Contacts of the helix formed by residues 319 - 332 (chain A) in PDB entry 2CFZ
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 ALA 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A LEU* 3.6 36.5 - - + +
317A ARG 3.5 5.7 + - - -
318A ASP* 1.3 69.4 + - - +
320A LEU* 1.3 60.7 + - - +
322A TRP* 3.4 4.9 - - - +
323A SER* 2.9 30.1 + - - -
365A TYR* 3.6 25.7 - - + +
369A HIS* 3.9 17.1 - - + -
415A VAL* 4.6 3.6 - - + -
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Residues in contact with LEU 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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318A ASP* 3.1 10.2 + - - +
319A ALA* 1.3 75.9 - - - +
321A GLY* 1.3 66.8 + - - +
323A SER* 3.2 9.5 + - - -
324A LYS* 3.0 56.4 + - + +
366A GLY* 6.0 2.7 - - - -
369A HIS* 3.8 42.5 - - + +
370A ASP* 4.6 5.6 - - - +
419A TYR* 4.7 4.3 - - - +
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Residues in contact with GLY 321 (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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278A GLY 5.6 1.6 - - - -
279A THR* 4.3 2.2 - - - -
318A ASP* 3.1 24.1 + - - -
320A LEU* 1.3 76.0 - - - +
322A TRP* 1.3 61.4 + - - +
324A LYS* 3.2 9.3 + - - +
325A TYR* 2.9 41.1 + - - -
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Residues in contact with TRP 322 (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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279A THR* 3.7 39.1 - - - +
280A GLU* 3.8 29.4 - - + -
299A GLU 4.0 7.0 - - - -
300A ASN* 3.0 30.2 + - - +
306A HIS* 3.6 34.5 - + + -
307A ASN 3.5 20.6 - - - -
308A LEU* 3.7 22.0 - - + -
317A ARG* 4.0 5.2 - - + -
318A ASP 3.1 16.9 + - - +
319A ALA* 3.4 7.6 - - - +
320A LEU 3.2 0.2 - - - -
321A GLY* 1.3 75.9 - - - +
323A SER* 1.3 63.8 + - - +
325A TYR* 3.5 2.1 + - - +
326A ILE* 3.2 34.7 + - + +
365A TYR* 3.6 23.7 - + + -
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Residues in contact with SER 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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319A ALA 2.9 18.0 + - - -
320A LEU* 3.6 8.5 - - - -
322A TRP* 1.3 77.4 - - - +
324A LYS* 1.3 63.0 + - - +
326A ILE* 3.3 4.0 + - - +
327A ASN 3.1 17.0 + - - -
362A ARG* 2.7 46.5 + - - +
365A TYR* 4.1 4.2 - - - +
366A GLY* 3.7 18.8 + - - -
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 3.0 53.2 + - + +
321A GLY* 3.8 7.0 - - - +
323A SER* 1.3 76.4 - - - +
325A TYR* 1.3 59.3 + - + +
327A ASN* 3.1 10.3 + - - +
328A GLN* 2.8 42.2 + - - +
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Residues in contact with TYR 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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274A GLN* 3.5 13.9 + - - -
275A ASN 3.5 14.8 + - - -
276A THR* 3.6 28.7 - - + -
277A PRO* 3.4 39.6 - - + +
279A THR* 3.6 19.1 - - + -
286A ASN* 4.7 2.1 + - - -
300A ASN* 5.5 2.5 - - - +
321A GLY* 2.9 29.4 + - - +
322A TRP 3.9 4.3 - - - +
324A LYS* 1.3 73.6 - - + +
326A ILE* 1.3 64.8 + - + +
328A GLN* 3.4 29.5 + - - -
329A ALA* 3.1 19.4 + - - +
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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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297A MET* 4.7 2.7 - - + -
300A ASN* 3.9 19.1 - - + +
301A VAL* 3.9 17.3 - - + -
322A TRP* 3.2 38.6 + - + +
323A SER 3.7 5.6 - - - +
325A TYR* 1.3 74.8 - - + +
327A ASN* 1.3 60.4 + - - +
329A ALA* 3.2 7.3 + - - +
330A LEU* 2.9 27.1 + - + +
358A LEU* 3.3 45.9 - - + +
361A GLN* 3.9 11.4 - - + +
362A ARG* 3.8 7.2 - - + +
365A TYR* 3.9 17.3 - - + -
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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 SER 3.1 9.8 + - - +
324A LYS* 3.1 13.6 + - - +
326A ILE* 1.3 78.0 - - - +
328A GLN* 1.3 56.5 + - + +
330A LEU* 3.2 6.4 + - - +
331A HIS* 2.9 62.1 + - - -
362A ARG* 3.1 45.3 + - + +
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Residues in contact with GLN 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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260A GLU* 5.3 6.9 + - - -
274A GLN* 3.8 11.8 - - - +
324A LYS* 2.8 36.0 + - - +
325A TYR* 3.7 33.6 - - - +
326A ILE 3.3 0.4 - - - -
327A ASN* 1.3 72.8 - - + +
329A ALA* 1.3 58.0 + - - +
331A HIS* 3.6 4.5 + - - +
332A ARG* 3.0 36.4 + - - +
1658A PEG 5.0 0.2 + - - -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLN* 3.4 25.3 - - - +
286A ASN* 3.8 10.8 - - - +
295A LEU* 4.7 1.2 - - + +
297A MET* 3.9 20.4 - - + -
325A TYR 3.1 14.5 + - - +
326A ILE 3.6 4.0 - - - +
328A GLN* 1.3 72.8 - - - +
330A LEU* 1.3 61.1 + - - +
333A PHE* 2.8 41.2 + - + +
334A GLY 3.2 5.1 + - - -
358A LEU* 4.9 2.7 - - + -
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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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326A ILE 2.9 12.7 + - - +
327A ASN* 3.2 14.3 + - - +
329A ALA* 1.3 75.9 - - - +
331A HIS* 1.3 69.0 + - + +
334A GLY* 3.0 24.8 + - - -
335A ARG* 3.3 12.5 + - - +
355A VAL* 4.1 26.7 - - + -
358A LEU* 3.9 34.2 - - + +
359A GLU* 3.7 26.0 - - + +
362A ARG* 3.6 29.4 - - - +
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Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASN* 2.9 55.0 + - - +
328A GLN* 4.2 4.0 - - - +
330A LEU* 1.3 84.3 - - + +
332A ARG* 1.3 57.5 + - - +
335A ARG* 3.0 25.4 + - - +
362A ARG* 4.7 4.9 + - - -
1658A PEG 3.0 60.5 + - - +
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Residues in contact with ARG 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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260A GLU* 5.3 8.9 + - - +
263A ASP* 4.9 2.6 + - - -
272A THR* 3.6 24.7 - - - +
273A PHE 5.1 2.0 + - - -
274A GLN* 4.4 21.2 - - - +
328A GLN* 3.0 22.4 + - - +
330A LEU 3.3 0.2 - - - -
331A HIS* 1.3 79.3 - - - +
333A PHE* 1.3 92.4 + - + +
335A ARG* 3.1 17.8 + - - +
336A GLN* 3.0 18.9 - - - +
1658A PEG 3.7 16.8 - - - +
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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