Contacts of the helix formed by residues 304 - 317 (chain D) in PDB entry 6APL
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 SER 304 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303D PRO* 1.3 74.7 - - - +
305D THR* 1.3 59.7 + - - +
306D GLY* 3.8 4.1 + - - -
307D ALA* 2.8 17.7 + - - +
308D LEU* 2.8 24.6 + - - +
325D PHE* 5.5 0.3 - - - -
351D HIS* 3.5 24.1 + - - -
353D LEU* 4.1 14.1 - - - +
356D GLU* 2.6 37.9 + - - -
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Residues in contact with THR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 4.1 5.6 - - + -
179D ASN* 3.6 35.0 + - - +
198D GLY 4.0 6.7 - - - +
199D PHE* 3.9 22.0 - - - +
200D THR* 4.2 17.8 - - - +
203D THR* 5.2 2.6 + - - -
230D ILE* 4.4 11.4 - - + +
303D PRO 3.6 1.6 + - - -
304D SER* 1.3 71.7 - - - +
306D GLY* 1.3 56.4 - - - +
308D LEU* 3.0 14.9 + - - +
309D MSE 2.9 31.1 + - + +
351D HIS* 4.7 4.7 + - - -
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Residues in contact with GLY 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLY* 5.8 0.2 - - - -
178D LEU* 3.9 23.9 - - - +
179D ASN* 4.9 2.8 - - - +
304D SER* 3.1 5.8 + - - -
305D THR* 1.3 78.1 - - - +
307D ALA* 1.3 60.6 + - - +
309D MSE 3.3 2.3 + - - +
310D LEU 3.0 18.7 + - - -
325D PHE* 3.2 29.9 - - - -
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Residues in contact with ALA 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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288D LEU* 4.1 12.3 - - + -
303D PRO* 4.2 2.7 - - + -
304D SER* 2.8 31.0 + - - +
306D GLY* 1.3 72.3 - - - +
308D LEU* 1.3 63.0 + - - +
310D LEU* 3.9 0.3 - - - +
311D LEU* 3.2 29.9 + - - +
325D PHE* 3.9 1.4 - - - -
356D GLU* 3.5 21.5 - - - +
360D TRP* 3.6 23.6 - - + -
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Residues in contact with LEU 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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111D PRO* 6.5 0.2 - - + -
230D ILE* 3.8 35.9 - - + -
275D LEU* 4.0 14.5 - - + +
280D ILE* 4.7 13.9 - - + -
283D LEU* 4.6 17.3 - - + +
302D MSE 5.7 4.3 - - - -
303D PRO* 3.5 42.6 - - + +
304D SER 2.8 10.9 + - - +
305D THR* 3.0 21.3 + - - +
307D ALA* 1.3 74.8 - - - +
309D MSE 1.3 69.0 + - + +
311D LEU* 4.0 1.8 - - + +
312D THR* 3.0 32.2 + - - -
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Residues in contact with MSE 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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153D VAL* 4.0 9.0 - - + +
176D PHE* 4.3 23.8 - - + -
177D ARG 4.6 0.9 - - - +
178D LEU* 3.7 36.6 - - + -
198D GLY* 3.8 21.5 - - - +
228D ILE* 4.0 24.2 - - + -
230D ILE* 3.7 29.6 - - + -
275D LEU* 4.3 4.0 - - + -
305D THR* 2.9 18.1 + - + +
306D GLY 3.3 1.1 + - - +
308D LEU* 1.3 83.4 - - + +
310D LEU* 1.3 65.3 + - - +
312D THR* 3.4 14.4 + - + +
313D ALA* 3.0 22.7 + - - +
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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
----------------------------------------------------------
153D VAL* 3.8 19.7 - - + +
306D GLY 3.0 15.5 + - - +
307D ALA 3.9 3.8 - - - +
309D MSE 1.3 77.4 - - - +
311D LEU* 1.3 57.5 + - - +
313D ALA* 3.1 6.8 + - - +
314D LEU* 3.0 45.9 + - + +
320D VAL* 4.8 2.2 - - + -
322D ALA* 4.0 12.3 - - + -
325D PHE* 3.6 33.0 - - + -
360D TRP* 3.6 39.3 - - + -
369D LEU* 4.0 22.2 - - + -
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Residues in contact with LEU 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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84D PHE* 5.9 0.9 - - + -
279D PHE* 4.5 1.6 - - - -
283D LEU* 3.6 47.3 - - + -
287D PHE* 4.6 17.0 - - + -
288D LEU* 4.4 22.0 - - + -
303D PRO* 5.8 1.1 - - + -
307D ALA 3.2 19.3 + - - +
308D LEU* 5.7 1.1 - - + -
310D LEU* 1.3 72.3 - - - +
312D THR* 1.3 65.6 + - - +
314D LEU* 3.1 22.0 + - + +
315D HIS* 2.8 28.0 + - + +
359D LEU* 4.2 20.0 - - + -
360D TRP* 4.2 11.0 - - + -
363D LEU* 4.8 4.9 - - + -
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Residues in contact with THR 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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90D VAL* 3.9 10.5 - - + -
137D LEU* 3.6 31.0 - - + -
176D PHE* 4.2 12.3 - - + -
228D ILE* 6.5 1.1 - - + -
275D LEU* 3.7 14.2 - - + +
279D PHE* 3.4 25.1 - - - -
308D LEU 3.0 19.1 + - - -
309D MSE 3.5 13.4 - - + +
310D LEU 3.3 0.2 - - - -
311D LEU* 1.3 75.3 - - - +
313D ALA* 1.3 62.0 + - - +
315D HIS* 3.2 2.6 + - - +
316D THR* 2.9 29.0 + - - +
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Residues in contact with ALA 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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151D CYS* 4.5 0.7 - - + -
153D VAL* 3.6 26.7 - - + -
176D PHE* 3.9 16.4 - - + -
309D MSE 3.0 8.0 + - - +
310D LEU 3.1 9.4 + - - +
312D THR* 1.3 74.6 - - - +
314D LEU* 1.3 65.6 + - - +
316D THR* 3.8 6.5 - - - -
317D CYS* 2.9 32.9 + - - +
320D VAL* 3.2 17.3 - - + +
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Residues in contact with LEU 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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67D ARG* 4.7 0.3 + - - -
70D LEU* 3.2 31.4 - - + +
84D PHE* 4.0 16.7 - - + -
86D LEU* 4.2 6.4 - - - +
310D LEU* 3.0 49.0 + - + +
311D LEU* 3.1 20.8 + - + +
313D ALA* 1.3 78.3 - - - +
315D HIS* 1.3 65.5 + - + +
316D THR 3.7 0.3 + - - -
317D CYS 4.1 0.7 - - - +
320D VAL* 3.5 24.5 - - + -
360D TRP* 5.7 0.2 - - + -
363D LEU* 4.8 12.3 - - + -
368D ILE* 3.7 33.0 - - + +
369D LEU* 4.8 4.0 - - + -
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Residues in contact with HIS 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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67D ARG* 4.8 6.2 + - - -
84D PHE* 3.8 21.7 - + - -
85D ASN 3.7 18.8 - - - -
86D LEU* 3.9 28.8 - - + +
88D ILE* 5.0 2.0 - - + -
90D VAL* 4.4 9.1 - - + +
279D PHE* 4.0 18.9 - + + -
282D TYR* 2.9 37.1 + + - -
283D LEU* 4.0 13.9 - - + -
287D PHE* 4.4 4.9 - + - -
311D LEU* 2.8 28.3 + - + +
312D THR 3.2 3.6 + - - +
313D ALA 3.2 0.4 - - - -
314D LEU* 1.3 79.8 - - + +
316D THR* 1.3 63.5 + - - +
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Residues in contact with THR 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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67D ARG* 5.5 2.5 - - - -
90D VAL* 3.8 22.9 - - + -
137D LEU* 4.5 17.6 - - + +
138D PHE* 3.6 34.9 - - + -
149D ILE* 4.1 13.5 - - - +
176D PHE* 4.6 2.1 - - - -
312D THR* 2.9 24.3 + - - +
313D ALA* 3.8 1.7 - - - -
315D HIS* 1.3 83.7 - - - +
317D CYS* 1.3 66.8 + - - +
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Residues in contact with CYS 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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67D ARG* 4.0 10.6 + - - -
70D LEU* 3.3 20.6 - - - +
138D PHE* 4.2 4.3 - - - -
149D ILE* 4.0 10.3 - - - +
151D CYS* 2.0 50.5 - - + -
176D PHE* 4.2 1.6 - - - -
313D ALA* 2.9 24.4 + - - +
314D LEU 4.1 0.3 - - - +
316D THR* 1.3 90.5 - - - +
318D ASP* 1.3 65.3 + - - +
319D GLN 3.6 1.3 - - - +
320D VAL* 3.8 11.4 - - + -
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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