Contacts of the helix formed by residues 304 - 321 (chain D) in PDB entry 3P9K
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 304 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D GLU* 4.7 13.5 + - + +
303D ALA* 1.3 76.3 - - - +
305D PRO* 1.3 77.5 - - + +
306D SER* 2.9 14.7 + - - -
307D SER* 2.7 37.7 + - - -
308D GLN* 3.1 25.3 + - - +
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Residues in contact with PRO 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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15C ASP* 4.8 13.2 - - + +
18C MET* 4.2 21.6 - - + +
19C PHE* 4.1 24.7 - - + +
22C GLN* 3.9 25.6 - - - +
304D ASN* 1.3 88.3 - - + +
306D SER* 1.3 56.9 + - - +
308D GLN* 3.8 4.0 - - - +
309D GLY* 3.1 22.9 + - - -
352D ASN* 4.6 0.9 + - - -
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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
----------------------------------------------------------
18C MET* 3.9 19.9 - - - -
304D ASN* 2.9 16.8 + - - -
305D PRO* 1.3 78.3 - - - +
307D SER* 1.3 66.8 + - - -
309D GLY 3.2 8.3 + - - -
310D VAL* 3.2 13.4 + - - +
352D ASN* 2.8 37.8 + - - +
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Residues in contact with SER 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D PRO* 4.4 12.8 - - - -
301D PRO* 4.1 26.7 - - - -
302D GLU 4.1 3.4 - - - -
303D ALA* 3.0 27.0 + - - -
304D ASN* 2.7 19.1 + - - -
306D SER* 1.3 74.0 + - - +
308D GLN* 1.3 64.2 + - - +
310D VAL* 3.1 9.0 + - - +
311D PHE* 3.1 33.5 + - - -
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Residues in contact with GLN 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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22C GLN* 2.7 35.2 + - - +
83C SER* 2.9 39.7 + - - +
84C TYR* 3.4 32.8 - - + +
303D ALA* 4.0 7.5 + - - +
304D ASN* 3.1 29.2 + - - +
305D PRO* 3.8 1.1 - - - +
307D SER* 1.3 82.0 + - - +
309D GLY* 1.3 56.4 + - - +
311D PHE* 3.1 11.1 + - - +
312D HIS* 2.9 36.9 + - - -
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Residues in contact with GLY 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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18C MET 5.8 0.2 - - - -
21C LEU* 5.9 2.9 - - - -
22C GLN* 5.0 10.7 - - - +
305D PRO 3.1 20.0 + - - -
306D SER 3.6 2.2 - - - -
307D SER 3.1 0.4 - - - -
308D GLN* 1.3 80.2 - - - +
310D VAL* 1.3 57.6 + - - +
312D HIS* 3.2 27.9 - - - +
313D VAL* 3.3 14.8 + - - +
352D ASN* 4.9 4.3 - - - -
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Residues in contact with VAL 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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295D CYS* 4.2 19.7 - - + -
296D ILE 4.4 13.7 - - - +
297D LEU* 3.4 29.8 - - + +
298D PRO* 4.8 4.5 - - + -
306D SER 3.2 13.0 + - - +
307D SER* 3.1 11.0 + - - +
309D GLY* 1.3 73.2 - - - +
311D PHE* 1.3 64.5 + - + +
313D VAL* 3.6 6.0 + - - +
314D ASP* 3.2 16.3 + - - +
326D GLU* 3.5 17.2 - - + +
352D ASN* 3.9 26.5 - - + +
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Residues in contact with PHE 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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76C ARG 6.0 0.2 - - - +
79C ARG* 3.6 48.5 - - + +
80C LEU* 3.7 20.9 - - + +
83C SER* 3.6 32.8 - - - -
297D LEU* 3.7 23.3 - - + -
298D PRO* 4.6 7.2 - - + -
301D PRO* 4.0 28.7 - - + -
307D SER* 3.1 28.4 + - - -
308D GLN 3.1 5.1 + - - +
310D VAL* 1.3 75.2 - - - +
312D HIS* 1.3 65.4 + - - +
314D ASP* 3.4 6.6 + - - +
315D MET* 3.1 27.2 + - - +
328D TYR* 5.4 1.1 - - - -
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Residues in contact with HIS 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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22C GLN* 3.4 33.9 + - + +
25C SER* 2.7 41.3 + - - +
26C SER* 4.1 5.8 - - - -
28C VAL* 3.8 17.3 - - + +
29C LEU* 5.3 2.5 + - + +
80C LEU* 4.0 14.8 - - + -
84C TYR* 2.7 31.1 + + - -
308D GLN 2.9 27.3 + - - -
309D GLY* 3.2 11.0 - - - +
310D VAL 3.2 0.2 - - - -
311D PHE* 1.3 76.8 - - - +
313D VAL* 1.3 64.0 + - + +
315D MET* 3.1 5.4 + - - +
316D ILE* 2.9 27.0 + - - +
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Residues in contact with VAL 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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25C SER* 5.8 0.7 - - - +
263D TRP* 4.8 9.6 - - + +
266D HIS* 3.8 21.5 - - + +
295D CYS* 4.8 11.4 - - - -
309D GLY 3.3 16.1 + - - +
310D VAL* 3.6 7.4 + - - +
312D HIS* 1.3 76.5 - - + +
314D ASP* 1.3 57.8 + - - +
316D ILE* 3.1 9.4 + - - +
317D MET* 2.8 38.8 + - + +
326D GLU* 3.1 23.1 - - - +
604D CIY 4.4 25.4 - - + -
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Residues in contact with ASP 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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76C ARG* 2.8 63.0 + - - +
79C ARG* 3.0 30.1 + - - +
297D LEU* 5.3 1.1 - - + -
310D VAL 3.2 13.5 + - - +
311D PHE* 3.5 13.2 - - - +
312D HIS 3.2 0.4 - - - -
313D VAL* 1.3 78.3 - - - +
315D MET* 1.3 57.8 + - - +
317D MET* 3.2 3.2 + - - +
318D LEU 3.0 9.9 + - - -
325D ARG* 3.6 1.2 - - - +
326D GLU* 2.9 40.9 + - + +
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Residues in contact with MET 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.9 12.6 - - + -
32C THR* 3.5 18.4 - - + +
76C ARG* 3.6 31.4 - - - +
77C ILE* 3.9 12.3 - - + -
80C LEU* 3.9 23.1 - - + -
137D TRP* 3.8 13.6 - - + -
140D LEU* 3.9 26.2 - - + -
311D PHE 3.1 16.7 + - - +
312D HIS 3.6 6.5 - - - +
314D ASP* 1.3 74.7 - - - +
316D ILE* 1.3 60.1 + - - +
318D LEU* 3.3 23.5 + - + +
319D ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 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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25C SER* 3.7 25.1 - - - -
28C VAL* 3.8 12.8 - - + -
128D ASN* 3.6 23.6 - - + +
133D LEU* 6.0 0.2 - - + -
137D TRP* 4.7 7.2 - - + -
312D HIS 2.9 22.2 + - - +
313D VAL* 3.1 9.4 + - - +
315D MET* 1.3 77.6 - - - +
317D MET* 1.3 77.8 + - + +
319D ALA* 3.2 5.5 + - - +
320D HIS* 3.0 43.0 + - + +
604D CIY 3.8 27.6 - - + +
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Residues in contact with MET 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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76C ARG* 4.0 0.2 - - - +
266D HIS* 3.3 31.4 - - + +
267D ASP* 3.4 19.1 - - - +
313D VAL* 2.8 19.9 + - + +
314D ASP* 3.4 7.6 - - - +
316D ILE* 1.3 92.6 - - + +
318D LEU* 1.3 60.6 + - - +
321D ASN* 2.9 46.3 + - - +
324D GLY* 3.5 21.6 - - - +
325D ARG* 3.7 2.7 - - - +
326D GLU* 3.8 13.9 - - - +
604D CIY 3.7 32.5 - - + -
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Residues in contact with LEU 318 (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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73C MET* 4.1 44.9 - - + +
76C ARG* 3.4 37.4 - - + +
77C ILE* 4.4 9.9 - - + -
140D LEU* 4.1 18.4 - - + -
150D PRO* 3.3 19.7 - - + +
314D ASP 3.0 7.4 + - - +
315D MET* 3.5 35.7 - - + +
317D MET* 1.3 79.6 - - - +
319D ALA* 1.3 62.0 + - - +
321D ASN 4.5 5.1 - - - +
324D GLY 4.4 1.8 - - - -
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Residues in contact with ALA 319 (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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136D SER* 3.5 6.0 + - - -
137D TRP* 4.0 28.7 - - + +
140D LEU* 5.2 3.1 - - + +
150D PRO* 3.4 16.1 - - + +
151D PHE 3.1 23.9 + - - -
315D MET 2.9 16.4 + - - +
316D ILE 3.2 4.7 + - - +
318D LEU* 1.3 79.9 - - - +
320D HIS* 1.3 77.1 + - + +
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Residues in contact with HIS 320 (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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133D LEU* 3.1 63.8 - - + +
136D SER* 2.7 29.4 + - - -
137D TRP* 4.6 7.1 + - - -
149D ILE* 3.6 13.7 - - - +
151D PHE* 3.7 11.9 - - + +
152D ASN* 4.4 0.9 - - - +
159D ALA* 3.6 23.5 + - + +
316D ILE* 3.0 38.0 + - + +
319D ALA* 1.3 86.9 - - + +
321D ASN* 1.3 72.8 + - - +
322D PRO* 4.3 1.4 - - - +
604D CIY 5.4 4.9 - + + -
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Residues in contact with ASN 321 (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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149D ILE* 3.8 13.9 - - - +
159D ALA* 3.9 10.9 - - - +
160D PHE* 3.9 14.0 - - - -
267D ASP* 3.3 42.1 + - - +
317D MET* 2.9 41.3 + - - +
318D LEU* 4.5 2.6 - - - +
320D HIS* 1.3 84.1 - - - +
322D PRO* 1.3 72.2 - - + +
323D GLY* 3.0 9.2 + - - -
324D GLY* 3.6 3.6 + - - -
604D CIY 3.4 17.5 + - - -
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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