Contacts of the helix formed by residues 304 - 323 (chain A) in PDB entry 7CAL
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 SER 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A VAL* 3.2 21.4 + - - -
301A HIS* 4.2 8.8 + - - -
302A TRP 3.5 1.8 - - - -
303A THR* 1.3 77.3 - - - +
305A ARG* 1.3 68.6 + - - +
307A ARG* 3.9 17.0 - - - +
308A THR* 3.3 29.7 + - - +
346A LEU* 4.3 3.5 - - - +
311B ASP* 5.0 5.0 + - - -
314B ARG* 4.4 10.9 + - - -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP 4.7 5.1 + - - +
303A THR* 3.4 0.8 - - - +
304A SER* 1.3 85.6 + - - +
306A THR* 1.3 64.2 + - - +
308A THR* 3.9 2.3 + - - -
309A PHE* 3.4 22.5 + - - +
341A PHE* 3.5 39.2 + - + -
345A GLY* 4.0 26.5 - - - -
346A LEU* 3.9 23.2 - - + +
314B ARG* 4.8 21.5 - - - +
318B GLU* 3.9 28.9 + - - -
322B ARG* 5.1 2.2 - - - +
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A THR* 4.3 9.5 + - - -
305A ARG* 1.3 80.5 + - - +
307A ARG* 1.3 57.7 + - - +
309A PHE* 4.0 10.2 - - + +
310A ARG* 3.3 24.9 + - - +
341A PHE* 4.6 6.8 - - + -
186D GLU* 4.3 28.9 + - + +
187D LYS* 4.2 26.8 - - + +
193D TYR* 4.4 13.6 - - + -
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 4.3 17.2 + - - +
303A THR 3.3 18.0 + - - +
304A SER* 3.9 25.2 + - - +
305A ARG 3.3 0.6 - - - -
306A THR* 1.3 76.5 - - - +
308A THR* 1.3 71.5 + - - +
309A PHE 3.2 1.1 - - - -
310A ARG* 3.3 1.8 + - - +
311A ASP* 3.1 25.5 + - - +
193D TYR* 4.3 16.6 + - + +
297D ASN* 2.9 37.2 + - - +
298D LEU* 6.2 0.2 - - - -
300D VAL* 5.0 12.9 - - - +
301D HIS* 3.6 48.1 + - + +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 3.3 18.0 + - - +
307A ARG* 1.3 89.3 - - - +
309A PHE* 1.3 63.8 + - - +
311A ASP* 3.7 13.6 - - - +
312A SER* 3.4 20.4 + - - -
346A LEU* 3.3 34.8 - - + +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG 3.4 16.8 + - - +
306A THR* 4.0 9.2 - - + +
307A ARG 3.2 0.8 - - - -
308A THR* 1.3 82.9 + - - +
310A ARG* 1.3 81.2 + - + +
311A ASP 3.2 0.2 - - - -
312A SER* 3.2 8.0 + - - -
313A VAL* 3.2 47.0 + - + +
337A ILE* 4.0 15.0 - - + -
338A CYS* 4.2 12.3 - - + -
341A PHE* 3.8 54.1 - + + -
346A LEU* 4.5 4.0 - - + +
187D LYS* 4.0 23.8 - - + -
189D ILE* 4.2 11.7 - - + -
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 3.3 18.3 + - + +
307A ARG 3.3 6.5 + - - +
309A PHE* 1.3 95.8 - - + +
311A ASP* 1.3 62.2 + - - +
313A VAL* 4.1 13.3 - - - +
314A ARG* 3.4 23.0 + - - +
185D LEU 4.2 1.6 + - - -
186D GLU* 2.4 40.9 + - - +
188D ASP 3.1 21.8 + - - +
189D ILE* 4.1 15.0 + - - +
191D PHE 2.4 29.1 + - - -
192D ASN* 4.0 8.1 + - - +
193D TYR* 4.1 31.2 - - + +
301D HIS* 4.5 10.0 + - + -
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 3.1 15.6 + - - +
308A THR* 3.8 13.1 - - - +
309A PHE 3.2 0.4 - - - -
310A ARG* 1.3 79.2 - - - +
312A SER* 1.3 57.5 + - - +
313A VAL 3.4 0.2 - - - -
314A ARG* 2.5 37.6 + - - +
315A ALA* 2.9 28.6 + - - +
301D HIS* 2.6 28.5 + - - -
304D SER* 5.0 4.5 + - - -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A THR 3.4 10.3 + - - -
309A PHE* 3.2 13.6 + - - -
311A ASP* 1.3 76.5 - - - +
313A VAL* 1.3 66.0 + - - +
315A ALA* 4.0 6.8 - - - +
316A ALA* 3.2 23.4 + - - +
337A ILE* 3.7 23.0 - - - +
351D THR* 5.4 1.2 - - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PHE* 3.2 44.2 + - + +
310A ARG* 4.5 12.3 - - - +
312A SER* 1.3 78.3 + - - +
314A ARG* 1.3 63.4 + - - +
316A ALA* 3.4 2.4 + - - +
317A SER* 3.1 26.3 + - - +
334A LEU* 4.1 19.3 - - + +
337A ILE* 3.9 16.8 - - + -
338A CYS* 4.9 2.0 - - - -
189D ILE* 3.8 29.2 - - + +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ARG 3.4 15.7 + - - +
311A ASP* 2.5 36.2 + - - +
312A SER 3.3 0.4 - - - -
313A VAL* 1.3 81.3 - - - +
315A ALA* 1.3 56.3 + - - +
317A SER* 3.3 5.9 + - - +
318A GLU* 3.0 48.3 + - + +
194D PHE* 3.9 19.8 - - - -
301D HIS* 3.8 29.4 + - - -
302D TRP 5.0 4.0 + - - -
304D SER* 4.4 9.5 + - - -
305D ARG* 4.8 19.8 - - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP 2.9 17.9 + - - +
312A SER* 3.6 7.8 + - - +
313A VAL 3.3 0.2 - - - -
314A ARG* 1.3 77.6 - - - +
316A ALA* 1.3 57.5 + - - +
317A SER 3.4 0.2 - - - -
318A GLU* 4.0 14.0 - - - +
319A PHE* 3.4 21.5 + - - +
322A ARG* 5.6 0.9 + - - -
347D LYS* 4.5 7.9 - - + +
351D THR* 3.7 22.7 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER 3.2 18.3 + - - +
313A VAL 3.7 3.6 - - - +
314A ARG 3.2 0.4 - - - -
315A ALA* 1.3 75.4 - - - +
317A SER* 1.3 61.2 + - - +
319A PHE* 4.0 5.6 - - - +
320A ALA* 3.7 19.9 + - - +
330A GLN* 5.0 0.5 + - - -
333A MET* 4.0 21.0 - - + +
334A LEU* 4.7 7.5 - - + +
337A ILE* 3.7 21.3 - - + -
351D THR* 4.2 17.9 - - + -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 3.1 19.6 + - - +
314A ARG* 3.3 6.0 + - - -
316A ALA* 1.3 75.3 - - - +
318A GLU* 1.3 63.4 + - - +
319A PHE 3.3 0.9 - - - -
320A ALA 3.8 2.3 + - - +
321A SER* 3.3 23.6 + - - -
330A GLN* 4.6 11.7 + - - +
334A LEU* 3.8 23.7 - - - +
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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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314A ARG* 3.0 43.1 + - + +
315A ALA* 4.1 10.7 - - - +
317A SER* 1.3 77.5 - - - +
319A PHE* 1.3 60.6 + - - +
321A SER* 4.1 2.9 - - - -
322A ARG* 3.3 48.4 + - + +
305D ARG* 3.9 32.7 + - - -
345D GLY* 5.3 2.1 - - - -
346D LEU 5.7 0.5 + - - -
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA 3.4 15.4 + - - +
316A ALA* 4.0 6.0 - - - +
317A SER 3.3 0.2 - - - -
318A GLU* 1.3 81.3 - - - +
320A ALA* 1.3 62.9 + - - +
321A SER 3.2 1.5 + - - -
322A ARG* 3.8 11.1 + - - +
323A ASN* 3.3 51.0 + - - +
325A LEU* 4.5 5.8 - - + -
333A MET* 4.2 17.7 - - + -
348D GLN* 3.8 33.7 - - + -
351D THR* 4.9 7.2 - - + -
352D LEU* 3.6 30.3 - - + -
363D ILE* 3.9 36.3 - - + -
367D LEU* 4.8 2.0 - - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 3.7 13.8 + - - +
317A SER 3.8 1.3 + - - +
318A GLU 3.4 0.4 - - - -
319A PHE* 1.3 78.7 - - - +
321A SER* 1.3 56.4 + - - +
323A ASN 4.5 0.7 - - - -
324A GLN* 4.3 0.7 - - - -
325A LEU* 3.5 48.4 + - + +
330A GLN* 3.4 42.2 + - + +
333A MET* 4.1 7.0 - - - -
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER 3.3 17.8 + - - -
318A GLU* 4.2 4.7 - - - -
319A PHE 3.2 0.8 - - - -
320A ALA* 1.3 79.5 - - - +
322A ARG* 1.3 63.0 + - - +
323A ASN 3.3 1.1 - - - -
324A GLN* 3.7 6.2 + - - +
330A GLN* 5.4 2.9 - - - +
118C HIS* 3.0 29.5 + - - -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA 5.6 0.8 + - - -
318A GLU* 3.3 35.0 + - + +
319A PHE* 4.2 18.5 - - - +
321A SER* 1.3 78.1 - - - +
323A ASN* 1.3 71.3 + - - +
324A GLN* 3.3 8.5 + - - +
117C SER 6.0 0.4 - - - +
118C HIS* 4.2 24.4 - - + +
120C TYR* 3.5 19.6 + - - +
305D ARG* 5.1 2.8 - - - +
342D LYS 4.8 5.5 + - - -
343D THR* 2.9 23.6 + - - +
344D GLU 3.7 8.9 + - - -
345D GLY* 3.4 23.4 - - - +
348D GLN* 3.6 24.5 + - - +
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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
----------------------------------------------------------
319A PHE* 3.3 46.1 + - - +
321A SER 3.3 0.2 - - - -
322A ARG* 1.3 90.6 + - - +
324A GLN* 1.3 71.9 + - - +
325A LEU* 3.4 6.9 + - + -
348D GLN* 5.6 0.2 + - - -
366D TYR* 4.7 2.6 - - - -
367D LEU* 3.4 44.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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