Contacts of the helix formed by residues 13 - 32 (chain L) in PDB entry 3E8E
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 GLU 13 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L SER* 1.3 74.1 + - - +
15L VAL* 3.4 6.1 - - - +
16L LYS* 3.2 19.5 + - - +
17L GLU* 2.9 35.3 + - - +
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Residues in contact with SER 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLU* 1.3 81.9 - - - +
15L VAL* 1.3 67.3 + - - +
17L GLU* 3.0 20.4 + - - +
18L PHE* 2.9 23.7 + - - +
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Residues in contact with VAL 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLU 5.2 3.6 - - - +
14L SER* 1.3 77.0 - - - +
16L LYS* 1.3 54.3 + - - +
18L PHE* 3.1 5.2 + - - +
19L LEU* 2.8 64.7 + - + +
155L GLU* 3.6 21.5 - - - +
292L LYS* 4.9 11.7 - - - +
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Residues in contact with LYS 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLU* 3.2 18.7 + - - +
14L SER 3.1 0.4 - - - -
15L VAL* 1.3 79.9 - - - +
17L GLU* 1.3 60.9 + - + +
19L LEU* 4.5 4.6 - - - +
20L ALA* 3.4 23.7 + - - +
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLU* 2.9 40.1 + - - +
14L SER* 3.0 18.2 + - - +
16L LYS* 1.3 77.6 - - + +
18L PHE* 1.3 62.2 + - - +
20L ALA* 4.0 3.7 - - - +
21L LYS* 3.4 27.0 + - - +
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Residues in contact with PHE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L SER 2.9 12.6 + - - +
15L VAL* 3.6 9.6 - - - +
17L GLU* 1.3 75.8 - - - +
19L LEU* 1.3 76.1 + - + +
21L LYS* 3.2 9.4 + - + +
22L ALA* 2.9 41.1 + - + +
99L ASN 5.7 2.5 - - - -
100L PHE* 4.4 22.2 - + - -
156L TYR* 4.9 5.2 - + - -
306L TYR* 3.1 36.1 - + - -
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L VAL* 2.8 54.5 + - + +
16L LYS* 4.5 4.9 - - - +
18L PHE* 1.3 88.8 - - + +
20L ALA* 1.3 58.0 + - - +
22L ALA* 3.4 7.4 + - - +
23L LYS* 2.9 31.3 + - - +
155L GLU* 4.6 17.3 - - + +
156L TYR* 5.7 7.4 - - + -
159L SER* 3.7 35.3 + - - +
160L LEU* 5.2 1.2 - - - +
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Residues in contact with ALA 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LYS 3.4 19.3 + - - +
17L GLU* 4.0 5.8 - - - +
18L PHE 3.2 0.2 - - - -
19L LEU* 1.3 77.4 - - - +
21L LYS* 1.3 63.6 + - + +
23L LYS* 3.6 6.9 + - - +
24L GLU* 3.3 32.0 + - - +
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Residues in contact with LYS 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLU 3.4 13.8 + - - +
18L PHE* 3.2 14.5 + - + +
20L ALA* 1.3 79.5 - - + +
22L ALA* 1.3 62.1 + - - +
24L GLU* 3.5 18.6 + - - +
25L ASP* 3.3 20.6 + - - +
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Residues in contact with ALA 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE* 2.9 28.7 + - + +
19L LEU* 3.7 8.7 - - - +
21L LYS* 1.3 75.9 - - - +
23L LYS* 1.3 59.8 + - - +
25L ASP* 3.3 6.4 + - - +
26L PHE* 2.9 29.6 + - - +
156L TYR* 4.1 28.8 + - + +
159L SER* 6.1 0.7 - - - +
160L LEU* 4.4 4.3 - - + +
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LEU 2.9 18.1 + - - +
20L ALA* 3.9 7.6 - - - +
22L ALA* 1.3 72.2 - - - +
24L GLU* 1.3 65.4 - - - +
26L PHE* 3.5 1.3 + - + +
27L LEU* 3.1 43.0 + - + +
159L SER 3.8 21.3 - - - +
160L LEU* 3.5 22.4 - - + +
161L ASP* 4.4 10.5 + - - -
190L ARG* 4.4 4.7 - - - +
192L LYS* 4.8 2.4 - - - +
31P GLU* 3.4 32.1 + - - +
32P ASN* 4.8 4.8 + - - +
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Residues in contact with GLU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L ALA* 3.3 21.1 + - - +
21L LYS* 3.6 19.6 - - - +
23L LYS* 1.3 79.1 - - - +
25L ASP* 1.3 61.6 + - - +
27L LEU* 3.3 6.7 + - - +
28L LYS* 3.1 39.3 + - - +
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Residues in contact with ASP 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L LYS 3.3 9.3 + - - +
22L ALA* 3.3 9.7 + - - +
24L GLU* 1.3 76.5 - - - +
26L PHE* 1.3 65.4 + - - +
28L LYS* 3.6 17.0 + - - +
29L LYS* 3.1 53.5 + - - +
97L ALA 4.8 1.7 - - - +
99L ASN* 4.7 13.2 + - - +
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Residues in contact with PHE 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ALA 2.9 18.0 + - - +
23L LYS 3.8 2.5 - - - +
25L ASP* 1.3 76.8 + - - +
27L LEU* 1.3 62.1 + - + +
29L LYS* 3.2 3.8 + - - +
30L TRP* 2.7 73.3 + + + +
94L ILE* 4.6 1.6 - - - -
97L ALA* 3.4 43.3 - - + +
98L VAL* 4.2 6.3 - - + -
156L TYR* 5.1 2.5 - - - +
160L LEU* 3.8 35.9 - - + -
162L LEU* 3.9 23.1 - - + -
190L ARG* 3.5 33.4 - - - -
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Residues in contact with LEU 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L LYS* 3.1 37.4 + - + +
24L GLU* 3.3 6.0 + - - +
26L PHE* 1.3 91.5 - - + +
28L LYS* 1.3 60.5 + - - +
30L TRP* 3.7 11.0 - - + +
31L GLU* 2.9 32.6 + - - +
190L ARG* 4.0 13.2 - - - +
31P GLU* 3.4 42.4 - - + +
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Residues in contact with LYS 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLU* 3.1 29.2 + - - +
25L ASP* 3.7 20.0 + - - +
26L PHE 3.3 0.2 - - - -
27L LEU* 1.3 76.6 - - - +
29L LYS* 1.3 60.1 + - + +
31L GLU* 4.6 2.2 - - - -
32L ASN* 3.0 39.2 + - - +
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Residues in contact with LYS 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ASP* 3.1 40.3 + - - +
26L PHE 3.2 4.2 + - - +
28L LYS* 1.3 76.2 - - + +
30L TRP* 1.3 65.4 + - - +
32L ASN* 3.2 23.3 - - - +
33L PRO* 3.2 0.9 - - - +
96L GLN* 3.1 40.1 + - - +
97L ALA* 3.7 27.7 + - - +
98L VAL 4.9 2.6 + - - -
99L ASN* 4.6 12.7 - - - +
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Residues in contact with TRP 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PHE* 2.7 54.0 + + + +
27L LEU* 3.7 21.8 - - + +
29L LYS* 1.3 75.4 - - - +
31L GLU* 1.3 64.1 + - + +
33L PRO* 3.6 6.1 - - - +
90L ASN* 5.7 5.4 - - - -
93L ARG* 3.1 92.5 + - + +
94L ILE* 3.7 26.9 - - + -
96L GLN* 4.1 3.8 - - - +
97L ALA* 3.9 1.2 - - - +
190L ARG* 3.6 43.4 - - + +
93P ARG* 6.1 1.0 - - - +
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Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L LEU 2.9 18.0 + - - +
28L LYS* 3.7 4.3 - - - +
30L TRP* 1.3 81.6 - - + +
32L ASN* 1.3 71.1 + - - +
33L PRO* 3.2 8.9 - - - +
93L ARG* 5.1 1.9 + - - +
23P LYS* 3.2 19.7 + - - +
27P LEU* 3.4 24.1 - - + +
30P TRP* 5.4 1.4 - - - -
190P ARG* 3.1 31.6 + - - -
192P LYS* 2.7 41.2 + - - -
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Residues in contact with ASN 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L LYS* 3.0 25.1 + - - +
29L LYS* 3.2 12.3 - - - +
31L GLU* 1.3 91.5 - - - +
33L PRO* 1.3 66.9 - - - +
34L ALA 3.8 0.5 + - - -
96L GLN* 4.4 0.5 - - - +
23P LYS* 4.7 5.6 + - - +
192P LYS* 3.7 17.7 + - - +
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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