Contacts of the helix formed by residues 24 - 36 (chain B) in PDB entry 3E0D
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 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLN* 4.1 12.6 - - - +
22B ALA 3.4 4.8 + - - +
23B ALA* 1.3 71.2 - - - +
25B LEU* 1.3 66.0 + - - +
26B GLN* 3.2 4.0 + - + +
27B ASP* 3.5 27.6 + - - +
28B LEU* 3.1 25.5 + - - +
563B MET 5.8 0.2 + - - -
564B ARG 4.2 16.3 + - - -
565B LEU* 4.4 1.1 - - - +
566B GLU 4.4 0.2 - - - +
567B GLY* 3.0 53.8 - - - +
568B LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.8 31.6 - - + +
15B GLN* 3.2 18.6 - - - +
16B PHE* 3.9 18.6 - - + -
23B ALA 3.6 1.6 + - - -
24B LYS* 1.3 71.7 - - - +
26B GLN* 1.3 61.3 + - - +
28B LEU* 4.1 4.8 - - + +
29B LEU* 3.2 33.2 + - + +
44B MET* 5.5 0.7 - - + -
52B GLY 4.8 0.2 - - - +
55B GLU* 3.4 36.3 - - + +
56B PHE* 3.7 48.9 - - + +
59B LYS* 4.6 9.2 - - + +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 3.2 3.2 - - + +
25B LEU* 1.3 76.0 - - - +
27B ASP* 1.3 61.9 + - + +
28B LEU 3.1 1.8 - - - -
29B LEU* 3.0 21.3 + - - +
30B LYS* 3.2 28.7 + - - +
59B LYS* 4.4 29.8 - - - +
63B MET* 4.2 28.0 - - - +
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 3.5 30.4 + - - +
26B GLN* 1.3 78.1 - - + +
28B LEU* 1.3 63.5 + - - +
30B LYS* 3.4 25.8 - - + +
31B TRP* 3.2 24.1 + - - +
216B VAL* 3.4 22.7 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 4.1 19.3 - - + +
14B THR* 4.0 25.8 - - + -
23B ALA* 4.2 9.6 - - + +
24B LYS 3.1 15.9 + - - +
25B LEU* 4.1 7.4 - - - +
26B GLN 3.1 0.8 - - - -
27B ASP* 1.3 81.3 + - - +
29B LEU* 1.3 58.9 + - + +
31B TRP* 3.3 2.9 + - - +
32B VAL* 3.1 30.1 + - + +
42B LEU* 3.8 25.4 - - + -
56B PHE* 5.0 2.9 - - + -
216B VAL* 3.9 20.0 - - + -
251B VAL* 3.5 31.6 - - + -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.2 20.4 + - + +
26B GLN* 3.0 8.2 + - - +
28B LEU* 1.3 79.3 - - + +
30B LYS* 1.3 58.6 + - - +
32B VAL* 3.8 2.9 + - - +
33B LYS* 3.2 24.6 + - - +
42B LEU* 3.8 23.8 - - + -
56B PHE* 4.0 18.2 - - + +
59B LYS* 3.9 15.7 - - + +
60B ALA* 3.5 46.0 - - + +
63B MET* 4.2 13.9 - - - +
65B VAL* 3.8 25.1 - - + +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN* 3.2 27.9 + - - +
27B ASP* 3.4 32.7 - - + +
29B LEU* 1.3 75.0 - - - +
31B TRP* 1.3 58.9 + - + +
33B LYS* 3.2 7.1 + - + +
34B GLU* 2.7 62.7 + - + +
63B MET* 4.3 19.2 - - + -
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Residues in contact with TRP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP 3.2 19.7 + - - +
28B LEU 3.3 2.9 + - - +
30B LYS* 1.3 75.9 - - + +
32B VAL* 1.3 62.6 - - - +
34B GLU* 4.0 17.0 - - + -
35B THR* 2.6 50.7 + - + +
216B VAL* 3.7 21.8 + - + -
217B ARG* 3.7 42.5 - - + +
251B VAL* 3.0 47.5 + - + +
252B LYS 5.6 0.2 - - - -
253B THR* 5.5 7.2 - - - -
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS* 5.5 1.8 - - - +
28B LEU* 3.1 17.2 + - + +
29B LEU* 4.0 6.3 - - - +
30B LYS 3.3 0.2 - - - -
31B TRP* 1.3 77.9 - - - +
33B LYS* 1.3 56.7 + - - +
35B THR* 3.5 3.3 + - - -
36B THR* 3.0 32.7 + - - +
40B PRO* 4.2 15.9 - - + -
41B ALA 4.0 20.4 - - - +
42B LEU* 4.0 30.3 - - + -
65B VAL* 4.4 11.9 - - + -
251B VAL* 4.1 21.3 - - + -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LYS* 5.5 3.5 - - - +
291A MET 4.6 9.8 - - - -
292A VAL* 3.5 26.7 - - - +
29B LEU 3.2 16.4 + - - +
30B LYS* 3.2 10.0 + - - +
32B VAL* 1.3 81.3 - - - +
34B GLU* 1.3 63.2 + - + +
36B THR 3.4 19.7 - - - +
37B PRO* 3.5 32.8 + - - +
40B PRO* 4.1 22.0 - - + +
63B MET* 4.0 29.0 + - + +
64B GLY* 4.8 5.8 + - - +
65B VAL* 4.2 6.3 - - + -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.7 52.6 + - + +
31B TRP* 3.9 20.1 + - + +
33B LYS* 1.3 74.7 - - + +
35B THR* 1.3 64.7 + - - +
37B PRO* 4.6 6.6 - - - +
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TRP* 2.6 47.7 + - + -
32B VAL* 4.0 3.8 - - - -
34B GLU* 1.3 80.0 - - - +
36B THR* 1.3 63.2 + - - +
37B PRO* 3.3 9.8 - - - +
251B VAL* 6.5 0.7 - - - -
252B LYS 5.0 2.9 - - - +
253B THR* 3.8 33.0 - - + +
254B PRO* 3.9 15.9 - - + -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LYS* 4.4 23.1 - - + -
7B PHE 3.8 17.8 + - - +
32B VAL* 3.0 12.9 + - - +
33B LYS 3.4 7.5 - - - +
35B THR* 1.3 84.3 + - - +
37B PRO* 1.3 65.7 - - + +
38B GLU* 3.5 25.1 - - + +
40B PRO* 3.3 27.1 - - + +
254B PRO* 4.7 7.2 - - + +
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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