Contacts of the helix formed by residues 322 - 333 (chain D) in PDB entry 1YCH
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 VAL 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D ASP* 4.5 13.5 - - + -
289D LEU* 3.9 21.5 - - + -
309D VAL* 3.8 28.7 - - + -
310D GLY 4.0 7.0 - - - +
311D SER* 4.0 16.2 - - - +
318D ILE* 2.9 28.7 - - + -
319D LEU* 3.0 12.4 + - + +
321D VAL* 1.3 80.0 - - - +
323D SER* 1.3 63.3 - - - +
324D PRO 3.5 0.2 - - - -
325D LEU* 3.6 5.6 + - + +
326D LEU* 3.5 20.9 + - + +
355D LEU* 4.1 3.1 - - + -
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Residues in contact with SER 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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323C SER* 3.6 19.3 - - - -
327C ASP* 2.8 37.7 + - - +
318D ILE* 4.0 10.1 - - - +
319D LEU 3.8 0.4 + - - -
320D PRO* 3.1 10.6 + - - +
322D VAL* 1.3 75.7 - - - +
324D PRO* 1.3 76.0 - - - +
326D LEU* 3.0 11.7 + - - +
327D ASP* 3.0 25.4 + - - +
358D ARG* 4.3 0.8 + - - +
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Residues in contact with PRO 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C PRO* 3.5 28.8 - - + +
321C VAL* 5.3 1.1 - - - -
323C SER* 4.3 2.5 - - - +
324C PRO* 3.4 21.8 - - + -
294D ARG* 3.7 20.9 - - + -
320D PRO 3.3 14.4 - - - +
321D VAL* 3.5 13.2 - - - +
323D SER* 1.3 90.6 - - - +
325D LEU* 1.3 60.5 + - - +
327D ASP* 3.6 0.3 + - - -
328D ASP* 3.1 25.6 + - - +
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Residues in contact with LEU 325 (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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258D ALA* 4.1 20.2 - - + -
289D LEU* 4.2 26.5 - - + -
294D ARG* 4.1 12.6 - - + +
297D VAL* 4.0 18.4 - - + -
298D ILE* 3.7 27.6 - - + -
301D ILE* 4.6 4.5 - - + -
307D VAL* 5.7 0.7 - - + -
309D VAL* 4.1 25.8 - - + -
321D VAL 5.0 1.0 + - - +
322D VAL 3.6 9.0 + - - +
323D SER 3.2 0.8 - - - -
324D PRO* 1.3 77.9 - - - +
326D LEU* 1.3 64.5 + - + +
328D ASP* 3.5 2.9 + - - +
329D LEU* 3.0 42.0 + - + +
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Residues in contact with LEU 326 (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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309D VAL* 4.1 22.0 - - + -
318D ILE* 4.2 10.1 - - + -
322D VAL* 3.5 22.4 - - + +
323D SER* 3.0 7.4 + - - +
325D LEU* 1.3 77.4 - - + +
327D ASP* 1.3 66.8 + - - +
329D LEU* 3.0 16.4 + - + +
330D VAL* 3.1 18.0 + - - +
354D ILE* 5.3 0.9 - - + -
355D LEU* 3.7 28.0 - - + +
358D ARG* 4.0 42.4 - - + +
359D LEU* 4.5 21.1 - - + +
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Residues in contact with ASP 327 (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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317C ASP* 3.2 46.3 - - - +
318C ILE* 4.7 6.5 - - + +
320C PRO* 5.0 6.5 - - + +
323C SER* 3.3 19.6 + - - +
327C ASP* 4.4 0.2 - - - +
354C ILE* 4.8 1.2 - - - +
358C ARG* 2.6 41.4 + - - -
323D SER 3.0 11.3 + - - +
324D PRO* 4.4 1.8 - - + +
326D LEU* 1.3 76.1 - - - +
328D ASP* 1.3 61.3 + - - +
330D VAL* 3.6 5.4 + - - +
331D GLY* 3.3 9.7 + - - -
358D ARG* 3.2 20.9 + - - -
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Residues in contact with ASP 328 (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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314C ILE* 6.1 1.0 - - - +
315C ASN* 5.4 3.6 + - - -
320C PRO* 3.5 16.2 - - + +
198D ASN* 4.4 3.3 - - - +
294D ARG* 3.6 23.8 + - - +
295D ASN* 5.4 0.5 - - - +
298D ILE* 3.3 28.7 - - + +
324D PRO 3.1 20.0 + - - +
325D LEU* 3.5 7.4 - - - +
326D LEU 3.1 0.2 - - - -
327D ASP* 1.3 76.9 - - - +
329D LEU* 1.3 59.8 + - - +
331D GLY* 3.7 1.4 + - - -
332D LEU* 3.0 46.8 + - - +
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Residues in contact with LEU 329 (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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201D MET* 4.8 4.3 - - + -
298D ILE* 3.8 17.9 - - + -
301D ILE* 3.7 25.1 - - + -
307D VAL* 4.2 16.6 - - + -
309D VAL* 5.1 0.4 - - + -
325D LEU* 3.0 31.6 + - + +
326D LEU* 3.0 7.2 + - + +
328D ASP* 1.3 75.0 - - - +
330D VAL* 1.3 68.4 + - - +
332D LEU* 4.4 1.8 - - - +
333D ARG 3.0 18.0 + - - -
334D PRO* 3.4 24.9 - - + +
359D LEU* 4.3 11.2 - - + -
362D ALA* 3.5 9.8 - - + +
364D ILE* 3.7 26.0 - - + -
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Residues in contact with VAL 330 (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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317C ASP* 3.4 15.0 - - - +
326D LEU 3.1 16.1 + - - +
327D ASP* 3.8 11.4 - - - +
329D LEU* 1.3 81.1 - - - +
331D GLY* 1.3 62.9 + - - +
333D ARG* 3.5 18.5 + - - +
358D ARG* 3.4 35.4 - - + +
361D ALA* 3.7 27.5 - - + +
362D ALA* 3.7 9.8 - - - +
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Residues in contact with GLY 331 (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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315C ASN* 3.6 41.3 - - - +
316C ASN* 5.6 1.7 + - - -
317C ASP* 4.3 6.5 - - - -
202D PRO* 3.8 7.8 - - - +
327D ASP 3.3 11.1 + - - -
328D ASP* 4.1 2.2 - - - -
329D LEU 3.2 0.4 - - - -
330D VAL* 1.3 83.2 - - - +
332D LEU* 1.3 58.0 + - - +
333D ARG* 3.4 9.0 + - - +
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Residues in contact with LEU 332 (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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315C ASN* 4.1 13.5 - - - +
197D ALA 3.9 4.5 - - - +
198D ASN* 3.4 30.5 - - - +
199D ILE 4.9 0.4 - - - +
201D MET* 3.1 19.0 - - + +
202D PRO* 3.2 45.6 - - + +
298D ILE* 3.8 28.0 - - + -
328D ASP* 3.0 45.2 + - - +
329D LEU* 4.2 1.8 - - - +
330D VAL 3.4 0.2 - - - -
331D GLY* 1.3 74.2 - - - +
333D ARG* 1.3 68.6 + - - +
334D PRO 3.5 1.0 - - - -
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Residues in contact with ARG 333 (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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316C ASN* 4.3 19.3 - - - +
201D MET 4.3 7.3 - - - +
202D PRO* 4.6 16.7 + - + +
329D LEU 3.0 10.3 + - - -
330D VAL 3.5 14.8 + - - +
331D GLY 4.0 7.3 + - - +
332D LEU* 1.3 79.4 - - - +
334D PRO* 1.4 73.1 - - - +
335D LYS* 3.3 5.2 + - - +
361D ALA 5.8 1.1 - - - +
362D ALA 4.4 6.3 - - - +
363D LYS* 5.7 9.4 - - + -
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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