Contacts of the helix formed by residues 51 - 61 (chain E) in PDB entry 4F2N
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 SER 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E GLY* 3.7 4.2 - - - -
49E VAL 4.1 0.2 + - - -
50E MET* 1.3 76.7 - - - +
52E PRO* 1.3 75.5 - - - +
53E ARG* 3.6 7.3 + - - +
54E GLN 3.1 14.9 + - - -
55E LEU 3.1 18.2 + - - -
199E LYS* 4.3 1.6 - - - +
200E ASP* 2.6 34.4 + - - -
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Residues in contact with PRO 52 (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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42E TYR 4.8 2.4 - - - +
43E LYS* 3.4 23.0 - - - +
44E ASP* 4.0 13.0 - - - +
45E GLY* 3.6 14.4 + - - +
50E MET 4.5 0.7 - - - +
51E SER* 1.3 88.6 - - - +
53E ARG* 1.3 56.5 + - - +
55E LEU* 3.4 1.7 + - - +
56E GLU* 2.9 30.7 + - - +
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Residues in contact with ARG 53 (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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51E SER* 3.3 6.3 + - - +
52E PRO* 1.3 76.6 - - - +
54E GLN* 1.3 61.2 + - - +
56E GLU* 2.9 36.5 + - - +
57E LEU* 2.9 46.9 + - + +
61E LYS* 5.3 10.3 - - - +
199E LYS* 3.7 29.2 - - - +
202F GLU* 2.7 35.5 + - - +
203F ASN* 5.3 0.8 + - - -
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E MET* 4.2 14.6 - - + -
51E SER* 3.1 13.5 + - - +
53E ARG* 1.3 77.7 - - - +
55E LEU* 1.3 61.6 + - - +
57E LEU* 3.8 6.2 - - - +
58E HIS* 3.1 23.8 + - + +
195E HIS 2.8 26.3 + - - -
196E ALA* 3.3 17.6 + - - +
197E TYR* 3.2 13.5 - - - -
199E LYS* 3.1 36.8 + - + +
200E ASP* 3.2 33.5 + - - +
198F TYR* 4.9 2.0 + - - -
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Residues in contact with LEU 55 (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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38E LEU* 4.4 5.8 - - + -
40E PHE* 3.9 17.0 - - + -
42E TYR* 3.8 25.6 - - - +
45E GLY* 3.7 33.7 - - - +
46E ILE* 4.0 10.3 - - + +
50E MET* 5.0 6.7 - - + +
51E SER 3.1 15.4 + - - +
52E PRO 4.0 2.7 - - - +
54E GLN* 1.3 74.7 - - - +
56E GLU* 1.3 60.2 + - - +
58E HIS* 3.1 2.5 + - - -
59E TYR* 2.8 40.4 + - + +
112E TRP* 3.6 36.6 - - + -
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Residues in contact with GLU 56 (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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42E TYR* 4.6 15.8 + - + +
43E LYS* 6.0 4.4 - - - +
52E PRO 2.9 19.0 + - - +
53E ARG* 2.9 40.8 + - - +
55E LEU* 1.3 78.2 - - - +
57E LEU* 1.3 57.8 + - - +
59E TYR* 5.1 0.7 - - - -
60E SER* 2.8 50.3 + - - +
61E LYS* 3.5 5.2 + - + +
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Residues in contact with LEU 57 (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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53E ARG* 2.9 47.7 + - + +
54E GLN* 3.8 6.1 - - - +
56E GLU* 1.3 74.8 - - - +
58E HIS* 1.3 60.5 + - - +
61E LYS* 3.0 20.7 + - + +
62E HIS* 2.9 27.0 + - - -
199E LYS* 3.8 19.5 - - + +
198F TYR* 3.8 26.2 - - + +
202F GLU* 3.5 30.5 - - + +
203F ASN* 3.5 25.6 - - - +
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Residues in contact with HIS 58 (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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50E MET* 5.3 4.4 - - - +
54E GLN* 3.1 18.9 + - - +
55E LEU* 3.1 5.0 + - - +
57E LEU* 1.3 82.5 - - - +
59E TYR* 1.3 53.3 + - - +
62E HIS* 3.3 8.3 - - + +
63E HIS* 2.8 31.5 + - - +
108E HIS* 3.1 20.6 + + - -
111E PHE* 3.9 16.9 - + - -
112E TRP* 3.5 20.1 - + + -
191E ASP* 2.8 30.3 + - - -
195E HIS* 3.2 22.1 + + - +
196E ALA* 3.6 29.9 + - + -
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Residues in contact with TYR 59 (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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35E LEU* 3.5 42.4 + - + +
36E PRO* 2.5 35.4 + - + -
37E THR* 4.6 2.1 - - - -
38E LEU* 3.7 24.8 + - + +
42E TYR* 3.9 37.0 - + + -
55E LEU* 2.8 23.5 + - + +
56E GLU* 5.9 0.2 - - - -
58E HIS* 1.3 77.6 - - - +
60E SER* 1.3 70.3 + - - +
61E LYS 3.3 0.2 - - - -
63E HIS* 3.4 4.9 - - - +
64E SER 3.1 24.6 + - - -
112E TRP* 3.6 28.9 - - + -
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 4.9 3.9 - - - +
42E TYR* 3.9 19.1 - - - -
56E GLU* 2.8 31.8 + - - +
59E TYR* 1.3 87.9 - - - +
61E LYS* 1.3 70.9 + - - +
64E SER* 3.1 19.9 + - - -
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Residues in contact with LYS 61 (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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53E ARG* 5.3 11.7 - - - +
56E GLU* 4.3 4.9 - - - +
57E LEU* 3.0 26.0 + - + +
60E SER* 1.3 89.0 + - - +
62E HIS* 1.3 67.7 + - - +
63E HIS 3.6 0.2 - - - -
64E SER* 4.0 0.4 - - - -
65E ALA* 3.1 25.6 + - - +
203F ASN* 3.9 39.7 - - + +
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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
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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