Contacts of the helix formed by residues 307 - 320 (chain A) in PDB entry 4Z1F
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 ARG 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A PRO 5.4 0.4 + - - -
304A LYS* 3.2 36.8 + - - +
305A ASP 3.7 4.8 + - - +
306A VAL* 1.3 79.1 + - - +
308A GLU* 1.3 71.2 + - + +
309A TRP* 3.0 11.1 + - + +
310A GLN* 2.9 30.9 + - - +
311A HIS* 3.7 7.0 + - - -
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Residues in contact with GLU 308 (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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307A ARG* 1.3 76.8 - - + +
309A TRP* 1.3 64.1 + - - +
311A HIS* 3.0 12.3 + - - +
312A GLU* 2.9 42.5 + - + +
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Residues in contact with TRP 309 (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* 5.9 0.4 - - - -
307A ARG* 3.0 15.7 + - + +
308A GLU* 1.3 76.2 - - + +
310A GLN* 1.3 94.7 + - + +
312A GLU* 3.4 12.1 + - - +
313A GLU* 2.9 55.0 + - - +
316A ARG* 5.4 0.3 + - - -
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Residues in contact with GLN 310 (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* 3.4 24.0 + - - +
298A ILE* 4.0 12.2 - - + +
301A MET* 3.8 13.4 - - - +
305A ASP 3.9 4.9 - - - +
306A VAL* 3.5 21.7 - - + -
307A ARG 2.9 26.0 + - - +
309A TRP* 1.3 117.6 + - + +
311A HIS* 1.3 59.7 + - - +
313A GLU* 3.2 7.2 + - - +
314A PHE* 2.9 31.4 + - - +
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Residues in contact with HIS 311 (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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298A ILE* 4.2 2.3 - - - +
303A PRO 5.2 2.0 + - - -
306A VAL* 3.5 40.6 + - + +
307A ARG* 3.7 8.6 + - - -
308A GLU* 3.0 12.0 + - - +
310A GLN* 1.3 78.6 - - - +
312A GLU* 1.3 57.8 + - + +
315A TYR* 2.9 31.0 + - - +
325A PRO* 4.9 3.6 - - + -
328A THR* 3.8 26.9 - - + +
330A HIS* 4.4 14.3 + - + +
342A ILE* 4.0 22.4 - - + -
344A TYR* 2.9 38.9 + + + +
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Residues in contact with GLU 312 (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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308A GLU* 2.9 39.5 + - + +
309A TRP* 3.6 10.8 + - - +
311A HIS* 1.3 75.6 - - + +
313A GLU* 1.3 65.4 + - - +
315A TYR* 3.3 5.0 + - - +
316A ARG* 2.9 58.2 + - - +
324A LYS* 3.2 44.1 + - + +
325A PRO* 4.4 17.5 - - + -
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Residues in contact with GLU 313 (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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309A TRP* 2.9 42.4 + - - +
310A GLN* 3.5 6.5 - - - +
312A GLU* 1.3 77.5 - - - +
314A PHE* 1.3 56.8 + - - +
316A ARG* 3.3 13.4 + - - +
317A TYR* 3.0 26.6 + - - +
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Residues in contact with PHE 314 (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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280A PHE* 3.8 21.3 - + - -
295A LEU* 5.7 0.9 - - + -
296A GLN 5.2 1.8 - - - -
298A ILE* 3.6 30.7 - - + -
299A TRP* 3.5 27.1 - + - -
310A GLN 2.9 7.8 + - - +
313A GLU* 1.3 73.1 - - - +
315A TYR* 1.3 67.2 + - - +
317A TYR* 3.1 9.6 + + + +
318A VAL* 2.9 58.3 + - + +
342A ILE* 4.3 5.4 - - + -
344A TYR* 3.3 28.7 - + - +
366A TYR* 6.2 0.7 - + - -
390A VAL* 3.5 35.7 - - + -
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Residues in contact with TYR 315 (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 HIS 2.9 20.9 + - - +
312A GLU 3.6 2.0 - - - +
314A PHE* 1.3 77.4 - - - +
316A ARG* 1.3 62.0 + - + +
318A VAL* 3.6 0.8 - - - +
319A ALA* 2.9 56.6 + - + +
321A ALA* 3.9 11.1 - - + +
323A ASP* 2.9 44.1 + - - -
324A LYS 3.7 7.9 - - - -
325A PRO* 3.5 22.0 - - + -
344A TYR* 3.5 43.6 - + + -
346A PRO* 3.1 41.1 - - + +
388A ARG* 4.4 3.1 - - + -
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Residues in contact with ARG 316 (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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309A TRP 5.4 0.6 + - - -
312A GLU* 2.9 56.5 + - - +
313A GLU* 3.7 10.2 - - - +
315A TYR* 1.3 79.2 - - + +
317A TYR* 1.3 61.7 + - - +
320A GLN* 3.0 22.5 + - - -
321A ALA 3.3 25.9 + - - +
322A HIS* 3.7 15.3 + - - +
323A ASP 3.3 29.4 + - - +
324A LYS* 4.0 11.7 - - - +
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Residues in contact with TYR 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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275A THR 4.9 0.2 + - - -
276A LYS 5.7 0.5 + - - -
279A ASN* 3.1 24.8 + - - +
280A PHE* 3.4 31.3 - + - -
295A LEU* 3.8 25.8 - - + -
313A GLU 3.0 13.3 + - - +
314A PHE* 3.1 14.1 + + + +
316A ARG* 1.3 81.2 - - - +
318A VAL* 1.3 81.1 + - + +
320A GLN* 3.4 17.0 + - - +
366A TYR* 4.4 7.4 + - - -
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Residues in contact with VAL 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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314A PHE* 2.9 52.8 + - + +
315A TYR* 3.6 9.9 - - - +
317A TYR* 1.3 88.0 - - + +
319A ALA* 1.3 64.4 + - + +
320A GLN* 3.6 4.9 + - - +
344A TYR* 4.5 2.9 - - + -
362A SER 4.8 10.1 + - - +
364A ALA* 5.3 8.7 - - + -
366A TYR* 5.9 2.9 - - + -
388A ARG* 5.0 2.8 - - - -
389A GLY* 3.9 38.1 - - - +
390A VAL* 5.0 2.0 - - + -
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Residues in contact with ALA 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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315A TYR* 2.9 47.4 + - + +
318A VAL* 1.3 76.3 - - - +
320A GLN* 1.3 69.7 + - - +
321A ALA* 3.3 8.3 + - + +
388A ARG* 3.8 29.7 + - + +
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Residues in contact with GLN 320 (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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316A ARG 3.0 13.5 + - - -
317A TYR 4.0 11.2 - - - +
318A VAL 3.3 6.8 - - - +
319A ALA* 1.3 80.2 - - - +
321A ALA* 1.3 57.6 + - - +
322A HIS* 4.7 8.0 - - - -
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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