Contacts of the helix formed by residues 305 - 320 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLN* 5.4 1.2 + - - +
118C TYR* 3.4 35.2 - + + +
303C GLY 3.5 14.1 - - - -
304C PRO* 1.3 70.6 - - - +
306C ASN* 1.3 59.4 + - - +
307C HIS* 3.1 26.4 + + + -
308C ALA* 2.8 29.3 + - + +
309C ILE* 3.2 13.4 + - - +
118D TYR* 3.3 25.1 - - + -
119D SER* 3.5 15.7 + - - -
263D ARG* 3.6 33.6 - - + +
305D HIS* 5.8 5.8 + - - -
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Residues in contact with ASN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.9 17.3 + - + +
72C LYS* 3.2 27.1 + - - +
74C SER* 3.2 21.2 + - - -
81C ARG* 4.7 0.5 + - - -
89C ILE* 2.9 42.2 - - + +
92C LEU* 3.6 11.9 - - + +
93C GLU* 5.0 1.2 - - - +
304C PRO* 3.3 15.0 + - - +
305C HIS* 1.3 71.3 - - - +
307C HIS* 1.3 57.7 + - - +
309C ILE* 3.3 18.0 + - - +
310C ALA* 3.0 23.0 + - - +
263D ARG* 5.6 0.8 - - - +
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Residues in contact with HIS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA 4.0 8.3 - - - +
65C LEU* 3.4 45.4 - - + +
67C SER* 4.4 0.7 - - - +
69C LEU* 3.9 14.5 + - + +
70C ASN* 3.2 46.9 + - - +
305C HIS* 3.5 36.5 + + + -
306C ASN* 1.3 75.6 + - - +
308C ALA* 1.3 71.7 + - + +
310C ALA* 3.4 4.3 + - - +
311C GLY 3.2 15.4 + - - -
65D LEU* 4.1 11.8 - - + +
262D CYS* 5.9 0.2 - - - +
263D ARG* 4.3 12.1 + - + -
307D HIS* 5.8 3.9 + + - -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.8 14.1 - - + -
262C CYS* 3.3 10.8 - - - -
263C ARG 4.4 17.3 - - - +
264C ALA* 4.9 6.7 - - + -
305C HIS* 2.8 21.0 + - + +
307C HIS* 1.3 82.5 - - + +
309C ILE* 1.3 67.8 + - + +
311C GLY 3.0 2.1 + - - -
312C VAL* 2.9 23.1 + - - +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.5 12.8 - - + -
93C GLU* 4.6 14.6 - - + +
96C CYS* 3.7 26.9 - - + -
115C VAL* 3.6 38.6 - - + +
116C GLN* 4.6 4.0 - - + -
304C PRO* 4.4 16.8 - - + -
305C HIS 3.2 9.6 + - - +
306C ASN* 3.6 26.5 - - - +
307C HIS 3.3 0.2 - - - -
308C ALA* 1.3 78.9 - - + +
310C ALA* 1.3 62.4 + - - +
312C VAL* 3.2 8.7 + - - +
313C ALA* 2.9 21.7 + - - +
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.2 13.2 - - + -
69C LEU* 3.5 31.0 - - + -
92C LEU* 3.8 19.5 - - + +
306C ASN 3.0 6.8 + - - +
307C HIS 3.5 10.1 - - - +
308C ALA 3.1 0.2 - - - -
309C ILE* 1.3 76.7 - - - +
311C GLY* 1.3 63.1 + - - +
313C ALA* 3.2 5.2 + - - +
314C VAL* 3.1 25.5 + - - +
33D VAL* 4.7 7.9 - - + +
37D ILE* 4.9 0.2 - - + -
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Residues in contact with GLY 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.7 27.7 - - - +
64C ALA* 4.2 3.5 - - - +
65C LEU* 5.1 1.1 - - - -
262C CYS* 3.8 15.9 - - - -
307C HIS 3.2 7.2 + - - -
308C ALA 3.0 7.2 + - - -
310C ALA* 1.3 79.4 - - - +
312C VAL* 1.3 61.4 + - - +
314C VAL* 3.2 7.0 + - - +
315C ALA* 3.0 18.9 + - - +
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C CYS* 3.6 17.9 - - - -
115C VAL* 5.6 1.1 - - + -
255C THR* 3.6 43.3 - - + +
262C CYS* 3.8 6.3 - - - +
264C ALA* 4.1 12.3 - - + -
266C MSE 4.6 9.9 - - + -
308C ALA 2.9 17.0 + - - +
309C ILE* 3.2 10.7 + - - +
311C GLY* 1.3 76.8 - - - +
313C ALA* 1.3 54.5 + - - +
315C ALA* 3.0 9.1 + - + +
316C LEU* 2.7 46.7 + - + +
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Residues in contact with ALA 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.6 5.4 - - + -
95C LEU* 5.0 1.3 - - + -
96C CYS* 3.7 29.1 - - + +
99C ARG* 2.9 30.3 + - - +
309C ILE 2.9 12.8 + - - +
310C ALA* 3.5 11.0 - - - +
312C VAL* 1.3 76.4 - - - +
314C VAL* 1.3 62.4 + - - +
316C LEU* 3.3 6.7 + - - +
317C LYS 3.1 13.9 + - - -
33D VAL* 4.2 11.7 - - + -
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 3.6 34.1 - - + +
61C VAL* 3.8 11.4 - - + +
64C ALA* 4.6 2.7 - - + -
310C ALA 3.1 15.9 + - - +
311C GLY* 3.4 9.9 - - - +
313C ALA* 1.3 74.3 - - - +
315C ALA* 1.3 63.1 + - - +
317C LYS* 3.3 6.1 + - + +
318C GLN* 3.2 28.4 + - + +
26D LEU* 3.7 24.9 - - + -
29D SER* 4.9 1.1 - - - +
30D ASP* 4.0 18.4 - - + +
33D VAL* 4.0 13.2 - - + -
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 3.8 10.8 - - + -
255C THR* 5.4 1.1 - - - +
259C LEU* 4.3 12.2 - - + +
260C ARG 4.2 3.6 - - - +
261C GLY* 3.6 32.3 - - - +
311C GLY 3.0 9.7 + - - +
312C VAL* 3.0 9.3 + - + +
314C VAL* 1.3 74.6 - - - +
316C LEU* 1.3 66.8 + - - +
318C GLN* 3.2 9.7 + - - +
319C ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C CYS* 3.6 13.9 - - - +
99C ARG* 3.4 12.3 - - + +
100C ALA* 3.2 40.8 - - + +
103C ALA* 3.8 22.4 - - + -
104C TYR* 4.6 11.0 - - + -
259C LEU* 4.8 11.0 - - + -
266C MSE 4.7 11.4 - - + -
312C VAL* 2.7 34.5 + - + +
313C ALA 3.5 8.5 - - - +
314C VAL 3.3 0.2 - - - -
315C ALA* 1.3 72.0 - - - +
317C LYS* 1.3 66.0 + - - +
319C ALA* 3.0 17.8 + - + +
320C MSE 3.3 17.3 + - - +
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Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ARG* 3.6 24.0 - - - +
313C ALA 3.1 3.4 + - - -
314C VAL 3.4 9.2 - - - +
316C LEU* 1.3 78.6 - - - +
318C GLN* 1.3 64.7 + - + +
320C MSE 3.0 32.8 + - + +
321C THR* 3.8 8.6 + - + +
28D ASP 5.1 0.4 + - - -
29D SER* 2.9 27.4 + - - +
30D ASP* 3.5 32.8 + - + +
31D ALA 4.4 3.0 - - - +
32D GLU* 5.5 1.0 - - - +
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Residues in contact with GLN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 3.0 38.8 + - - -
60C ALA* 3.4 21.8 - - - +
61C VAL* 4.9 0.5 - - - +
260C ARG* 4.8 6.5 + - - +
314C VAL* 3.2 17.3 + - - +
315C ALA* 3.2 11.9 + - - +
317C LYS* 1.3 80.5 - - + +
319C ALA* 1.3 59.7 + - - +
321C THR* 2.9 33.1 + - - -
324C PHE* 3.1 10.4 - - + +
21D MSE 4.0 29.2 + - + +
22D LEU* 4.1 9.5 - - - +
29D SER* 3.5 12.5 + - - +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA* 5.1 1.6 - - + -
237C ALA* 4.7 15.7 - - + +
238C ALA* 5.1 1.2 - - - -
259C LEU* 4.1 16.2 - - + -
315C ALA 2.9 12.4 + - - +
316C LEU* 3.0 17.2 + - + +
318C GLN* 1.3 77.5 - - - +
320C MSE 1.3 60.9 + - + +
321C THR 3.3 3.0 + - - +
324C PHE* 2.7 48.9 - - + +
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Residues in contact with MSE 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ARG* 3.9 32.5 - - + +
102C GLN* 3.9 18.8 - - - +
103C ALA* 3.8 32.8 - - + +
316C LEU 3.3 22.9 - - - +
317C LYS* 3.0 28.0 + - + +
319C ALA* 1.3 77.1 - - - +
321C THR* 1.3 64.5 + - - +
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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
------------------------------------------------------------
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