Contacts of the helix formed by residues 30 - 46 (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 ASP 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.0 27.4 + - + +
29C SER* 1.3 79.2 - - - +
31C ALA* 1.3 58.5 + - - +
32C GLU* 3.1 6.6 + - - +
33C VAL* 3.0 28.2 + - + +
34C TYR* 3.0 26.7 + - - +
99D ARG* 2.5 42.1 + - - -
314D VAL* 4.1 11.1 - - + -
317D LYS* 3.6 14.9 + - + +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS 4.1 12.8 - - - +
28C ASP 4.0 7.1 + - - +
30C ASP* 1.3 72.1 + - - +
32C GLU* 1.3 60.1 + - - +
34C TYR* 3.5 9.6 - - + +
35C SER* 2.8 30.8 + - - -
317D LYS* 4.5 3.4 - - - +
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP* 3.1 8.2 + - - +
31C ALA* 1.3 75.6 - - - +
33C VAL* 1.3 65.8 + - - +
35C SER* 3.2 8.2 + - - -
36C ILE* 3.1 30.4 + - + +
95D LEU* 3.7 27.5 - - + +
98D LYS* 5.1 4.7 + - - -
99D ARG* 3.1 20.8 + - - +
317D LYS* 6.1 0.4 - - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.3 8.1 - - + -
30C ASP* 3.0 31.3 + - + +
32C GLU* 1.3 80.0 - - - +
34C TYR* 1.3 64.0 + - - +
36C ILE* 3.3 9.7 + - - +
37C ILE* 3.0 37.3 + - + +
64D ALA* 5.1 0.4 - - + -
92D LEU* 4.6 8.7 - - + -
95D LEU* 3.9 15.0 - - + -
99D ARG* 3.9 9.9 - - - +
310D ALA* 4.7 12.8 - - + +
313D ALA* 4.2 13.9 - - + -
314D VAL* 4.2 17.5 - - + -
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.0 23.1 - - + +
27C LYS* 3.2 62.6 + - + -
30C ASP 3.0 20.4 + - - +
31C ALA* 3.5 9.0 - - + +
32C GLU 3.2 0.2 - - - -
33C VAL* 1.3 78.1 - - - +
35C SER* 1.3 64.6 + - - +
37C ILE* 3.4 4.6 + - - +
38C LYS* 2.8 65.9 + - + +
484C PHE* 4.7 16.4 - + - -
63D GLU* 5.6 1.1 - - - -
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA 2.8 21.4 + - - -
32C GLU* 3.4 8.3 - - - -
34C TYR* 1.3 76.7 - - - +
36C ILE* 1.3 64.2 + - - +
38C LYS* 3.1 7.8 + - - +
39C LYS* 2.9 43.4 + - - +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.1 19.9 + - + +
33C VAL* 3.3 8.5 + - - +
35C SER* 1.3 76.0 + - - +
37C ILE* 1.3 63.4 + - + +
39C LYS* 3.2 12.5 + - - +
40C GLU* 2.9 23.6 + - + +
69D LEU* 5.9 3.8 - - + -
88D PHE* 3.6 32.9 - - + +
91D GLU* 3.7 27.1 - - + +
92D LEU* 4.0 33.2 - - + +
95D LEU* 4.2 20.2 - - + -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.1 25.8 - - + -
33C VAL* 3.0 22.1 + - + +
34C TYR* 3.7 7.6 - - - +
36C ILE* 1.3 76.3 - - + +
38C LYS* 1.3 59.0 + - + +
40C GLU* 3.4 7.0 + - - +
41C SER* 2.9 24.9 + - - -
484C PHE* 3.4 35.8 - - + +
64D ALA* 4.3 10.3 - - + -
67D SER* 3.6 29.4 - - - +
68D SER* 3.8 4.9 + - - +
69D LEU* 3.8 23.6 - - + -
92D LEU* 6.2 0.9 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 2.8 55.1 + - + +
35C SER* 3.1 10.0 + - - +
37C ILE* 1.3 77.4 - - + +
39C LYS* 1.3 60.6 + - + +
41C SER* 3.2 5.4 + - - -
42C ASN* 2.9 30.0 + - - +
482C PRO 5.4 0.4 + - - -
483C ASP* 3.2 42.2 + - - +
484C PHE* 4.8 8.7 - - + +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C SER* 2.9 32.4 + - - +
36C ILE* 3.5 21.5 - - - +
38C LYS* 1.3 75.6 - - - +
40C GLU* 1.3 57.3 + - - +
42C ASN* 3.4 8.9 + - - +
43C ARG 3.1 20.3 + - - -
88D PHE* 3.4 38.7 - - + -
91D GLU* 3.3 31.0 + - - -
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 2.9 16.4 + - + +
37C ILE* 3.6 7.2 - - - +
39C LYS* 1.3 73.8 - - - +
41C SER* 1.3 65.8 + - - +
42C ASN 3.1 1.6 - - - -
43C ARG* 2.9 42.1 + - - +
44C GLN* 3.2 42.2 + - - +
68D SER* 4.2 4.7 - - - +
69D LEU* 4.3 20.6 - - + -
72D LYS* 4.6 4.7 - - + +
85D GLY 4.0 4.8 - - - +
88D PHE* 3.4 28.0 - - + +
89D ILE* 4.5 11.9 - - + +
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE 2.9 11.2 + - - -
38C LYS* 3.2 8.2 + - - -
40C GLU* 1.3 76.5 - - - +
42C ASN* 1.3 64.5 + - - +
44C GLN* 3.5 9.3 + - - +
45C ARG* 3.3 14.1 + - - +
478C LEU* 3.7 14.4 - - - +
483C ASP* 4.1 6.7 + - - -
484C PHE* 2.7 46.7 + - - -
68D SER* 3.8 8.4 + - - -
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Residues in contact with ASN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS 2.9 13.1 + - - +
39C LYS* 3.4 13.4 + - - +
41C SER* 1.3 75.2 - - - +
43C ARG* 1.3 59.1 + - - +
45C ARG* 2.7 61.0 + - - +
46C VAL* 3.1 18.9 + - - +
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Residues in contact with ARG 43 (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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39C LYS 3.1 12.2 + - - +
40C GLU* 2.9 44.2 + - - +
42C ASN* 1.3 82.9 - - - +
44C GLN* 1.3 71.8 + - - +
45C ARG 3.2 0.2 + - - -
46C VAL* 3.5 24.6 + - - +
47C GLY* 3.7 4.5 + - - -
49C GLU* 3.1 28.5 + - - -
54C GLU* 4.8 0.6 + - - -
383C ALA* 5.4 4.2 - - - +
72D LYS* 3.5 24.4 - - - +
84D GLY 5.0 0.2 + - - -
85D GLY* 3.2 33.1 + - - -
87D GLU* 5.9 1.3 - - - -
88D PHE* 4.0 17.7 - - + -
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Residues in contact with GLN 44 (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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40C GLU* 3.2 45.1 + - - +
41C SER* 3.7 7.4 - - - +
42C ASN 3.2 0.6 - - - -
43C ARG* 1.3 89.7 - - - +
45C ARG* 1.3 57.7 + - - +
47C GLY 3.8 6.3 - - - +
49C GLU* 5.0 7.6 - - - +
54C GLU* 6.1 0.2 - - - +
56C PHE* 3.4 40.8 - - + -
411C ARG* 2.9 20.4 + - - -
478C LEU* 4.1 9.2 - - + +
68D SER* 3.5 31.8 + - - +
69D LEU* 5.2 0.2 - - - +
71D ASN* 3.9 16.0 - - - +
72D LYS* 5.4 2.7 - - - +
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 3.3 6.7 + - - +
42C ASN* 2.7 47.9 + - - +
44C GLN* 1.3 73.5 - - - +
46C VAL* 1.3 89.4 + - - +
47C GLY 3.3 1.7 + - - -
411C ARG* 2.8 31.2 + - - +
473C ALA* 3.9 5.2 - - - +
474C SER* 3.5 25.0 + - - +
476C PHE 5.3 2.5 - - - +
478C LEU* 3.3 33.0 - - + -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASN* 3.5 27.6 - - - +
43C ARG* 3.6 8.8 - - - +
45C ARG* 1.3 108.4 - - - +
47C GLY* 1.3 56.5 + - - +
381C SER* 4.0 3.1 + - - -
470C GLU* 3.1 42.8 - - + +
473C ALA* 3.8 10.8 - - - -
474C SER* 3.6 13.5 - - - -
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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