Contacts of the helix formed by residues 302 - 314 (chain D) in PDB entry 4U8T
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 PRO 302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D ILE* 4.2 15.9 - - + -
285D PRO* 4.0 23.6 - - + -
286D ALA* 5.8 3.1 - - + +
300D GLU* 4.3 2.9 - - + +
301D ILE* 1.3 90.8 - - + +
303D ALA* 1.3 65.5 + - - +
304D THR* 3.3 4.4 + - - +
305D ILE* 3.5 14.1 + - + +
306D SER* 3.0 23.2 + - - -
215F GLU* 3.6 35.0 - - + +
244F ASN* 5.3 0.9 - - - +
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Residues in contact with ALA 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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178D SER 4.7 7.2 - - - +
180D PHE* 3.7 23.1 - - + -
301D ILE 3.7 1.0 + - - -
302D PRO* 1.3 73.9 - - - +
304D THR* 1.3 64.3 + - - +
306D SER* 3.4 3.1 + - - -
307D LYS* 3.1 39.1 + - - +
215F GLU* 3.9 13.8 + - - +
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Residues in contact with THR 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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302D PRO* 3.3 3.2 - - - +
303D ALA* 1.3 78.6 - - - +
305D ILE* 1.3 68.3 + - + +
307D LYS* 3.2 20.7 + - - +
308D SER* 3.3 15.9 + - - +
215F GLU* 4.9 4.0 + - - -
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Residues in contact with ILE 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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282D PHE* 3.6 33.7 - - + -
283D LEU 3.3 29.8 - - - +
284D ILE* 4.6 3.4 - - + -
285D PRO* 4.3 14.4 - - + -
301D ILE* 3.7 17.7 - - + -
302D PRO* 3.5 21.1 + - + +
303D ALA 3.4 0.4 - - - -
304D THR* 1.3 80.0 - - + +
306D SER* 1.3 62.7 + - - +
308D SER* 3.2 9.5 + - - -
309D ILE* 3.1 25.9 + - + +
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Residues in contact with SER 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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180D PHE* 3.1 46.8 - - - +
226D LEU* 5.4 4.3 - - - +
301D ILE* 3.4 13.9 - - - +
302D PRO 3.0 17.9 + - - -
303D ALA 3.5 4.9 - - - -
304D THR 3.2 0.2 - - - -
305D ILE* 1.3 79.3 - - - +
307D LYS* 1.3 52.0 + - - +
309D ILE* 3.0 10.8 + - - +
310D LEU* 2.8 37.8 + - - +
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Residues in contact with LYS 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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174D VAL* 4.4 33.0 + - + -
176D ASP* 5.1 9.1 + - - +
180D PHE* 4.7 9.0 - - + -
303D ALA* 3.1 27.5 + - - +
304D THR* 3.2 11.1 + - - +
306D SER* 1.3 78.5 - - - +
308D SER* 1.3 63.1 + - - +
310D LEU* 3.2 9.5 + - - +
311D LYS* 3.0 35.5 + - - +
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Residues in contact with SER 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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282D PHE* 3.8 26.7 - - - -
304D THR* 3.3 11.5 + - - +
305D ILE* 3.2 10.5 + - - -
306D SER 3.2 0.6 - - - -
307D LYS* 1.3 79.0 - - - +
309D ILE* 1.3 61.7 + - - +
311D LYS* 3.3 10.5 + - - +
312D LEU* 3.1 24.3 + - - +
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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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226D LEU* 4.4 17.3 - - + -
235D PHE* 6.4 0.9 - - + -
279D LEU* 3.7 20.0 - - + -
282D PHE* 3.6 21.1 - - + -
292D VAL* 3.9 33.9 - - + -
301D ILE* 4.7 2.5 - - + -
305D ILE* 3.1 30.0 + - + +
306D SER* 3.0 12.2 + - - +
308D SER* 1.3 75.4 - - - +
310D LEU* 1.3 64.7 + - + +
312D LEU* 3.1 17.0 + - - +
313D PHE* 3.1 31.7 + - + -
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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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172D ILE* 4.4 23.6 - - + +
174D VAL* 3.8 29.4 - - + -
180D PHE* 4.1 20.0 - - + -
224D TYR* 4.7 7.2 - - + -
226D LEU* 4.4 10.8 - - + -
238D VAL* 3.9 37.5 - - + -
306D SER* 2.8 18.3 + - - +
307D LYS* 3.2 12.1 + - - +
309D ILE* 1.3 75.4 - - + +
311D LYS* 1.3 61.7 + - + +
313D PHE* 3.2 17.1 + - + +
314D LYS* 3.4 18.9 + - - +
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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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307D LYS* 3.0 23.2 + - - +
308D SER* 3.7 11.7 - - - +
309D ILE 3.3 0.2 - - - -
310D LEU* 1.3 75.9 - - + +
312D LEU* 1.3 65.1 + - + +
314D LYS* 3.0 37.8 + - - +
315D TYR* 3.5 12.0 + - - +
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Residues in contact with LEU 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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272D ARG* 4.2 5.4 + - - -
274D VAL* 4.6 12.1 - - + +
278D SER* 3.4 33.0 - - - +
279D LEU* 4.0 16.4 - - + -
281D GLN* 5.5 1.3 - - - +
282D PHE* 4.3 13.0 - - + -
308D SER 3.1 14.2 + - - +
309D ILE* 3.1 10.4 + - - +
311D LYS* 1.3 77.8 - - + +
313D PHE* 1.3 60.7 + - - +
314D LYS 3.3 0.5 + - - -
315D TYR* 3.3 31.9 + - + +
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Residues in contact with PHE 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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168D ILE* 4.0 7.3 - - - +
226D LEU* 5.1 6.1 - - + -
235D PHE* 3.8 29.2 - + + -
237D GLY* 3.8 21.3 - - - -
238D VAL* 4.0 19.7 - - + -
270D VAL* 3.5 35.4 - - + +
272D ARG* 3.5 39.5 + - + -
274D VAL* 3.6 30.3 - - + -
279D LEU* 5.4 0.9 - - + -
309D ILE* 3.1 41.2 + - + -
310D LEU* 3.4 13.9 - - + +
311D LYS 3.1 0.4 - - - -
312D LEU* 1.3 76.9 - - + +
314D LYS* 1.3 57.8 + - + +
315D TYR 3.4 0.9 - - - -
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Residues in contact with LYS 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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168D ILE* 3.9 13.6 - - + +
169D PRO* 3.9 18.1 - - + +
170D PRO 4.0 15.7 + - - +
171D TRP* 4.5 2.0 - - - +
172D ILE* 3.7 61.6 + - + +
270D VAL* 5.6 0.2 - - + -
272D ARG* 4.3 1.3 - - - -
310D LEU* 3.4 11.8 + - - +
311D LYS* 3.0 29.8 + - - +
313D PHE* 1.3 77.3 - - - +
315D TYR* 1.3 59.5 + - - +
316D GLU* 3.7 3.8 + - - +
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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