Contacts of the helix formed by residues 47 - 61 (chain D) in PDB entry 2E9X
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 LYS 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ALA* 4.6 11.2 - - + -
44D LEU* 6.4 0.7 - - - -
45D GLU* 3.6 24.2 + - + +
46D SER* 1.3 80.7 + - - +
48D PRO* 1.3 65.2 - - - +
49D GLU* 3.3 2.9 - - - -
50D ILE* 3.1 41.2 + - + -
51D VAL* 3.1 18.9 + - - +
92D TYR* 3.5 26.5 + - + +
96D ARG* 5.4 0.4 - - - +
216D ALA* 4.4 15.0 + - - +
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Residues in contact with PRO 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.3 22.9 - - - +
47D LYS* 1.3 88.1 - - - +
49D GLU* 1.3 73.7 + - + +
50D ILE 3.0 0.3 + - - -
51D VAL* 3.3 4.7 + - + +
52D GLU* 2.9 49.2 + - + +
123D SER* 5.4 6.7 - - - -
124D PRO* 5.9 2.7 - - + -
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 6.3 2.5 - - + -
26D LEU* 4.3 2.1 - - - +
47D LYS 3.3 0.9 - - - -
48D PRO* 1.3 84.4 - - + +
50D ILE* 1.3 62.3 + - + +
52D GLU* 5.1 4.8 - - - +
53D CYS* 3.1 39.6 + - - +
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Residues in contact with ILE 50 (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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21D LEU* 5.9 1.3 - - + -
26D LEU* 4.0 13.7 - - + -
29D ARG* 3.8 40.6 - - + +
30D LEU* 3.9 36.3 - - + +
33D ALA* 4.8 3.4 - - + -
47D LYS* 3.1 38.5 + - + +
48D PRO 3.1 0.6 - - - -
49D GLU* 1.3 79.2 - - + +
51D VAL* 1.3 69.8 + - + +
53D CYS* 3.4 1.0 + - - +
54D VAL* 2.9 36.5 + - + +
92D TYR* 5.7 2.2 - - + -
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Residues in contact with VAL 51 (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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128A LEU* 5.1 13.0 - - + +
47D LYS 3.1 18.2 + - - +
48D PRO* 4.1 3.8 - - + +
50D ILE* 1.3 76.3 - - + +
52D GLU* 1.3 62.5 + - + +
54D VAL* 3.8 1.6 - - - +
55D MET* 2.9 46.2 + - + +
89D LEU* 4.3 20.3 - - + +
92D TYR* 4.2 24.0 - - + -
93D LEU* 4.4 23.8 - - + -
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 5.7 5.4 - - - +
48D PRO* 2.9 38.5 + - + +
49D GLU* 4.5 5.4 - - - +
51D VAL* 1.3 78.3 - - + +
53D CYS* 1.3 58.7 + - - +
55D MET* 3.2 8.5 + - - +
56D GLU* 3.0 27.9 + - - +
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Residues in contact with CYS 53 (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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21D LEU* 6.6 0.2 - - - -
26D LEU* 3.5 23.3 - - + -
49D GLU* 3.1 29.5 + - - +
52D GLU* 1.3 78.0 - - - +
54D VAL* 1.3 60.7 + - - +
56D GLU* 3.4 12.8 + - - +
57D GLN* 3.0 31.4 + - - +
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Residues in contact with VAL 54 (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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26D LEU* 3.7 25.8 - - + -
27D ILE* 4.4 6.3 - - + -
30D LEU* 4.2 18.8 - - + -
50D ILE* 2.9 34.0 + - + +
51D VAL 3.8 3.1 - - - +
53D CYS* 1.3 73.8 - - - +
55D MET* 1.3 67.5 + - - +
57D GLN* 3.3 5.6 + - + +
58D LEU* 2.9 23.9 + - + +
85D ILE* 3.6 29.6 - - + -
89D LEU* 4.0 20.2 - - + -
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Residues in contact with MET 55 (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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128A LEU* 4.1 15.7 - - - +
129A GLY* 4.1 24.9 - - - -
133A GLY 4.8 2.5 - - - +
134A LEU* 4.0 26.5 - - + -
51D VAL* 2.9 31.8 + - + +
52D GLU* 3.4 8.1 - - - +
54D VAL* 1.3 78.6 - - - +
56D GLU* 1.3 62.1 + - - +
58D LEU* 3.2 23.9 + - + +
59D GLU* 3.0 37.9 + - + +
86D ARG* 5.2 0.9 - - - +
89D LEU* 3.3 28.7 - - + -
93D LEU* 6.0 0.4 - - - -
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Residues in contact with GLU 56 (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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52D GLU 3.0 12.9 + - - +
53D CYS* 3.6 14.0 - - - +
54D VAL 3.2 0.2 - - - -
55D MET* 1.3 74.3 - - - +
57D GLN* 1.3 57.2 + - + +
59D GLU* 2.9 10.7 + - + +
60D HIS* 2.7 67.9 + - + +
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Residues in contact with GLN 57 (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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29B ILE* 3.5 35.9 - - + +
23D PRO* 3.6 29.1 - - + +
26D LEU* 4.2 15.0 - - + +
27D ILE* 5.9 2.9 - - + -
53D CYS 3.0 18.3 + - - +
54D VAL* 3.5 10.8 - - + +
56D GLU* 1.3 76.4 - - + +
58D LEU* 1.3 63.9 + - + +
60D HIS* 3.4 13.6 + - + +
61D MET* 3.1 28.3 + - - +
85D ILE* 6.2 0.9 - - + -
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Residues in contact with LEU 58 (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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134A LEU* 5.6 0.9 - - + -
29B ILE* 5.8 1.1 - - + -
54D VAL 2.9 15.3 + - - +
55D MET* 3.5 35.2 - - + +
57D GLN* 1.3 78.9 - - + +
59D GLU* 1.3 61.6 + - + +
61D MET* 3.5 2.7 + - - -
62D GLU* 2.9 28.7 + - - +
82D MET* 3.6 34.7 - - + +
85D ILE* 3.7 30.5 - - + -
86D ARG* 3.8 41.3 - - + +
89D LEU* 4.4 6.5 - - + -
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Residues in contact with GLU 59 (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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129A GLY* 4.0 6.6 - - - -
130A GLY* 3.1 34.8 + - - -
131A ASP* 4.3 13.1 + - - +
55D MET* 3.0 23.7 + - + +
56D GLU* 2.9 11.7 + - + +
58D LEU* 1.3 75.2 - - + +
60D HIS* 1.3 65.1 + - + +
62D GLU* 3.0 29.7 + - + +
63D GLU* 3.5 10.6 + - - +
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Residues in contact with HIS 60 (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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56D GLU* 2.7 59.8 + - + +
57D GLN* 3.8 15.9 - - - +
59D GLU* 1.3 74.4 - - + +
61D MET* 1.3 60.1 + - - +
62D GLU 3.1 0.4 - - - -
63D GLU* 3.0 40.0 + - - +
64D ASN* 4.2 3.3 + - - -
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Residues in contact with MET 61 (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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27B TYR 4.9 2.5 - - - +
29B ILE* 4.3 26.9 - - + -
57D GLN* 3.1 21.2 + - - +
58D LEU 4.0 0.7 - - - +
59D GLU 3.2 0.2 - - - -
60D HIS* 1.3 75.8 - - - +
62D GLU* 1.3 57.3 + - - +
63D GLU 3.2 3.8 - - - -
64D ASN* 3.1 31.7 + - - +
78D HIS* 3.5 48.9 - - + +
81D GLU* 5.0 2.2 - - - +
82D MET* 3.4 41.5 - - + +
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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