Contacts of the helix formed by residues 253 - 268 (chain D) in PDB entry 5HP1
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 THR 253 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C PRO* 5.5 1.7 - - + +
251D SER 5.6 1.1 - - - +
252D TRP* 1.3 74.2 - - - +
254D VAL* 1.3 65.9 + - - +
255D ASN* 3.6 8.0 + - - +
256D ASP* 3.0 42.2 + - - +
257D ILE* 3.1 18.9 + - - +
289D LEU 3.7 9.2 - - - -
290D THR* 3.6 20.4 - - + +
291D GLU 3.2 7.6 - - - -
292D VAL* 4.2 12.3 - - + -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TYR* 4.3 7.9 - - - +
253D THR* 1.3 72.2 - - - +
255D ASN* 1.3 62.7 + - - +
257D ILE* 3.3 3.8 + - - +
258D GLN* 3.0 41.7 + - - +
283D LEU* 4.0 11.4 - - + +
287D LYS* 4.0 20.0 - - + +
288D ALA 3.3 27.8 - - - +
289D LEU* 3.4 9.2 + - + +
291D GLU* 2.7 26.4 + - + +
293D ILE* 3.7 25.5 - - + +
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C GLU* 4.4 6.7 + - - -
433C PRO* 3.6 27.7 - - + +
532C TYR* 2.7 35.8 + - - -
534C ALA* 4.4 3.3 - - - +
253D THR* 3.2 6.5 + - - +
254D VAL* 1.3 74.4 - - - +
256D ASP* 1.3 72.0 + - - +
258D GLN* 3.2 12.5 + - - +
259D LYS* 2.9 36.1 + - - +
289D LEU* 2.7 28.2 + - + +
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Residues in contact with ASP 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C GLU* 5.7 0.7 - - - +
249D LYS* 3.4 36.3 + - + +
251D SER 4.0 2.3 - - - +
252D TRP* 3.7 21.8 - - + -
253D THR* 3.0 38.5 + - - +
255D ASN* 1.3 83.4 + - - +
257D ILE* 1.3 58.7 + - - +
259D LYS* 3.2 7.9 + - - +
260D LEU* 2.8 29.4 + - - +
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Residues in contact with ILE 257 (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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252D TRP* 3.6 27.4 - - + -
253D THR 3.1 25.8 + - - +
254D VAL 4.0 3.6 - - - +
256D ASP* 1.3 73.5 - - - +
258D GLN* 1.3 61.6 + - - +
260D LEU* 3.7 7.1 - - + +
261D VAL* 2.8 36.0 + - + +
279D LEU* 3.8 33.2 - - + +
282D LEU* 5.2 7.2 - - + -
283D LEU* 3.9 16.8 - - + -
293D ILE* 3.5 33.7 - - + +
295D LEU* 5.1 11.2 - - + -
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Residues in contact with GLN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TYR* 3.6 34.6 + - - -
496C VAL* 4.1 5.0 - - - +
534C ALA* 4.8 6.2 - - - +
535C TRP 4.9 5.4 - - - +
536C VAL* 3.7 32.1 - - + +
537C PRO* 5.1 1.6 - - - +
542C ILE* 3.9 13.7 - - + +
543C GLY* 4.9 2.2 - - - -
254D VAL* 3.0 24.1 + - - +
255D ASN* 3.7 9.1 - - - +
257D ILE* 1.3 77.3 - - - +
259D LYS* 1.3 64.3 + - + +
261D VAL* 3.8 2.9 - - - +
262D GLY* 2.9 21.5 + - - -
283D LEU* 3.6 19.1 - - + +
289D LEU* 3.4 21.1 - - - +
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Residues in contact with LYS 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C TYR* 3.5 25.0 + - - -
533C LEU 5.0 1.8 + - - -
534C ALA* 4.2 6.6 - - - +
535C TRP* 4.0 28.0 + - - +
255D ASN* 2.9 28.3 + - - +
256D ASP* 3.5 8.3 - - - +
258D GLN* 1.3 77.0 - - + +
260D LEU* 1.3 59.0 + - - +
262D GLY* 3.2 2.5 + - - -
263D LYS* 2.8 31.2 + - - +
422D LEU 4.8 12.1 + - - +
423D VAL* 5.6 1.0 - - - +
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Residues in contact with LEU 260 (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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246D LEU* 3.6 41.5 - - + -
247D PRO* 5.8 1.6 - - + +
252D TRP* 3.9 30.5 - - + -
256D ASP 2.8 16.8 + - - +
257D ILE* 3.7 7.6 - - + +
259D LYS* 1.3 76.6 - - - +
261D VAL* 1.3 59.0 + - + +
263D LYS* 3.3 5.6 + - + +
264D LEU* 2.9 37.6 + - + +
279D LEU* 4.1 20.0 - - + -
295D LEU* 6.0 0.2 - - + -
303D LEU* 3.9 21.5 - - + -
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Residues in contact with VAL 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C PRO* 4.4 5.8 - - + -
540C LYS* 5.1 1.1 - - + -
542C ILE* 3.8 27.1 - - + -
257D ILE* 2.8 30.0 + - + +
258D GLN* 3.9 4.0 - - - +
260D LEU* 1.3 70.7 - - - +
262D GLY* 1.3 62.4 + - - +
264D LEU* 4.7 0.4 - - - -
265D ASN* 2.9 28.6 + - + +
276D VAL* 4.0 22.6 - - + +
279D LEU* 3.8 30.5 - - + -
280D SER* 3.9 21.3 - - - +
283D LEU* 5.0 2.2 - - + -
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Residues in contact with GLY 262 (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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535C TRP* 4.3 10.9 - - - -
537C PRO* 4.0 21.7 - - - +
258D GLN 2.9 14.9 + - - -
259D LYS* 3.7 2.9 - - - -
261D VAL* 1.3 78.2 - - - +
263D LYS* 1.3 61.4 + - - +
265D ASN* 3.9 2.4 + - - +
266D TRP* 3.0 24.6 + - - +
423D VAL* 3.7 10.8 - - - +
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Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 4.5 4.5 - - + -
245D VAL 3.6 22.8 + - - +
246D LEU* 4.2 20.2 - - + -
247D PRO* 4.4 9.8 - - + +
259D LYS 2.8 16.3 + - - +
260D LEU* 3.7 8.1 - - + +
262D GLY* 1.3 75.7 - - - +
264D LEU* 1.3 63.1 + - - +
266D TRP* 3.3 3.6 + - - +
267D ALA* 3.1 22.0 + - - +
423D VAL* 3.6 17.1 - - + +
424D LYS 3.2 26.4 + - - +
425D LEU* 3.7 31.9 + - + +
427D TYR* 3.8 22.4 - - - +
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Residues in contact with LEU 264 (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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246D LEU* 3.5 33.0 - - + -
260D LEU* 2.9 31.0 + - + +
263D LYS* 1.3 76.1 - - - +
265D ASN* 1.3 58.4 + - - +
267D ALA* 3.3 5.4 + - + +
268D SER 3.0 22.9 + - - -
274D ILE* 3.4 29.0 - - + +
276D VAL* 3.7 15.7 - - + -
279D LEU* 3.5 31.9 - - + -
303D LEU* 4.4 1.6 - - + -
306D ASN* 3.6 31.2 - - + +
310D LEU* 4.6 3.4 - - + -
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Residues in contact with ASN 265 (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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535C TRP* 4.9 4.9 - - - -
537C PRO* 3.7 26.2 - - + +
540C LYS* 3.1 32.5 + - + +
261D VAL* 2.9 20.4 + - + +
262D GLY 4.0 3.3 + - - +
264D LEU* 1.3 74.7 - - - +
266D TRP* 1.3 65.6 + - - +
268D SER* 2.3 30.3 + - - -
269D GLN* 4.2 3.6 + - - +
274D ILE* 5.3 0.2 - - - -
276D VAL* 4.2 14.9 - - + +
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Residues in contact with TRP 266 (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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535C TRP* 5.7 7.0 - + + -
262D GLY 3.0 18.3 + - - +
263D LYS 3.7 3.8 - - - +
265D ASN* 1.3 81.2 - - - +
267D ALA* 1.3 63.5 + - - +
268D SER 3.2 1.0 + - - -
269D GLN* 3.0 43.0 + - - +
270D ILE* 3.9 13.6 + - + -
346D PHE* 3.5 27.1 - + - -
423D VAL* 4.5 22.9 - - + -
425D LEU* 3.2 38.6 - - + -
426D TRP* 4.9 7.6 - + - -
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Residues in contact with ALA 267 (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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244D ILE* 4.2 25.4 - - + -
263D LYS 3.1 13.5 + - - +
264D LEU* 3.3 12.1 + - + +
266D TRP* 1.3 85.0 - - - +
268D SER* 1.3 53.7 + - - +
270D ILE* 2.6 31.5 + - - +
271D TYR* 3.0 13.6 + - + -
274D ILE* 4.1 15.5 - - + -
310D LEU* 4.7 5.8 - - + -
425D LEU* 4.6 2.2 - - + +
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Residues in contact with SER 268 (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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264D LEU 3.0 12.5 + - - -
265D ASN* 2.3 35.1 + - - -
267D ALA* 1.3 75.3 - - - +
269D GLN* 1.3 61.9 + - - +
271D TYR 3.1 28.2 - - - +
272D PRO* 3.4 12.0 - - - +
274D ILE* 4.2 19.5 - - - +
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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