Contacts of the helix formed by residues 305 - 320 (chain D) in PDB entry 1EJI
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 HIS 305 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.3 25.1 - - + -
119C SER* 3.3 18.8 + - - -
263C ARG* 3.6 33.6 - - + +
305C HIS* 5.8 5.6 + - - -
116D GLN 5.4 1.4 + - - -
118D TYR* 3.4 36.8 - + + +
303D GLY 3.5 9.0 - - - -
304D PRO* 1.3 69.3 - - - +
306D ASN* 1.3 59.3 + - - +
307D HIS* 3.1 26.3 + + + -
308D ALA* 2.8 30.2 + - + +
309D ILE* 3.3 12.7 + - - +
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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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263C ARG* 5.7 0.6 - - - +
69D LEU* 3.9 17.5 + - + +
72D LYS* 3.1 29.3 + - - +
74D SER* 3.2 19.0 + - - +
81D ARG* 5.0 0.3 + - - -
89D ILE* 3.0 42.4 - - + +
92D LEU* 3.5 12.1 - - + +
93D GLU* 5.1 1.7 - - - +
304D PRO* 3.3 16.6 + - - +
305D HIS* 1.3 71.4 - - - +
307D HIS* 1.3 55.8 + - - +
309D ILE* 3.3 16.7 + - - +
310D ALA* 3.0 23.6 + - - +
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Residues in contact with HIS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 4.1 11.5 - - + +
263C ARG* 4.3 12.2 + - + -
307C HIS* 5.8 3.7 + - - -
64D ALA 4.0 8.1 - - - +
65D LEU* 3.4 45.4 - - + +
67D SER* 4.4 0.7 - - - +
69D LEU* 3.8 14.3 + - + +
70D ASN* 3.2 48.0 + - - +
305D HIS* 2.9 35.5 + + + +
306D ASN* 1.3 75.2 + - - +
308D ALA* 1.3 72.4 + - + +
310D ALA* 3.4 4.5 + - - +
311D GLY 3.2 15.8 + - - -
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 3.9 15.7 - - + -
262D CYS* 3.3 10.0 - - - -
263D ARG 4.4 17.0 - - - +
264D ALA* 4.8 6.3 - - + -
305D HIS* 2.8 21.9 + - + +
307D HIS* 1.3 81.8 - - + +
309D ILE* 1.3 68.1 + - + +
311D GLY 3.0 2.1 + - - -
312D VAL* 2.9 22.6 + - - +
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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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92D LEU* 4.5 13.0 - - + -
93D GLU* 4.6 14.4 - - + +
96D CYS* 3.9 26.6 - - + -
115D VAL* 3.5 38.6 - - + +
116D GLN* 4.5 4.9 - - + -
304D PRO* 4.4 20.2 - - + -
305D HIS 3.3 9.6 + - - +
306D ASN* 3.5 22.7 - - - +
308D ALA* 1.3 78.8 - - + +
310D ALA* 1.3 62.0 + - - +
312D VAL* 3.2 9.5 + - - +
313D ALA* 2.9 21.3 + - - +
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Residues in contact with ALA 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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33C VAL* 4.7 7.2 - - + +
37C ILE* 4.9 0.2 - - + -
64D ALA* 4.2 13.7 - - + -
69D LEU* 3.4 32.8 - - + -
92D LEU* 3.9 19.5 - - + -
306D ASN 3.0 6.0 + - - +
307D HIS 3.5 8.5 - - - +
308D ALA 3.2 0.2 - - - -
309D ILE* 1.3 77.7 - - - +
311D GLY* 1.3 62.7 + - - +
313D ALA* 3.1 4.9 + - - +
314D VAL* 3.1 26.0 + - - +
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Residues in contact with GLY 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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61D VAL* 3.8 24.6 - - - +
64D ALA* 4.3 3.3 - - - +
65D LEU* 5.1 1.3 - - - -
262D CYS* 3.7 16.6 - - - -
307D HIS 3.2 7.0 + - - -
308D ALA 3.0 8.0 + - - -
310D ALA* 1.3 79.4 - - - +
312D VAL* 1.3 61.6 + - - +
314D VAL* 3.2 6.8 + - - +
315D ALA* 3.0 21.8 + - - +
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Residues in contact with VAL 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D CYS* 3.7 18.2 - - - -
115D VAL* 5.6 1.3 - - + -
255D THR* 3.8 40.8 - - + +
262D CYS* 3.7 6.9 - - - +
264D ALA* 4.1 12.3 - - + -
266D MSE 4.5 9.4 - - + -
308D ALA 2.9 18.3 + - - +
309D ILE* 3.2 11.2 + - - +
311D GLY* 1.3 76.4 - - - +
313D ALA* 1.3 58.4 + - - +
315D ALA* 3.0 8.6 + - + +
316D LEU* 2.7 42.1 + - + +
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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
----------------------------------------------------------
33C VAL* 4.2 11.7 - - + -
92D LEU* 4.6 5.6 - - + -
95D LEU* 5.0 1.3 - - + -
96D CYS* 4.0 27.8 - - + +
99D ARG* 2.9 30.2 + - - +
309D ILE 2.9 13.2 + - - +
310D ALA* 3.4 10.8 - - - +
312D VAL* 1.3 76.5 - - - +
314D VAL* 1.3 62.8 + - - +
316D LEU* 3.3 7.1 + - - +
317D LYS 3.1 13.9 + - - -
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.7 24.9 - - + -
29C SER* 4.8 3.1 - - - +
30C ASP* 4.1 16.6 - - + +
33C VAL* 4.2 12.8 - - + -
60D ALA* 3.7 33.9 - - + +
61D VAL* 3.8 11.2 - - + +
64D ALA* 4.6 2.5 - - + -
310D ALA 3.1 15.3 + - - +
311D GLY* 3.4 10.3 - - - +
312D VAL 3.1 0.4 - - - -
313D ALA* 1.3 76.3 - - - +
315D ALA* 1.3 62.5 + - - +
317D LYS* 3.2 6.3 + - + +
318D GLN* 3.2 29.5 + - + +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D VAL* 3.8 11.0 - - + -
255D THR* 5.5 1.1 - - - +
259D LEU* 4.3 12.7 - - + +
260D ARG 4.2 4.3 - - - +
261D GLY* 3.6 31.6 - - - +
311D GLY 3.0 10.6 + - - +
312D VAL* 3.0 8.8 + - - +
314D VAL* 1.3 73.8 - - - +
316D LEU* 1.3 66.9 + - - +
318D GLN* 3.2 9.3 + - - +
319D ALA* 2.9 23.4 + - - +
324D PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 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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96D CYS* 3.5 14.6 - - - +
99D ARG* 3.5 11.2 - - + +
100D ALA* 3.2 39.9 - - + +
103D ALA* 3.8 23.7 - - + +
104D TYR* 4.6 10.5 - - + -
259D LEU* 4.9 11.0 - - + -
266D MSE 4.7 10.8 - - + -
312D VAL* 2.7 33.7 + - + +
313D ALA* 3.5 9.2 - - - +
315D ALA* 1.3 72.0 - - - +
317D LYS* 1.3 65.0 + - - +
319D ALA* 3.0 19.5 + - + +
320D MSE 3.3 15.2 + - - +
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Residues in contact with LYS 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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28C ASP 5.0 0.6 + - - -
29C SER* 2.7 28.6 + - - +
30C ASP* 3.6 30.4 + - + +
31C ALA 4.5 2.0 - - - +
99D ARG* 3.6 23.5 - - - +
313D ALA 3.1 3.2 + - - -
314D VAL 3.4 9.6 - - - +
315D ALA 3.2 0.2 - - - -
316D LEU* 1.3 79.6 - - - +
318D GLN* 1.3 64.9 + - + +
320D MSE 3.0 32.3 + - + +
321D THR* 3.8 8.4 + - + +
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Residues in contact with GLN 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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21C MSE 3.9 30.3 + - + +
22C LEU* 4.0 9.7 - - - +
29C SER* 3.5 12.0 + - - +
58D SER* 3.1 38.1 + - - -
60D ALA* 3.3 22.4 - - - +
61D VAL* 4.8 1.4 - - - +
260D ARG* 4.8 5.7 + - - +
314D VAL* 3.2 17.2 + - - +
315D ALA* 3.2 11.6 + - - +
317D LYS* 1.3 81.4 - - + +
319D ALA* 1.3 59.8 + - - +
321D THR* 2.8 33.6 + - - -
324D PHE* 3.2 10.2 - - + +
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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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103D ALA* 5.1 4.7 - - + -
237D ALA* 4.7 16.1 - - + +
238D ALA* 5.1 1.2 - - - -
259D LEU* 4.1 15.7 - - + -
315D ALA 2.9 13.6 + - - +
316D LEU* 3.0 14.6 + - + +
318D GLN* 1.3 76.5 - - - +
320D MSE 1.3 61.0 + - + +
321D THR 3.2 2.5 + - - +
324D PHE* 2.8 47.8 - - + +
325D LYS* 6.0 0.2 - - - +
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Residues in contact with MSE 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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99D ARG* 3.8 32.5 - - + +
102D GLN* 3.8 19.5 - - - +
103D ALA* 3.8 33.7 - - + +
316D LEU 3.3 22.7 - - - +
317D LYS* 3.0 28.2 + - + +
319D ALA* 1.3 75.6 - - - +
321D THR* 1.3 64.9 + - - +
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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
------------------------------------------------------------
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