 1.3 66.2 + - + +
328A ALA* 3.4 10.0 + - - +
329A ASP* 3.3 16.8 - - - +
271B LYS* 5.4 1.6 + - - +
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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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266A LYS* 3.3 53.6 - - + +
267A GLN 4.0 20.0 - - - +
268A VAL* 3.7 22.7 - - + +
322A ALA* 3.2 18.8 - - + +
323A ASN* 3.4 8.7 - - - +
324A ALA 3.0 0.6 - - - -
325A ALA* 1.3 76.4 - - + +
327A PHE* 1.3 61.2 + - - +
329A ASP* 2.9 28.5 + - + +
330A SER 3.5 4.2 + - - -
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Residues in contact with PHE 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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268A VAL* 4.0 26.2 - - + +
273A VAL* 4.4 8.3 - - + -
289A LEU* 4.1 7.2 - - + -
292A TYR* 3.8 28.9 - + + -
293A LEU* 3.7 22.0 - - + -
296A GLN* 6.6 0.2 - - + -
323A ASN 2.7 14.3 + - - +
324A ALA* 2.6 21.9 + - - +
326A ILE* 1.3 66.1 - - - +
328A ALA* 1.3 54.4 + - - -
329A ASP 2.9 11.3 + - - -
330A SER* 3.0 14.3 + - - -
333A GLN* 3.0 50.9 + - + -
336A ILE* 4.0 31.2 - - + -
337A CYS* 4.0 19.1 - - - -
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Residues in contact with ALA 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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293A LEU* 4.7 2.0 - - + -
296A GLN* 3.8 36.8 - - + +
324A ALA 2.7 12.7 + - - +
325A ALA* 3.4 14.6 - - - +
326A ILE 3.1 0.2 - - - -
327A PHE* 1.3 73.0 - - - +
329A ASP* 1.3 58.6 + - - +
333A GLN* 3.8 14.3 + - - +
271B LYS* 3.1 37.8 + - + +
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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