Contacts of the helix formed by residues 3 - 16 (chain F) in PDB entry 2EHO
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 CYS 3 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0F MSE 3.4 9.3 + - - -
1F MSE 3.3 1.6 - - - -
2F PHE* 1.3 81.9 - - - +
4F GLU* 1.3 64.1 + - - +
5F LYS 3.2 3.8 + - - +
6F ALA* 3.4 7.2 + - + +
7F MSE 3.3 21.6 + - + +
35F GLU* 4.4 4.9 - - - -
68F SER* 3.4 24.9 - - - -
71F ARG* 3.4 24.9 - - + -
72F ASN* 3.2 42.0 - - - +
75F CYS* 5.7 0.2 - - - -
71H TRP* 3.9 6.3 - - + -
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Residues in contact with GLU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 4.2 11.3 - - - +
2F PHE* 2.9 19.4 + - + +
3F CYS* 1.3 77.5 - - - +
5F LYS* 1.3 61.7 + - - +
7F MSE 3.5 5.0 - - - +
8F GLU* 3.4 21.4 + - - +
11F ARG* 3.8 15.9 + - - -
1004F SO4 5.8 1.1 - - - +
29H HIS* 3.1 34.0 + - - -
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Residues in contact with LYS 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 5.2 0.8 - - - +
3F CYS* 3.2 1.0 - - - +
4F GLU* 1.3 75.4 - - - +
6F ALA* 1.3 65.0 + - - +
7F MSE 3.1 1.8 - - - -
8F GLU* 2.6 56.8 + - - +
9F LEU* 3.4 6.6 + - - +
27F ASP* 5.6 0.6 - - - +
28F GLY* 3.8 22.1 - - - +
31F GLN* 3.5 45.4 + - + +
32F VAL* 4.0 19.6 - - + +
35F GLU* 4.2 21.6 + - - +
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Residues in contact with ALA 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F CYS* 3.4 9.4 + - + +
4F GLU 3.4 0.4 - - - -
5F LYS* 1.3 79.0 - - - +
7F MSE 1.3 57.2 + - - +
9F LEU* 2.9 29.1 + - + +
10F ILE* 3.1 10.6 + - - +
32F VAL* 3.9 20.0 - - + +
72F ASN* 3.7 22.8 + - - +
75F CYS* 3.6 30.0 - - + +
76F THR 5.3 0.4 - - - +
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Residues in contact with MSE 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PHE 4.8 0.4 - - - +
3F CYS* 3.3 10.2 + - + +
4F GLU* 3.5 12.1 - - - +
5F LYS 3.1 0.2 - - - -
6F ALA* 1.3 80.7 - - - +
8F GLU* 1.3 58.0 + - - +
10F ILE* 3.8 5.6 - - + +
11F ARG* 3.0 46.5 + - - +
71F ARG* 2.9 31.0 - - - +
75F CYS* 3.1 27.6 - - - -
25H ILE* 3.4 26.2 - - + +
26H LEU* 4.0 19.3 - - - -
29H HIS* 3.4 37.5 - - + +
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Residues in contact with GLU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F GLU* 3.4 9.7 + - - +
5F LYS* 2.6 63.0 + - + +
7F MSE 1.3 76.6 - - - +
9F LEU* 1.3 62.5 + - + +
11F ARG* 3.8 18.0 - - - +
12F GLU* 3.0 30.5 + - - +
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LYS* 3.4 7.4 + - - +
6F ALA* 2.9 13.6 + - + +
8F GLU* 1.3 81.1 - - + +
10F ILE* 1.3 67.3 + - + +
12F GLU* 3.3 11.7 + - - +
13F LEU 3.4 7.6 + - - -
25F ASN* 3.2 39.5 - - - +
28F GLY* 3.8 19.1 - - - -
29F LEU* 4.3 11.0 - - + +
32F VAL* 4.1 23.8 - - + -
75F CYS* 5.6 0.7 - - + +
76F THR* 5.1 7.9 - - - -
79F TYR* 3.7 47.7 - - + -
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ALA 3.1 10.9 + - - +
7F MSE 3.8 11.4 - - + +
9F LEU* 1.3 81.1 - - + +
11F ARG* 1.3 64.4 + - - +
13F LEU* 3.1 9.9 + - - +
14F HIS* 3.1 18.0 + - - +
75F CYS* 3.5 28.0 - - + +
78F ALA* 4.2 0.4 - - + -
79F TYR* 3.9 11.2 - - + +
22H LEU* 3.7 32.5 - - + +
25H ILE* 3.2 43.5 - - + -
26H LEU* 4.1 20.6 - - + -
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Residues in contact with ARG 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F GLU* 3.8 14.5 + - - -
7F MSE 3.0 44.7 + - - +
8F GLU* 3.8 29.9 - - - +
10F ILE* 1.3 79.3 - - - +
12F GLU* 1.3 56.4 + - - +
14F HIS* 3.1 7.1 + - + +
15F ARG* 2.8 74.1 + - + +
26H LEU* 4.6 19.9 - - + +
29H HIS* 4.0 11.1 + - - -
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Residues in contact with GLU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 4.5 16.4 - - - +
11B ARG* 6.1 1.0 - - - -
15B ARG* 4.5 14.1 + - - +
8F GLU 3.0 19.2 + - - +
9F LEU* 3.6 7.0 - - - +
10F ILE 3.3 0.2 - - - -
11F ARG* 1.3 75.1 - - - +
13F LEU* 1.3 61.5 + - + +
15F ARG* 3.8 2.4 + - - +
16F ALA* 3.4 20.3 + - - +
22F PRO* 4.3 23.2 - - + +
23F ALA 4.7 6.3 + - - +
25F ASN* 3.3 32.1 + - - +
79F TYR* 4.3 6.8 + - - -
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU 3.4 4.5 + - - +
10F ILE* 3.1 10.0 + - - +
12F GLU* 1.3 77.8 - - + +
14F HIS* 1.3 65.0 + - - +
16F ALA* 3.2 12.7 + - - +
21F LEU* 6.1 0.2 - - + -
22F PRO* 3.7 28.5 - - + -
79F TYR* 3.4 57.0 - - + +
82F ASP* 3.7 30.3 - - + +
83F ARG* 4.1 12.6 - - + +
86F ARG* 2.9 28.4 + - - +
22H LEU* 4.0 9.2 - - + -
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Residues in contact with HIS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE 3.1 11.5 + - - +
11F ARG* 3.1 9.4 + - + +
13F LEU* 1.3 74.1 - - - +
15F ARG* 1.3 66.3 + - + +
16F ALA 3.0 12.3 + - - +
17F PRO* 5.2 0.7 - - - +
86F ARG* 4.7 1.7 + - - +
22H LEU* 4.3 20.1 - - + +
23H ASP* 3.0 29.1 + - - -
26H LEU* 3.7 30.8 - - + +
115H HIS* 5.8 1.4 + - - -
170H GLU* 5.0 12.9 + - + +
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Residues in contact with ARG 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 4.1 24.9 - - - +
8B GLU* 3.3 45.9 - - + +
11F ARG* 2.8 56.4 + - + +
12F GLU* 4.2 1.8 - - - +
14F HIS* 1.3 77.1 - - + +
16F ALA* 1.3 56.9 + - - +
17F PRO* 3.0 16.5 - - - +
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Residues in contact with ALA 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 6.3 0.2 - - - -
15B ARG* 4.9 7.2 - - - +
12F GLU 3.4 13.1 + - - +
13F LEU 3.2 16.3 + - - +
14F HIS 3.0 6.5 - - - +
15F ARG* 1.3 75.9 - - - +
17F PRO* 1.3 71.8 - - + +
18F GLU 3.4 1.6 + - - -
20F GLN* 4.1 6.7 - - + +
22F PRO* 3.9 20.9 - - + -
86F ARG* 3.2 25.1 + - - +
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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