Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 4CQ8
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 ASN 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A THR* 3.3 17.5 - - - +
319A VAL* 1.3 83.0 - - + +
321A ILE* 1.3 66.7 + - - +
322A VAL* 3.2 30.8 + - - +
323A ASP* 3.2 43.7 + - - +
362A ASN* 5.5 0.9 + - - -
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Residues in contact with ILE 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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314A LYS* 3.9 32.8 - - + +
318A THR* 4.3 0.4 - - - +
319A VAL 3.9 3.6 + - - -
320A ASN* 1.3 75.4 + - - +
322A VAL* 1.3 60.3 + - + +
324A ASP* 3.0 6.9 + - - +
325A LEU* 3.0 46.5 + - + +
342A ASN 4.5 3.4 - - - +
343A VAL* 4.2 19.1 - - + -
351A LEU* 3.7 28.7 - - + -
354A ASN* 3.7 29.4 - - - +
363A ILE* 3.8 18.2 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASN* 3.2 20.7 + - - +
321A ILE* 1.3 74.7 - - + +
323A ASP* 1.4 56.1 + - - +
325A LEU* 3.3 10.6 + - + +
326A LYS* 2.9 53.6 + - + +
362A ASN* 3.8 23.6 - - - +
363A ILE* 3.9 29.8 - - + -
366A SER* 3.7 23.3 - - - +
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Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A THR* 4.9 3.5 - - + +
319A VAL* 5.8 1.6 - - - +
320A ASN* 3.2 37.1 + - - +
322A VAL* 1.4 75.1 - - - +
324A ASP* 1.3 63.2 + - - +
326A LYS* 3.8 16.6 + - - +
327A TYR* 3.1 27.8 + - - +
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Residues in contact with ASP 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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252A PRO* 3.4 30.0 - - + +
253A ARG* 5.0 1.9 + - - -
313A GLY 3.8 11.7 - - - +
314A LYS* 3.4 4.8 - - + -
315A ASN* 2.8 23.7 + - - +
318A THR* 2.7 39.6 + - + +
320A ASN 3.9 0.2 + - - -
321A ILE 3.0 9.6 + - - +
323A ASP* 1.3 77.5 - - - +
325A LEU* 1.4 63.1 + - - +
327A TYR* 3.4 1.7 + - - +
328A CYS* 3.1 27.7 + - - -
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Residues in contact with LEU 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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312A ILE* 3.8 44.0 - - + +
313A GLY* 4.0 12.8 - - - +
321A ILE* 3.0 34.2 + - + +
322A VAL* 3.3 14.6 + - + +
324A ASP* 1.4 74.8 - - - +
326A LYS* 1.4 57.0 + - + +
328A CYS* 3.2 5.2 + - - +
329A ILE* 2.9 34.9 + - - +
341A ILE* 4.1 10.1 - - + -
342A ASN 5.8 0.2 - - - +
363A ILE* 3.7 30.7 - - + -
367A VAL* 3.9 22.2 - - + -
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 2.9 43.3 + - + +
323A ASP* 3.8 14.5 + - - +
325A LEU* 1.4 72.4 - - + +
327A TYR* 1.3 66.1 + - - +
329A ILE* 3.3 4.7 + - + +
330A ASN* 2.9 32.3 + - - +
366A SER* 4.7 9.8 - - - +
367A VAL* 5.9 0.4 - - - -
369A GLU* 6.0 1.1 - - - +
370A GLU* 3.3 44.6 - - + +
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Residues in contact with TYR 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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252A PRO* 3.5 40.6 + - + -
283A CYS* 4.1 11.4 - - + -
284A ASP* 2.6 36.4 + - - -
323A ASP 3.1 17.7 + - - +
324A ASP* 3.6 5.8 - - - +
325A LEU 3.4 0.2 - - - -
326A LYS* 1.3 76.7 - - - +
328A CYS* 1.3 62.5 + - - +
330A ASN* 3.4 6.9 + - - +
331A LYS* 3.2 22.0 + - + +
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Residues in contact with CYS 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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250A ILE* 4.3 11.0 - - + -
251A THR 4.0 6.5 - - - -
252A PRO* 3.9 26.5 - - - -
283A CYS* 3.7 20.6 - - - -
312A ILE* 3.6 31.2 - - + -
313A GLY 4.6 1.8 - - - -
324A ASP 3.1 17.5 + - - +
325A LEU 3.2 6.9 + - - +
327A TYR* 1.3 72.7 - - - +
329A ILE* 1.3 60.8 + - - +
331A LYS* 3.1 1.4 + - - +
332A ILE* 2.8 36.9 + - - +
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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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312A ILE* 4.0 12.1 - - + -
325A LEU 2.9 25.4 + - - +
326A LYS* 3.7 4.3 - - + +
328A CYS* 1.3 73.6 - - - +
330A ASN* 1.3 60.4 + - - +
332A ILE* 5.1 0.7 - - - -
333A GLY* 2.9 33.1 + - - +
334A ARG 4.5 0.3 + - - -
339A ILE* 4.8 8.5 - - + -
367A VAL* 3.7 46.9 - - + +
370A GLU* 3.8 18.8 - - + +
371A ILE* 3.7 41.5 - - + +
374A LEU* 4.0 12.2 - - + +
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Residues in contact with ASN 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 LYS* 2.9 25.9 + - - +
327A TYR* 3.8 6.8 - - - +
329A ILE* 1.3 75.8 - - - +
331A LYS* 1.3 58.5 + - - +
370A GLU* 2.7 35.2 + - - +
373A ASN* 6.1 0.2 - - - +
374A LEU* 3.6 26.4 - - + +
467B LYS* 5.0 11.6 + - - -
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Residues in contact with LYS 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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283A CYS* 3.6 19.3 - - - +
284A ASP* 2.8 43.1 + - - +
287A THR* 3.4 43.3 - - - +
288A GLU* 6.2 0.4 - - - +
291A ILE* 5.8 2.5 - - - -
327A TYR* 3.2 14.0 + - + +
328A CYS 3.1 2.2 + - - -
330A ASN* 1.3 80.2 - - - +
332A ILE* 1.3 58.0 + - - +
333A GLY 3.8 0.2 - - - -
334A ARG* 5.2 1.5 + - - +
335A TYR* 3.5 12.6 - - - -
467B LYS* 5.8 11.2 - - - +
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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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247A ILE* 4.4 0.9 - - + -
250A ILE* 3.9 24.7 - - + -
283A CYS* 4.5 2.2 - - - -
286A VAL* 4.1 11.0 - - + -
287A THR* 3.4 37.9 - - + +
290A LEU* 3.8 28.0 - - + -
310A VAL* 3.9 28.9 - - + -
312A ILE* 4.8 1.8 - - + -
328A CYS 2.8 24.7 + - - +
331A LYS* 1.3 72.3 - - - +
333A GLY* 1.3 63.9 + - - +
334A ARG 3.3 3.1 - - - -
335A TYR* 3.0 19.1 + - + -
336A ALA* 3.5 7.3 + - - +
339A ILE* 4.5 6.7 - - + -
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Residues in contact with GLY 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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328A CYS 3.8 0.2 + - - -
329A ILE* 2.9 23.9 + - - -
331A LYS 3.8 0.2 - - - -
332A ILE* 1.3 78.0 - - - +
334A ARG* 1.3 60.0 + - - +
335A TYR 3.2 0.9 + - - -
336A ALA* 3.3 9.7 + - - +
339A ILE* 4.3 17.7 - - - -
374A LEU* 4.4 5.6 - - - -
416A TRP* 4.3 4.3 - - - -
424A PRO* 3.5 27.6 - - - +
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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