Contacts of the helix formed by residues 309 - 325 (chain D) in PDB entry 4C3P
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 LYS 309 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D HIS* 3.6 27.6 + - - +
307D ASP 3.2 1.6 - - - -
308D GLU* 1.3 100.5 - - + +
310D VAL* 1.3 61.4 + - - +
311D ASP 3.2 0.4 - - - -
312D LEU* 3.3 17.2 + - + -
313D TRP 3.5 1.2 + - - -
368D PRO* 3.3 39.0 - - + +
369D SER 4.2 7.9 + - - -
371D ARG* 2.8 50.2 + - + +
372D PRO 3.5 22.7 + - - +
373D MET* 4.3 10.3 - - - +
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Residues in contact with VAL 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 3.4 29.6 - - + +
299A GLU* 4.1 6.7 + - + +
300A MET* 3.5 24.2 - - + -
253D ILE* 3.3 22.7 - - + -
255D ARG* 4.2 17.2 - - + +
306D HIS 4.3 2.4 + - - +
307D ASP* 3.1 25.8 + - - +
308D GLU 2.9 0.8 + - - -
309D LYS* 1.3 78.3 - - - +
311D ASP* 1.3 69.4 + - - +
312D LEU 3.3 1.0 + - - -
313D TRP* 3.3 16.1 + - - +
314D SER* 3.5 9.2 + - - -
371D ARG* 4.0 6.7 - - - +
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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
----------------------------------------------------------
244D LEU* 3.7 29.7 - - + +
248D HIS* 2.6 33.0 + - + +
253D ILE* 3.6 7.2 - - - +
254D HIS* 3.1 26.4 + - - +
255D ARG* 2.7 35.7 + - - +
257D ILE* 5.4 1.2 - - - +
308D GLU 2.9 9.8 + - - +
310D VAL* 1.3 76.6 - - - +
312D LEU* 1.3 64.2 + - + +
314D SER* 3.7 8.2 - - - -
315D LEU* 3.4 15.4 + - - +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D HIS* 5.1 0.2 - - + -
308D GLU* 3.8 36.6 - - + +
309D LYS* 3.7 11.4 - - + +
310D VAL 3.2 0.6 - - - -
311D ASP* 1.3 79.4 - - + +
313D TRP* 1.3 67.2 + - - +
315D LEU* 3.3 5.0 + - + +
316D GLY 3.3 14.2 + - - -
363D LEU* 3.3 36.9 - - + +
371D ARG* 4.2 11.7 - - + -
372D PRO* 2.8 40.2 - - + +
373D MET 4.0 9.4 - - - -
374D LEU* 4.2 19.3 - - + +
377D VAL* 4.4 5.2 - - + -
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Residues in contact with TRP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP 4.7 1.2 + - - -
295A TYR 3.6 18.0 + - - -
296A LEU 3.9 6.3 + - - -
297A PRO* 3.5 29.7 - - + +
298A PRO* 3.8 19.5 - - + -
309D LYS 3.5 3.4 + - - -
310D VAL 3.3 11.3 + - - +
312D LEU* 1.3 77.3 - - - +
314D SER* 1.3 66.3 + - - +
316D GLY* 2.8 14.7 + - - -
317D VAL* 3.1 24.8 + - + +
329D PHE* 3.5 29.7 - + - -
341D ILE* 4.3 8.1 - - + -
344D VAL* 4.1 18.6 - - + -
363D LEU 3.8 10.2 + - - -
364D LEU* 3.7 34.5 - - + +
365D LYS 3.4 21.1 - - - -
371D ARG* 3.4 26.7 - - - +
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Residues in contact with SER 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 3.6 17.4 + - - +
297A PRO* 5.3 2.3 - - - +
255D ARG 3.0 26.1 + - - -
256D ASP* 4.5 0.3 - - - -
257D ILE* 4.0 26.6 + - - -
310D VAL 3.5 6.4 + - - -
311D ASP* 3.7 10.8 - - - -
313D TRP* 1.3 84.6 - - - +
315D LEU* 1.3 61.7 + - - +
317D VAL* 3.3 3.4 + - - +
318D LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE* 4.1 28.1 - - + +
240D LEU* 3.6 34.8 - - + -
241D ALA* 4.2 20.2 - - + -
244D LEU* 3.7 17.9 - - + -
257D ILE* 5.3 2.9 - - + -
311D ASP 3.4 5.8 + - - +
312D LEU* 3.3 11.6 + - - +
313D TRP 3.1 1.0 - - - -
314D SER* 1.3 79.9 - - - +
316D GLY* 1.3 58.7 + - - +
318D LEU* 3.3 6.6 + - + +
319D CYS* 2.9 30.1 + - - +
363D LEU* 4.4 8.3 - - + -
374D LEU* 4.2 16.8 - - + -
377D VAL* 4.3 12.8 - - + -
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Residues in contact with GLY 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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312D LEU 3.3 4.6 + - - -
313D TRP 2.8 8.3 + - - -
315D LEU* 1.3 77.3 - - - +
317D VAL* 1.3 58.1 + - - +
319D CYS* 3.3 4.1 + - - +
320D TYR* 3.0 29.5 + - - +
360D ILE* 4.0 8.3 - - - +
363D LEU* 3.8 28.4 - - - +
364D LEU* 4.1 13.2 - - - -
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP 4.1 15.0 - - - +
295A TYR* 3.4 36.8 - - + +
313D TRP* 3.1 34.8 + - + +
314D SER* 3.7 9.2 - - - +
316D GLY* 1.3 74.8 - - - +
318D LEU* 1.3 58.4 + - - +
320D TYR* 3.6 2.1 + - - +
321D GLU* 2.9 26.9 + - - +
327D PRO* 4.2 4.0 - - + -
328D PRO* 4.2 19.2 - - + +
329D PHE* 4.4 7.9 - - + -
364D LEU* 3.7 11.9 - - + -
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 3.9 22.4 - - + -
237D ILE* 4.5 4.3 - - + -
240D LEU* 3.7 24.0 - - + -
257D ILE* 3.4 39.9 - - + +
259D PRO* 4.4 8.5 - - + -
262D LEU* 4.0 15.5 - - + -
314D SER* 3.0 22.6 + - - +
315D LEU* 3.7 6.5 - - + +
317D VAL* 1.3 73.4 - - - +
319D CYS* 1.3 60.6 + - - +
321D GLU* 4.2 3.6 - - - +
322D PHE* 2.8 58.8 + - + -
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Residues in contact with CYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D THR* 3.9 19.3 - - - -
237D ILE* 4.0 21.3 - - + +
315D LEU 2.9 17.5 + - - +
316D GLY* 3.6 6.3 - - - +
318D LEU* 1.3 74.9 - - - +
320D TYR* 1.3 68.9 + - - +
322D PHE* 3.4 1.4 + - - +
323D LEU* 3.2 27.0 + - - +
356D ALA 5.3 0.9 - - - -
359D LEU* 4.3 11.0 - - - -
360D ILE* 3.9 22.4 - - + -
363D LEU* 5.4 2.9 - - + -
382D TRP* 4.2 17.3 - - - -
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Residues in contact with TYR 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 GLY 3.0 17.4 + - - +
317D VAL 3.7 3.6 - - - +
319D CYS* 1.3 78.7 - - - +
321D GLU* 1.3 57.3 + - - +
323D LEU* 3.2 1.0 + - - -
324D VAL* 2.9 57.8 + - + +
326D LYS* 3.2 27.6 + - + -
327D PRO 3.9 0.4 - - - -
328D PRO* 3.5 45.3 + - + +
346D PHE* 4.0 7.9 - + - -
347D THR* 2.9 28.3 + - - -
348D PHE* 3.9 30.1 - + - -
349D PRO* 3.7 10.5 - - + +
360D ILE* 3.6 14.5 - - + +
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Residues in contact with GLU 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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295A TYR* 2.6 38.6 + - - -
222D LEU* 3.7 20.2 - - + +
259D PRO* 3.6 15.2 - - + +
317D VAL 2.9 18.2 + - - +
318D LEU* 3.6 6.2 - - - +
319D CYS 3.2 0.2 - - - -
320D TYR* 1.3 73.6 - - - +
322D PHE* 1.3 63.8 + - + +
325D GLY* 2.8 30.3 + - - +
326D LYS* 3.4 21.1 - - - -
327D PRO* 3.2 28.2 - - + +
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Residues in contact with PHE 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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218D VAL* 3.7 27.6 - - + -
222D LEU* 4.2 9.6 - - + -
227D LYS* 3.6 3.1 - - - +
228D PHE* 2.7 53.0 + + + -
233D THR* 3.3 33.2 - - + +
236D TYR* 4.0 28.0 - + + -
237D ILE* 4.0 15.3 - - + -
240D LEU* 4.4 4.0 - - + -
259D PRO* 4.5 15.3 - - + -
262D LEU* 4.2 12.6 - - + -
270D LEU* 5.3 0.2 - - + -
318D LEU* 2.8 44.5 + - + +
321D GLU* 1.3 75.5 - - + +
323D LEU* 1.3 56.7 + - - +
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Residues in contact with LEU 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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227D LYS* 3.5 12.2 - - - +
228D PHE 3.8 14.8 - - - +
230D GLU* 4.0 29.2 - - + +
233D THR* 3.7 18.4 - - + +
319D CYS* 3.2 22.1 + - - +
320D TYR 3.2 4.0 + - - +
322D PHE* 1.3 80.6 - - - +
324D VAL* 1.3 65.5 + - + +
351D PHE* 3.4 19.1 - - + -
352D VAL* 4.9 10.3 - - + -
356D ALA* 3.8 28.5 - - + -
360D ILE* 4.4 7.4 - - + -
382D TRP* 4.0 12.1 - - + -
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LYS* 4.0 13.4 + - - +
320D TYR* 2.9 55.6 + - + +
323D LEU* 1.3 82.3 - - + +
325D GLY* 1.3 59.1 + - - +
326D LYS* 3.9 19.5 + - - +
349D PRO* 3.7 23.6 - - + -
351D PHE* 4.3 7.2 - - + -
352D VAL* 3.9 26.2 - - + -
360D ILE* 6.1 0.4 - - + -
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Residues in contact with GLY 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LEU* 4.4 9.5 - - - +
226D SER 3.3 26.6 - - - +
227D LYS* 4.0 2.6 - - - +
321D GLU* 2.8 21.5 + - - +
323D LEU 3.7 0.2 - - - -
324D VAL* 1.3 79.0 - - - +
326D LYS* 1.3 60.6 + - - +
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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
------------------------------------------------------------
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