Contacts of the helix formed by residues 304 - 323 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASP* 5.0 5.4 + - - -
314A ARG* 4.4 10.7 + - - -
300D VAL* 3.2 19.8 + - - -
301D HIS* 4.2 9.2 + - - -
302D TRP 3.5 2.0 - - - -
303D THR* 1.3 77.8 - - - +
305D ARG* 1.3 67.8 + - - +
306D THR 3.5 0.2 - - - -
307D ARG* 3.9 17.0 - - - +
308D THR* 3.3 30.0 + - - +
346D LEU* 4.3 3.9 - - - +
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Residues in contact with ARG 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 4.8 21.5 - - - +
318A GLU* 3.9 28.9 + - - -
322A ARG* 5.1 2.2 - - - +
302D TRP 4.7 4.9 + - - +
303D THR* 3.4 0.6 - - - +
304D SER* 1.3 86.4 + - - +
306D THR* 1.3 63.9 + - - +
308D THR* 3.9 2.3 + - - -
309D PHE* 3.4 22.5 + - - +
341D PHE* 3.5 37.9 + - + -
345D GLY* 4.0 26.5 - - - -
346D LEU* 4.0 22.0 - - + +
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Residues in contact with THR 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C GLU* 4.3 30.4 + - + +
187C LYS* 4.1 26.3 - - + +
193C TYR* 4.4 14.1 - - + -
303D THR* 4.3 9.3 + - - -
305D ARG* 1.3 80.4 + - - +
307D ARG* 1.3 58.3 + - - +
309D PHE* 4.0 11.5 - - + +
310D ARG* 3.3 25.1 + - - +
341D PHE* 4.6 6.4 - - + -
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Residues in contact with ARG 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C TYR* 4.3 16.4 + - + +
297C ASN* 2.9 36.0 + - - +
298C LEU* 6.2 0.7 - - - -
300C VAL* 5.0 13.5 - - - +
301C HIS* 3.6 47.3 + - + +
300D VAL* 4.3 17.2 + - - +
303D THR 3.3 18.1 + - - +
304D SER* 3.8 25.8 + - - +
305D ARG 3.3 1.0 - - - -
306D THR* 1.3 76.9 - - - +
308D THR* 1.3 73.3 + - - +
309D PHE 3.2 1.3 - - - -
310D ARG* 3.3 2.0 + - - -
311D ASP* 3.1 25.1 + - - +
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Residues in contact with THR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D SER* 3.3 17.7 + - - +
307D ARG* 1.3 90.5 - - - +
309D PHE* 1.3 64.4 + - - +
311D ASP* 3.7 14.1 - - - +
312D SER* 3.4 20.8 + - - -
346D LEU* 3.3 32.6 - - + +
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Residues in contact with PHE 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LYS* 4.0 24.2 - - + -
189C ILE* 4.2 12.1 - - + -
305D ARG 3.4 16.6 + - - +
306D THR* 4.0 9.6 - - + +
307D ARG 3.2 0.6 - - - -
308D THR* 1.3 81.7 + - - +
310D ARG* 1.3 82.5 + - + +
311D ASP 3.2 0.2 - - - -
312D SER* 3.2 7.8 + - - -
313D VAL* 3.2 46.0 + - + +
337D ILE* 4.0 16.4 - - + -
338D CYS* 4.2 11.7 - - + -
341D PHE* 3.8 54.3 - + + -
346D LEU* 4.7 3.1 - - + -
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU 4.2 1.6 + - - -
186C GLU* 2.4 42.0 + - - +
187C LYS 4.1 0.4 - - - -
188C ASP 3.1 21.8 + - - +
189C ILE* 4.1 14.7 + - - +
191C PHE 2.4 29.3 + - - -
192C ASN* 4.0 8.3 + - - +
193C TYR* 4.1 30.1 - - + +
301C HIS* 4.5 8.9 + - + -
306D THR 3.3 18.7 + - - +
307D ARG 3.3 6.3 + - - +
309D PHE* 1.3 94.5 - - + +
311D ASP* 1.3 62.9 + - - +
312D SER 3.5 0.2 - - - -
313D VAL* 4.1 13.2 - - - +
314D ARG* 3.4 21.8 + - - +
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Residues in contact with ASP 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C HIS* 2.6 28.1 + - - -
304C SER* 5.0 4.5 + - - -
307D ARG* 3.1 15.5 + - - +
308D THR* 3.8 13.9 - - - +
309D PHE 3.2 0.4 - - - -
310D ARG* 1.3 79.0 - - - +
312D SER* 1.3 57.4 + - - +
314D ARG* 2.5 38.7 + - - +
315D ALA* 2.9 28.2 + - - +
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C THR* 5.4 1.2 - - - +
308D THR 3.4 11.2 + - - -
309D PHE* 3.2 13.1 + - - -
311D ASP* 1.3 76.4 - - - +
313D VAL* 1.3 66.7 + - - +
315D ALA* 4.0 6.3 - - - +
316D ALA* 3.2 24.1 + - - +
337D ILE* 3.7 23.4 - - - +
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Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ILE* 3.7 29.4 - - + +
309D PHE* 3.2 44.2 + - + +
310D ARG* 4.5 12.8 - - - +
312D SER* 1.3 78.4 + - - +
314D ARG* 1.3 62.4 + - - +
316D ALA* 3.4 2.4 + - - +
317D SER* 3.1 26.5 + - - +
334D LEU* 4.1 19.0 - - + +
337D ILE* 3.9 17.0 - - + -
338D CYS* 4.9 2.0 - - - -
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Residues in contact with ARG 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C PHE* 3.9 20.0 - - - -
301C HIS* 3.8 28.3 + - - -
302C TRP 5.0 4.0 + - - -
304C SER* 4.4 9.3 + - - -
305C ARG* 4.8 20.2 - - - +
310D ARG 3.4 15.8 + - - +
311D ASP* 2.5 37.1 + - - +
312D SER 3.3 0.2 - - - -
313D VAL* 1.3 80.4 - - - +
315D ALA* 1.3 57.2 + - - +
317D SER* 3.3 5.9 + - - -
318D GLU* 3.0 47.2 + - + +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LYS* 4.6 7.4 - - + +
351C THR* 3.7 23.5 + - - +
311D ASP 2.9 18.5 + - - +
312D SER* 4.1 7.2 - - - +
313D VAL 3.3 0.2 - - - -
314D ARG* 1.3 77.8 - - - +
316D ALA* 1.3 57.5 + - - +
318D GLU* 4.0 13.6 - - - +
319D PHE* 3.4 22.0 + - - +
322D ARG* 5.6 1.0 + - - -
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C THR* 4.2 17.2 - - + +
312D SER 3.2 17.4 + - - +
313D VAL 3.4 3.6 + - - +
314D ARG 3.2 0.4 - - - -
315D ALA* 1.3 75.6 - - - +
317D SER* 1.3 60.5 + - - +
319D PHE* 4.0 4.7 - - - -
320D ALA* 3.7 19.9 + - - +
330D GLN* 5.0 0.2 + - - -
333D MET* 4.0 21.3 - - + +
334D LEU* 4.7 7.6 - - + +
337D ILE* 3.7 22.4 - - + -
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Residues in contact with SER 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D VAL* 3.1 19.9 + - - +
314D ARG* 3.3 6.3 + - - -
316D ALA* 1.3 75.6 - - - +
318D GLU* 1.3 62.1 + - - +
319D PHE 3.3 0.7 - - - -
320D ALA 4.0 1.9 - - - +
321D SER* 3.3 23.9 + - - -
330D GLN* 4.6 11.7 + - - +
334D LEU* 3.8 22.9 - - - +
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C ARG* 3.9 32.5 + - - -
345C GLY* 5.3 2.3 - - - -
346C LEU 5.7 0.3 + - - -
314D ARG* 3.0 44.6 + - + +
315D ALA* 4.1 10.6 - - - +
317D SER* 1.3 77.7 - - - +
319D PHE* 1.3 61.9 + - - +
321D SER* 4.2 2.6 - - - -
322D ARG* 3.3 47.5 + - + +
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Residues in contact with PHE 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C GLN* 3.8 34.1 - - + -
351C THR* 4.9 7.2 - - + -
352C LEU* 3.6 28.5 - - + -
363C ILE* 3.9 38.1 - - + -
367C LEU* 4.8 2.0 - - + -
315D ALA 3.4 16.4 + - - +
316D ALA* 4.0 6.0 - - - +
317D SER 3.3 0.4 - - - -
318D GLU* 1.3 81.6 - - - +
320D ALA* 1.3 62.4 + - - +
321D SER 3.2 0.9 + - - -
322D ARG* 4.2 10.3 - - - +
323D ASN* 3.3 53.2 + - - +
325D LEU* 4.5 5.8 - - + -
333D MET* 4.2 17.9 - - + -
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Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ALA 3.7 14.2 + - - +
317D SER 3.8 1.7 + - - +
318D GLU 3.4 0.4 - - - -
319D PHE* 1.3 77.8 - - - +
321D SER* 1.3 58.0 + - - +
323D ASN 4.5 0.9 - - - -
324D GLN* 4.3 0.5 - - - -
325D LEU* 3.5 48.0 + - + +
330D GLN* 3.4 42.0 + - + +
333D MET* 4.1 6.3 - - - -
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Residues in contact with SER 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B HIS* 3.1 27.9 + - - -
317D SER 3.3 18.2 + - - -
318D GLU* 4.2 3.8 - - - -
319D PHE 3.2 0.4 - - - -
320D ALA* 1.3 78.3 - - - +
322D ARG* 1.3 63.9 + - - +
323D ASN 3.3 1.3 - - - -
324D GLN* 3.7 6.6 + - - +
330D GLN* 5.4 2.7 - - - +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B SER 6.0 0.4 - - - +
118B HIS* 4.2 26.0 - - + +
120B TYR* 3.5 19.6 + - - +
305C ARG* 5.1 2.2 - - - +
342C LYS 4.8 5.3 + - - -
343C THR* 3.0 24.0 + - - +
344C GLU 3.7 9.1 + - - -
345C GLY* 3.4 22.6 - - - +
348C GLN* 3.6 24.4 + - - +
315D ALA 5.6 1.0 + - - -
318D GLU* 3.3 34.5 + - - +
319D PHE* 3.8 19.5 + - - +
321D SER* 1.3 78.4 - - - +
323D ASN* 1.3 70.3 + - - +
324D GLN* 3.6 8.3 + - - +
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Residues in contact with ASN 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C TYR* 4.6 2.9 - - - -
367C LEU* 3.4 44.0 - - + +
319D PHE* 3.3 45.6 + - - +
321D SER 3.3 0.2 - - - -
322D ARG* 1.3 89.7 + - - +
324D GLN* 1.3 71.3 + - - +
325D LEU* 3.4 7.9 + - + +
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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) + - + + + + + -
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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