Contacts of the helix formed by residues 300 - 319 (chain D) in PDB entry 1CCW
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 ASP 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B GLU* 4.7 1.2 - - - +
345B LYS* 2.9 30.4 + - - +
298D PRO* 3.3 2.2 - - - +
299D GLN* 1.3 78.6 - - - +
301D GLU* 1.3 59.3 + - - +
302D SER* 3.0 17.2 + - - -
303D LYS* 3.0 51.7 + - + +
304D ALA* 2.9 25.5 + - - +
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Residues in contact with GLU 301 (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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98C LYS* 3.3 26.7 + - - -
299D GLN 4.1 5.6 - - - +
300D ASP* 1.3 73.9 + - - +
302D SER* 1.3 62.2 + - - +
304D ALA* 3.2 10.3 + - - +
305D PHE* 3.1 32.7 + - + -
328D PRO* 3.7 33.2 - - + +
329D HIS* 3.6 17.3 + - - -
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Residues in contact with SER 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 3.9 9.1 - - - -
342B ALA* 3.2 48.5 - - - +
345B LYS* 4.1 9.2 + - - -
346B ALA* 3.5 14.4 - - - +
300D ASP* 3.0 10.9 + - - -
301D GLU* 1.3 74.5 - - - +
303D LYS* 1.3 66.9 + - - +
305D PHE* 3.2 11.6 + - - +
306D GLY 3.2 15.1 + - - -
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Residues in contact with LYS 303 (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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345B LYS* 4.1 34.1 - - + +
349B MET* 3.3 34.0 - - + +
298D PRO* 3.7 21.5 - - + -
300D ASP* 3.0 35.9 + - + +
302D SER* 1.3 76.0 - - - +
304D ALA* 1.3 62.8 + - - +
306D GLY 2.9 10.4 + - - -
307D VAL* 3.2 10.6 + - - +
475D LYS 5.4 2.8 + - - -
476D GLY* 5.1 9.5 - - - -
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D PHE* 3.7 26.6 - - + -
298D PRO* 3.8 7.7 - - - +
300D ASP 2.9 14.1 + - - +
301D GLU* 3.2 11.2 + - - +
303D LYS* 1.3 75.5 - - - +
305D PHE* 1.3 57.3 + - - +
307D VAL* 3.1 5.3 + - - +
308D ILE* 2.9 32.2 + - - +
328D PRO* 3.7 28.9 - - + +
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Residues in contact with PHE 305 (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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302B SER* 3.9 18.8 - - - -
305B PHE* 3.6 50.3 - + + -
309B VAL* 4.1 2.9 - - + +
346B ALA* 5.0 0.4 - - + -
301D GLU* 3.1 33.0 + - + -
302D SER 3.2 6.7 + - - +
304D ALA* 1.3 73.4 - - - +
306D GLY* 1.3 66.2 + - - +
308D ILE* 4.2 11.7 - - + -
309D VAL* 2.9 29.9 + - + +
328D PRO* 3.8 28.7 - - + -
342D ALA* 3.9 17.0 - - + -
343D GLY 4.6 0.4 - - - -
346D ALA* 3.7 31.9 - - + -
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Residues in contact with GLY 306 (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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309B VAL* 3.6 10.0 - - - +
346B ALA 3.9 21.1 - - - -
349B MET* 4.2 7.9 - - - -
350B ALA* 4.5 2.2 - - - -
353B MET* 5.3 0.7 - - - -
302D SER 3.2 7.4 + - - -
303D LYS 2.9 9.4 + - - -
305D PHE* 1.3 77.3 - - - +
307D VAL* 1.3 58.3 + - - +
310D THR* 2.8 34.3 + - - +
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Residues in contact with VAL 307 (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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349B MET* 3.8 29.6 - - + -
353B MET* 4.4 12.8 - - + -
254D GLU* 4.8 1.0 - - - +
292D GLN* 6.0 0.2 - - + -
293D TRP* 3.6 28.5 - - + +
297D PHE* 3.5 25.1 - - + -
298D PRO* 4.1 9.6 - - + -
303D LYS 3.2 7.2 + - - +
304D ALA 3.1 7.0 + - - +
306D GLY* 1.3 74.4 - - - +
308D ILE* 1.3 66.9 + - - +
310D THR* 3.2 5.9 + - - -
311D ALA* 3.0 26.3 + - - +
473D VAL* 4.0 12.3 - - + -
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Residues in contact with ILE 308 (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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292D GLN* 3.5 21.9 + - - +
297D PHE* 4.0 12.3 - - + -
304D ALA 2.9 25.7 + - - +
305D PHE* 3.8 15.5 - - + +
307D VAL* 1.3 76.6 - - - +
309D VAL* 1.3 68.4 + - + +
311D ALA* 3.6 3.4 - - - +
312D THR* 2.8 29.7 + - - +
326D LYS 3.4 24.5 - - - +
327D THR* 3.7 22.0 - - - +
328D PRO* 3.9 9.2 - - + -
343D GLY* 4.2 6.7 - - - +
346D ALA* 4.6 4.0 - - + -
347D THR* 3.7 20.0 - - - +
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Residues in contact with VAL 309 (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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305B PHE 4.1 4.9 - - - +
306B GLY* 3.6 28.0 - - - +
309B VAL* 3.5 23.1 - - + -
310B THR* 3.6 22.7 - - + +
305D PHE* 2.9 21.5 + - + +
308D ILE* 1.3 78.5 - - + +
310D THR* 1.3 67.3 + - - +
312D THR* 3.3 5.5 + - - -
313D THR* 2.9 26.2 + - - -
346D ALA* 4.0 26.0 - - + +
350D ALA* 3.9 6.3 - - + -
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Residues in contact with THR 310 (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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309B VAL* 3.7 1.8 - - + -
313B THR* 3.4 27.0 - - - +
350B ALA* 3.6 27.8 - - + +
353B MET* 4.4 13.3 - - + +
354B LEU* 4.3 17.3 - - + -
254D GLU* 4.9 3.3 + - - -
258D MET* 5.4 0.2 - - - +
306D GLY 2.8 25.0 + - - +
307D VAL* 3.2 9.2 + - - -
309D VAL* 1.3 77.5 - - - +
311D ALA* 1.3 62.9 + - - +
313D THR* 3.1 12.5 + - - -
314D ILE* 3.2 22.9 + - - +
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Residues in contact with ALA 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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254D GLU* 3.1 35.0 + - - +
290D PHE* 3.5 11.7 - - + -
292D GLN* 3.6 26.9 - - + -
293D TRP 4.3 0.2 - - - +
307D VAL 3.0 18.6 + - - +
308D ILE 3.6 4.9 - - - +
310D THR* 1.3 75.8 + - - +
312D THR* 1.3 63.2 + - - +
314D ILE* 3.3 4.0 + - - +
315D ALA* 3.0 17.7 + - - +
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Residues in contact with THR 312 (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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292D GLN* 2.9 19.6 + - - +
308D ILE 2.8 22.3 + - - -
309D VAL* 3.6 6.7 - - - -
310D THR 3.2 0.2 - - - -
311D ALA* 1.3 76.5 - - - +
313D THR* 1.3 56.7 + - - +
315D ALA* 3.2 7.1 + - - +
316D ALA* 2.9 28.3 + - + +
323D VAL* 4.9 3.4 - - + -
347D THR* 3.4 37.6 + - + +
350D ALA* 3.7 14.4 - - + -
351D LEU* 3.6 20.0 - - + +
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Residues in contact with THR 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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258B MET* 4.1 17.3 - - + -
310B THR* 3.4 26.7 - - + +
313B THR* 3.7 28.7 + - + -
258D MET* 4.1 2.5 - - + -
309D VAL 2.9 14.5 + - - -
310D THR 3.1 9.4 + - - -
312D THR* 1.3 75.8 - - - +
314D ILE* 1.3 63.4 + - - +
316D ALA* 3.3 1.2 + - - +
317D LEU* 3.0 36.0 + - + +
354D LEU* 3.8 21.8 - - + -
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Residues in contact with ILE 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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354B LEU* 5.3 6.3 - - + -
254D GLU* 3.6 25.6 - - - +
256D GLY 3.9 14.1 - - - +
258D MET* 3.8 33.9 - - + +
261D ASP* 3.6 28.9 - - + +
262D ILE* 4.0 13.2 - - + +
290D PHE* 3.5 21.5 - - + -
310D THR* 3.2 16.4 + - - +
311D ALA* 3.6 6.1 - - - +
313D THR* 1.3 75.9 - - - +
315D ALA* 1.3 56.6 + - - +
317D LEU* 3.4 1.4 + - - -
318D ALA* 2.9 29.1 + - - +
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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
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61D THR* 4.3 3.7 + - + -
290D PHE* 3.7 38.8 - - + -
311D ALA 3.0 9.7 + - - +
312D THR* 3.4 8.7 - - + +
314D ILE* 1.3 77.2 - - - +
316D ALA* 1.3 61.7 + - - +
318D ALA* 3.3 5.5 + - - +
319D GLY 3.2 3.8 + - - -
320D ALA* 3.1 29.4 + - + -
323D VAL* 4.0 21.1 - - + -
351D LEU* 5.3 0.2 - - + -
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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
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61D THR* 4.2 11.7 + - - -
312D THR 2.9 17.2 + - - +
313D THR 3.6 4.5 - - - +
315D ALA* 1.3 75.9 - - - +
317D LEU* 1.3 56.8 + - + +
319D GLY* 3.0 19.6 + - - -
351D LEU* 3.9 17.5 - - + +
354D LEU* 3.8 30.3 - - + +
357D GLN 3.4 12.7 - - - +
358D ARG* 3.8 7.3 + - - +
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Residues in contact with LEU 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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258B MET* 3.6 38.6 - - + -
359B MET* 5.4 0.2 - - + -
258D MET* 3.9 21.3 - - + -
262D ILE* 4.0 12.8 - - + -
266D ARG* 2.9 21.0 + - - -
313D THR* 3.0 23.2 + - + +
314D ILE 4.1 0.4 - - - +
316D ALA* 1.3 79.1 - - + +
318D ALA* 1.3 58.3 + - - +
319D GLY 3.2 0.4 + - - -
354D LEU* 5.1 7.9 - - + -
357D GLN* 3.7 39.5 - - + +
358D ARG* 3.6 12.3 - - - +
359D MET* 3.0 22.4 + - + +
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Residues in contact with ALA 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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261D ASP 5.2 0.2 - - - +
262D ILE* 3.9 25.5 - - + +
265D LEU* 3.7 27.2 - - + +
266D ARG* 3.7 24.9 + - - +
290D PHE* 5.3 2.5 - - + -
314D ILE* 2.9 20.0 + - + +
315D ALA* 3.5 7.2 - - - +
316D ALA 3.2 0.2 - - - -
317D LEU* 1.3 79.1 - - - +
319D GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 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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56D LYS* 4.8 9.5 + - - +
61D THR* 4.5 1.1 - - - -
265D LEU* 4.7 0.7 - - - -
269D GLU* 5.3 2.4 - - - +
288D THR* 4.1 3.4 + - - -
316D ALA 3.0 12.8 + - - -
317D LEU 3.2 1.4 + - - -
318D ALA* 1.3 78.9 - - - +
320D ALA* 1.3 65.5 + - - +
321D THR* 3.5 3.3 + - - -
358D ARG* 3.6 30.3 + - - +
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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
------------------------------------------------------------
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