Contacts of the helix formed by residues 310 - 323 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B GLU* 3.5 23.6 - - - +
305B SER 4.1 13.1 + - - -
308B LEU* 3.8 12.6 + - + +
309B PRO* 1.3 75.4 - - - +
311B PHE* 1.3 72.1 + - + +
312B LYS* 3.0 34.7 + - - +
313B ASP* 2.9 28.3 + - - +
314B VAL* 3.3 12.6 + - - +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU* 3.0 41.8 + - - +
218B LYS* 3.4 55.4 - - + -
219B ALA* 3.6 2.9 - - - +
222B GLU* 5.4 3.1 - - + -
310B ASN* 1.3 81.7 - - + +
312B LYS* 1.3 93.4 + - + +
314B VAL* 3.4 4.9 + - - +
315B ILE* 3.0 50.0 + - + +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASN* 3.0 18.4 + - - +
311B PHE* 1.3 113.4 - - + +
313B ASP* 1.3 61.4 + - - +
315B ILE* 3.8 10.1 - - + +
316B GLU* 3.1 28.9 + - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B VAL* 3.9 19.3 - - + -
308B LEU 4.0 2.6 - - - +
309B PRO* 3.3 8.7 - - - +
310B ASN* 2.9 36.2 + - - +
312B LYS* 1.3 75.5 - - - +
314B VAL* 1.3 64.8 + - - +
316B GLU* 3.3 7.4 + - - +
317B THR* 2.8 33.2 + - - +
362C TYR* 5.5 3.6 + - - -
365C LYS* 4.2 21.3 + - - -
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ILE* 4.0 28.9 - - + -
212B MET* 5.8 0.7 - - - -
215B GLU* 4.3 8.3 - - + +
216B SER* 4.4 4.9 - - - +
219B ALA* 3.6 19.1 - - + -
257B ILE* 4.0 10.2 - - + +
259B VAL* 3.8 28.5 - - + -
291B VAL* 4.1 10.5 - - + -
310B ASN 3.5 16.2 - - - +
311B PHE* 3.5 9.9 - - - +
312B LYS 3.3 0.2 - - - -
313B ASP* 1.3 77.3 - - - +
315B ILE* 1.3 56.3 + - - +
317B THR* 3.3 2.1 + - - -
318B ALA* 2.9 31.5 + - + +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.8 22.7 - - + +
222B GLU* 3.7 24.0 - - + -
223B LEU* 4.2 14.8 - - + +
226B GLU* 4.7 6.5 - - - +
311B PHE* 3.0 44.6 + - + +
312B LYS* 3.8 10.5 - - + +
313B ASP 3.3 0.2 - - - -
314B VAL* 1.3 74.9 - - - +
316B GLU* 1.3 65.1 + - + +
318B ALA* 3.9 1.7 - - - +
319B LYS* 3.1 43.8 + - + +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B LYS 3.1 16.4 + - - +
313B ASP* 3.8 8.6 - - - +
314B VAL 3.3 0.4 - - - -
315B ILE* 1.3 83.2 - - + +
317B THR* 1.3 59.3 + - - +
319B LYS* 3.7 6.4 + - - +
320B LYS* 3.0 41.7 + - - +
365C LYS* 4.7 21.6 + - - +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 4.2 9.4 - - + -
289B LEU* 3.8 32.8 - - + -
290B ARG 4.4 7.5 + - - +
291B VAL* 3.4 26.2 - - + +
313B ASP* 2.8 19.5 + - - +
314B VAL 3.9 0.9 - - - -
316B GLU* 1.3 75.2 - - - +
318B ALA* 1.3 64.6 + - - +
320B LYS* 2.9 27.1 + - - +
321B VAL* 3.0 12.6 + - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ILE* 3.8 27.1 - - + +
206B ILE* 5.0 2.5 - - + -
223B LEU* 4.0 25.4 - - + -
228B ILE* 5.8 0.2 - - + -
257B ILE* 4.1 11.7 - - + +
314B VAL 2.9 21.7 + - - +
315B ILE 3.9 3.1 - - - +
317B THR* 1.3 72.4 - - - +
319B LYS* 1.3 57.3 + - - +
321B VAL* 2.9 6.6 + - - +
322B MET* 2.8 32.6 + - + +
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 4.0 13.0 - - + -
226B GLU* 2.9 33.7 + - - +
228B ILE* 4.2 11.0 - - + -
315B ILE* 3.1 38.0 + - + +
316B GLU* 3.8 6.1 - - - +
318B ALA* 1.3 76.9 - - - +
320B LYS* 1.3 61.5 + - - +
322B MET* 3.2 7.7 + - - -
323B ASN* 3.0 44.9 + - - +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.9 21.9 - - + +
316B GLU* 3.0 36.0 + - - +
317B THR* 2.9 25.8 + - - +
319B LYS* 1.3 75.4 - - - +
321B VAL* 1.3 60.5 + - - +
323B ASN* 3.6 4.4 + - - +
324B PHE* 3.3 20.4 + - - +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ILE* 3.6 21.3 - - + -
255B ARG* 2.8 47.4 + - + -
256B ALA 4.4 5.6 - - - +
257B ILE* 3.6 23.8 - - + -
286B ALA* 3.9 12.8 - - + -
287B PRO 3.8 17.7 - - - +
289B LEU* 3.9 17.0 - - + -
317B THR 3.0 8.7 + - - +
318B ALA 2.9 9.7 + - - +
320B LYS* 1.3 76.8 - - - +
322B MET* 1.3 54.7 + - - +
324B PHE* 3.2 14.2 + - - +
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Residues in contact with MET 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASP* 3.7 29.8 - - + +
204B ILE* 4.0 15.3 - - + -
228B ILE* 3.9 37.9 - - + -
255B ARG* 3.7 44.5 + - - +
318B ALA 2.8 19.3 + - - +
319B LYS* 3.2 7.2 + - - +
321B VAL* 1.3 76.7 - - - +
323B ASN* 1.3 63.8 + - - +
324B PHE* 3.3 2.2 + - - +
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LYS* 3.0 36.7 + - - +
320B LYS* 3.8 5.1 - - - +
322B MET* 1.3 80.5 - - - +
324B PHE* 1.3 65.8 + - - +
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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