Contacts of the helix formed by residues 296 - 312 (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 296 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278D GLN* 4.5 4.3 - - - +
281D LYS* 6.3 0.4 - - + -
282D LEU* 3.5 29.2 - - + +
294D PRO 3.4 4.6 + - - -
295D LEU* 1.3 73.7 - - - +
297D GLU* 1.3 60.4 + - - +
298D GLU* 3.2 20.5 + - + +
299D ALA* 3.0 23.3 + - + +
300D GLU* 2.8 27.7 + - - +
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Residues in contact with GLU 297 (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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295D LEU 4.0 0.8 + - - -
296D THR* 1.3 75.3 + - - +
298D GLU* 1.3 61.3 + - - +
300D GLU* 3.2 14.1 + - - +
301D LEU* 2.8 51.1 + - + +
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Residues in contact with GLU 298 (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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278D GLN* 3.2 35.7 - - + +
296D THR* 3.2 21.9 + - + -
297D GLU* 1.3 82.0 + - - +
299D ALA* 1.3 53.3 + - - +
301D LEU* 3.1 12.9 + - + +
302D GLU* 2.6 36.9 + - - +
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Residues in contact with ALA 299 (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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278D GLN* 3.7 19.4 - - - +
279D LEU* 4.1 7.5 - - + +
282D LEU* 3.8 10.1 - - + -
295D LEU* 3.5 26.7 - - + -
296D THR* 3.0 25.6 + - + +
298D GLU* 1.3 75.9 - - - +
300D GLU* 1.3 55.8 + - - +
302D GLU* 3.5 2.1 - - - +
303D LEU* 2.7 33.3 + - - +
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Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D GLU* 5.3 4.0 - - - +
295D LEU* 4.1 33.2 - - + +
296D THR 2.8 21.3 + - - +
297D GLU* 3.4 16.4 - - - +
299D ALA* 1.3 77.1 - - - +
301D LEU* 1.3 64.0 + - + +
303D LEU* 3.7 6.8 - - - +
304D ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 301 (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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297D GLU* 2.8 36.8 + - + +
298D GLU* 3.1 14.6 + - + +
300D GLU* 1.3 73.2 - - + +
302D GLU* 1.3 58.0 + - - +
304D ALA* 3.2 8.2 + - + +
305D GLU* 2.8 31.6 + - - +
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Residues in contact with GLU 302 (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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275D LYS* 3.1 38.5 - - + +
276D VAL 3.6 0.7 - - - -
277D ARG* 2.7 25.9 + - - +
278D GLN* 3.0 19.5 + - + +
279D LEU* 2.6 40.9 + - + +
298D GLU 2.6 20.6 + - - +
299D ALA 3.5 3.8 - - - +
301D LEU* 1.3 73.5 - - - +
303D LEU* 1.3 56.2 + - - +
305D GLU* 3.3 8.3 + - + +
306D ASN* 2.9 35.7 + - - +
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Residues in contact with LEU 303 (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* 3.9 24.0 - - + -
248D GLU* 4.5 7.2 - - - +
252D TRP* 4.6 5.6 - - + -
260D LEU* 3.9 29.8 - - + -
264D LEU* 4.4 2.5 - - + -
279D LEU* 4.1 18.8 - - + +
295D LEU* 3.8 28.5 - - + -
299D ALA 2.7 17.7 + - - +
300D GLU* 3.7 6.3 - - - +
302D GLU* 1.3 74.0 - - - +
304D ALA* 1.3 56.2 + - - +
306D ASN* 3.0 6.0 + - - +
307D ARG* 2.9 60.0 + - - +
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Residues in contact with ALA 304 (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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300D GLU 2.9 16.7 + - - +
301D LEU* 3.7 10.3 - - + +
303D LEU* 1.3 76.0 - - - +
305D GLU* 1.3 64.1 + - - +
307D ARG* 3.2 14.6 + - - +
308D GLU* 3.0 30.6 + - - +
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Residues in contact with GLU 305 (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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273D GLY 4.9 4.8 - - - +
275D LYS* 6.0 4.0 - - + -
301D LEU 2.8 21.0 + - - +
302D GLU* 3.5 9.6 - - + +
304D ALA* 1.3 72.2 - - - +
306D ASN* 1.3 64.8 + - - +
308D GLU* 3.5 13.4 + - - +
309D ILE* 3.3 40.4 + - + +
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Residues in contact with ASN 306 (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* 5.1 2.2 - - + -
264D LEU* 3.6 38.9 - - + +
273D GLY 4.5 1.6 - - - +
274D ILE* 3.3 13.7 - - + +
275D LYS* 2.9 44.8 + - - +
279D LEU* 4.5 0.6 - - - +
302D GLU* 2.9 26.0 + - - +
303D LEU* 3.0 7.6 + - - +
305D GLU* 1.3 77.3 - - - +
307D ARG* 1.3 66.0 + - - +
309D ILE* 3.3 8.7 + - - +
310D LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 307 (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* 3.9 31.8 + - + +
247D PRO 3.2 21.6 + - - -
248D GLU* 2.5 39.1 + - - +
252D TRP* 4.9 1.4 - - - -
303D LEU* 2.9 50.0 + - - +
304D ALA* 3.5 11.7 - - - +
306D ASN* 1.3 73.1 - - - +
308D GLU* 1.3 68.2 + - - +
310D LEU* 3.3 8.7 + - + +
311D LYS* 3.2 35.5 + - - +
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Residues in contact with GLU 308 (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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304D ALA* 3.0 23.3 + - - +
305D GLU* 3.5 16.6 - - - +
307D ARG* 1.3 76.3 - - - +
309D ILE* 1.3 66.2 + - + +
311D LYS* 3.2 22.1 + - - +
312D GLU* 3.7 10.4 + - - +
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Residues in contact with ILE 309 (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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271D TYR* 3.5 38.5 - - + -
273D GLY* 3.3 37.5 - - - +
274D ILE* 4.0 11.9 - - + +
305D GLU* 3.3 30.5 + - + +
306D ASN* 3.3 8.6 + - - +
308D GLU* 1.3 77.8 - - + +
310D LEU* 1.3 62.6 + - - +
312D GLU* 3.1 37.3 - - - +
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Residues in contact with LEU 310 (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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243D PRO* 4.7 10.6 - - - +
244D ILE* 3.8 47.7 + - + +
245D VAL* 5.0 0.2 - - - -
246D LEU* 4.0 30.5 - - + +
264D LEU* 4.6 6.1 - - + -
267D ALA* 4.7 3.6 - - + -
271D TYR* 3.7 34.2 + - + -
274D ILE* 3.7 24.0 - - + -
306D ASN 3.0 20.7 + - - +
307D ARG* 3.3 8.5 + - - +
309D ILE* 1.3 74.9 - - - +
311D LYS* 1.3 61.0 - - - +
312D GLU 3.5 5.4 + - - +
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Residues in contact with LYS 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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243D PRO* 6.3 0.4 - - - -
245D VAL* 6.3 1.0 - - - +
307D ARG* 3.2 22.0 + - - +
308D GLU* 3.2 17.3 + - - +
310D LEU* 1.3 77.8 - - - +
312D GLU* 1.3 61.4 + - - +
313D PRO* 4.0 1.4 - - - +
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Residues in contact with GLU 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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271D TYR* 3.4 24.2 + - + -
308D GLU 3.7 8.7 + - - +
309D ILE* 3.1 34.9 - - - +
310D LEU 3.8 0.3 - - - +
311D LYS* 1.3 83.1 - - - +
313D PRO* 1.3 80.1 - - + +
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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