Contacts of the helix formed by residues 2 - 13 (chain E) in PDB entry 5EJK
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 LEU 2 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E PRO* 1.3 87.3 - - + +
3E ARG* 1.3 61.5 + - + +
5E ALA* 3.4 2.9 + - - +
6E LYS* 2.9 45.5 + - - +
25E ILE* 4.2 13.2 - - + -
29E GLN* 3.5 46.9 - - + +
32E GLU* 6.5 0.9 - - - -
33E VAL* 5.3 7.4 - - + +
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Residues in contact with ARG 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E PRO* 3.4 1.2 - - - +
2E LEU* 1.3 77.4 - - + +
4E GLU* 1.3 67.9 + - + +
6E LYS* 3.2 15.2 + - + +
7E ASP* 2.9 31.6 + - - +
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Residues in contact with GLU 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E PRO* 3.5 25.2 + - + +
2E LEU 3.4 0.2 - - - -
3E ARG* 1.3 77.8 - - + +
5E ALA* 1.3 57.1 + - - +
7E ASP* 3.2 10.0 + - - +
8E LEU* 2.9 39.5 + - + +
23E SER* 5.2 7.6 - - - -
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Residues in contact with ALA 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E PRO 2.9 19.6 + - - +
2E LEU* 3.7 4.0 - - - +
4E GLU* 1.3 73.4 - - - +
6E LYS* 1.3 66.6 + - - +
8E LEU* 3.2 12.9 + - - +
9E HIS* 2.9 24.6 + - - +
19E LEU* 4.0 19.6 - - + +
23E SER* 4.1 6.7 + - - +
25E ILE* 3.5 19.7 - - + -
30E ALA* 6.5 0.4 - - - -
33E VAL* 4.8 10.1 - - + -
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Residues in contact with LYS 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D GLU* 3.3 41.0 + - - +
2E LEU* 2.9 37.8 + - - +
3E ARG* 3.2 13.7 + - + +
5E ALA* 1.3 77.1 - - - +
7E ASP* 1.3 59.1 + - - +
9E HIS* 3.3 1.9 + - - +
10E THR* 2.9 37.8 + - + +
32E GLU* 5.4 8.1 + - - -
33E VAL* 4.4 27.6 - - + -
36E THR* 6.0 2.2 - - - +
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Residues in contact with ASP 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ARG* 2.9 21.2 + - - +
4E GLU* 3.6 9.8 - - - +
6E LYS* 1.3 78.8 - - - +
8E LEU* 1.3 63.9 + - + +
10E THR* 2.3 29.8 + - - +
11E ALA* 3.0 10.7 + - - +
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Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 6.2 2.5 - - + -
114B ARG* 5.7 11.9 - - - +
4E GLU* 2.9 26.4 + - + +
5E ALA* 3.6 10.5 - - + +
7E ASP* 1.3 78.0 - - + +
9E HIS* 1.3 58.3 + - - +
11E ALA* 3.4 3.1 + - - +
12E LEU* 2.9 38.4 + - + +
13E HIS 3.6 1.2 + - - -
14E ILE* 4.5 12.2 - - + +
19E LEU* 3.8 24.7 - - + -
22E ALA* 5.8 6.5 - - + -
23E SER* 5.4 8.7 - - - -
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Residues in contact with HIS 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ALA 2.9 16.2 + - - +
6E LYS 3.9 3.4 - - - +
8E LEU* 1.3 74.1 - - - +
10E THR* 1.3 65.6 + - + +
13E HIS* 2.7 43.3 + - - +
14E ILE 2.8 29.9 + - - +
15E GLY* 5.3 0.4 - - - -
19E LEU* 4.0 7.7 - - + +
33E VAL* 3.9 20.6 - - + -
34E VAL* 4.0 19.7 - - + +
37E CYS* 3.5 28.8 - - + +
40E CYS* 3.0 36.8 - - + +
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Residues in contact with THR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LYS* 2.9 27.1 + - + +
7E ASP* 2.3 36.1 + - - +
9E HIS* 1.3 81.4 - - + +
11E ALA* 1.3 62.3 + - - +
13E HIS* 3.2 17.8 + - - -
37E CYS* 6.2 0.9 - - - -
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Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 3.3 21.5 - - - +
191A LYS* 4.4 12.5 + - - +
137B ARG* 6.2 4.0 - - + +
138B TRP* 5.5 10.5 - - + -
7E ASP 3.0 9.5 + - - +
8E LEU* 4.1 2.7 - - - +
10E THR* 1.3 83.8 + - - +
12E LEU* 1.3 69.9 + - + +
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 4.3 7.4 - - - +
170A LEU* 4.3 4.5 - - + +
191A LYS* 3.9 29.2 - - + +
194A TYR* 3.7 19.7 - - + -
195A ALA* 3.8 20.0 - - + +
199A PHE* 3.6 32.8 - - + -
114B ARG* 5.5 2.0 - - - +
138B TRP* 4.1 20.9 - - + -
8E LEU* 2.9 18.1 + - + +
11E ALA* 1.3 81.6 - - + +
13E HIS* 1.3 71.0 + - - +
14E ILE* 3.4 21.9 + - + -
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Residues in contact with HIS 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 3.2 24.1 + - + +
169A VAL* 3.3 31.3 + - + +
170A LEU* 3.5 25.0 - - + +
173A GLY* 4.6 11.5 - - - -
9E HIS* 2.7 43.0 + - - -
10E THR* 3.2 20.3 + - - -
12E LEU* 1.3 73.1 - - - +
14E ILE* 1.3 65.3 + - - +
15E GLY* 3.6 0.7 + - - -
37E CYS* 3.8 18.8 - - - -
39E HIS* 4.7 8.1 - + + -
40E CYS* 3.1 29.1 - - - -
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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