Contacts of the helix formed by residues 310 - 323 (chain D) in PDB entry 1W88
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 ASN 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D GLU* 3.7 19.7 - - - +
305D SER 4.3 11.7 + - - -
308D LEU* 3.9 9.8 + - + +
309D PRO* 1.3 73.2 - - - +
311D PHE* 1.3 68.5 + - + +
312D LYS* 2.9 53.4 + - - +
313D ASP* 2.8 29.0 + - - +
314D VAL* 3.1 16.8 + - - +
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Residues in contact with PHE 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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215D GLU* 3.0 45.8 + - - +
218D LYS* 3.6 51.1 - - + -
219D ALA* 3.5 1.9 - - - +
222D GLU* 4.2 12.8 - - + -
310D ASN* 1.3 81.1 - - + +
312D LYS* 1.3 90.0 + - + +
314D VAL* 3.3 6.0 + - - +
315D ILE* 2.8 50.3 + - + +
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Residues in contact with LYS 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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310D ASN* 2.9 26.2 + - - +
311D PHE* 1.3 103.9 - - + +
313D ASP* 1.3 61.1 + - - +
315D ILE* 3.1 11.7 + - + +
316D GLU* 2.8 32.9 + - - +
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Residues in contact with ASP 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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362A TYR* 5.5 1.8 + - - -
365A LYS* 4.3 22.0 + - - -
291D VAL* 3.9 20.6 - - + -
308D LEU 3.9 2.1 - - - +
309D PRO* 3.3 9.4 - - - +
310D ASN* 2.8 38.0 + - - +
312D LYS* 1.3 75.9 - - - +
314D VAL* 1.3 58.0 - - - +
316D GLU* 3.7 9.0 - - - +
317D THR* 3.0 34.3 + - - +
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Residues in contact with VAL 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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206D ILE* 4.0 22.2 - - + -
212D MET* 5.8 0.4 - - - -
215D GLU* 4.5 6.7 - - + +
216D SER* 4.3 7.6 - - - +
219D ALA* 3.6 18.6 - - + -
257D ILE* 3.9 18.9 - - + +
259D VAL* 3.8 28.3 - - + -
291D VAL* 4.2 10.8 - - + -
310D ASN 3.1 15.1 + - - +
311D PHE* 3.5 11.9 - - - +
312D LYS 3.2 0.2 - - - -
313D ASP* 1.3 76.0 - - - +
315D ILE* 1.3 61.8 + - - +
318D ALA* 3.0 27.8 + - + +
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Residues in contact with ILE 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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219D ALA* 3.7 20.9 - - + +
222D GLU* 3.7 22.2 - - + -
223D LEU* 4.1 13.0 - - + +
226D GLU* 5.2 3.4 - - - +
311D PHE* 2.8 49.0 + - + +
312D LYS* 3.1 12.3 + - + +
314D VAL* 1.3 72.2 - - - +
316D GLU* 1.3 64.3 + - - +
318D ALA* 3.5 4.6 + - - +
319D LYS* 3.1 47.2 + - + +
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Residues in contact with GLU 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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361A ILE* 6.2 0.3 - - - +
365A LYS* 4.6 22.6 + - - +
312D LYS 2.8 20.3 + - - +
313D ASP* 3.7 10.7 - - - +
315D ILE* 1.3 75.1 - - - +
317D THR* 1.3 57.7 + - - +
319D LYS* 3.3 9.2 + - - +
320D LYS* 3.0 44.1 + - - +
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Residues in contact with THR 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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257D ILE* 3.9 10.3 - - + -
289D LEU* 3.7 35.2 - - + -
290D ARG 4.5 6.5 + - - +
291D VAL* 3.7 23.4 - - + +
313D ASP* 3.0 17.8 + - - +
314D VAL 4.3 0.7 - - - -
316D GLU* 1.3 74.2 - - - +
318D ALA* 1.3 65.8 + - - +
320D LYS* 3.4 19.9 + - - +
321D VAL* 3.1 22.5 + - - +
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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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204D ILE* 3.6 24.0 - - + +
206D ILE* 5.0 2.2 - - + -
223D LEU* 4.0 25.6 - - + -
257D ILE* 4.1 10.9 - - + +
314D VAL 3.0 19.1 + - - +
315D ILE 3.6 4.5 - - - +
316D GLU 3.3 0.2 - - - -
317D THR* 1.3 78.3 - - - +
319D LYS* 1.3 56.4 + - - +
321D VAL* 3.2 5.9 + - - +
322D MET* 2.9 31.5 + - + +
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Residues in contact with LYS 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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223D LEU* 4.1 12.6 - - + -
226D GLU* 3.1 38.8 + - - -
228D ILE* 4.4 13.7 - - + -
315D ILE* 3.1 35.4 + - + +
316D GLU* 3.6 6.7 - - - +
318D ALA* 1.3 69.3 - - - +
320D LYS* 1.3 67.0 + - - +
321D VAL 3.1 1.1 - - - -
322D MET* 3.0 8.1 + - - +
323D ASN* 2.8 41.7 + - - +
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Residues in contact with LYS 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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289D LEU* 3.7 24.0 - - + +
316D GLU* 3.0 30.3 + - - +
317D THR* 3.4 32.7 + - - +
319D LYS* 1.3 74.5 - - - +
321D VAL* 1.3 57.4 + - - +
323D ASN* 3.5 4.8 + - - +
324D PHE* 3.1 28.4 + - - +
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Residues in contact with VAL 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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204D ILE* 3.9 11.2 - - + -
255D ARG* 3.2 41.8 + - + -
256D ALA 4.3 6.7 - - - +
257D ILE* 3.5 19.3 - - + -
286D ALA* 3.7 12.1 - - + +
287D PRO* 4.1 9.2 - - + +
289D LEU* 3.8 24.2 - - + -
317D THR 3.1 15.3 + - - +
318D ALA 3.4 7.9 - - - +
319D LYS 3.1 0.8 - - - -
320D LYS* 1.3 74.6 - - - +
322D MET* 1.3 64.5 + - - +
324D PHE* 3.4 15.7 + - - +
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Residues in contact with MET 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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203D ASP* 4.0 24.0 - - + +
204D ILE* 3.9 23.3 - - + -
228D ILE* 4.1 34.5 - - + -
255D ARG* 3.4 43.4 + - - +
318D ALA 2.9 22.7 + - - +
319D LYS* 3.0 10.3 + - - +
321D VAL* 1.3 75.1 - - - +
323D ASN* 1.3 63.4 + - - +
324D PHE* 3.3 2.8 + - - +
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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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319D LYS* 2.8 45.0 + - - +
320D LYS* 3.6 5.2 - - - +
322D MET* 1.3 75.2 - - - +
324D PHE* 1.3 65.1 + - - +
154I LYS* 3.0 23.3 + - - +
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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
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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