Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 4FJV
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 ASN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A HIS* 3.6 10.2 + - + +
23A PRO 3.7 0.2 - - - -
24A GLU* 1.3 78.6 - - - +
26A ARG* 1.3 62.6 + - - +
27A ILE* 3.0 16.9 + - - +
28A TYR* 2.6 59.8 + - + +
29A ARG* 3.0 27.5 + - - +
198A GLU* 4.9 7.5 - - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU 3.9 3.2 + - - -
25A ASN* 1.3 72.2 + - - +
27A ILE* 1.3 83.6 + - + +
29A ARG* 3.5 10.2 + - - +
30A ARG* 2.9 32.0 + - - +
200A ASP* 3.3 29.3 + - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.0 11.8 + - - +
26A ARG* 1.3 105.1 - - + +
28A TYR* 1.3 66.6 + - - +
30A ARG* 3.3 11.9 + - - +
31A LYS* 3.0 34.5 + - - +
197A ASP 4.2 2.9 - - - +
198A GLU* 3.5 28.3 - - - +
199A MET 3.6 21.1 - - - +
200A ASP* 3.9 26.2 - - + +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A HIS* 3.5 46.7 - + + -
25A ASN* 2.6 36.5 + - + +
27A ILE* 1.3 72.2 - - - +
29A ARG* 1.3 57.3 + - - +
31A LYS* 3.2 3.8 + - - +
32A ILE* 2.8 36.1 + - + +
196A VAL* 4.0 17.3 + - + -
197A ASP* 3.8 19.0 - - - -
198A GLU* 3.6 38.4 + - + +
221A LYS* 3.9 20.2 - - + -
222A THR* 3.8 22.8 + - + +
303A GOL 5.8 1.0 - - - -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.9 47.3 + - + +
22A HIS* 3.5 19.2 + - + +
23A PRO* 3.7 21.6 + - - +
24A GLU* 5.5 0.2 - - - +
25A ASN 3.0 24.6 + - - +
26A ARG* 3.7 8.5 - - - +
28A TYR* 1.3 74.9 - - - +
30A ARG* 1.3 63.5 + - - +
32A ILE* 3.2 3.3 + - - +
33A GLU* 2.9 39.2 + - + +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 2.9 20.0 + - - +
27A ILE* 3.5 9.6 + - - +
29A ARG* 1.3 75.3 - - - +
31A LYS* 1.3 77.9 + - - +
33A GLU* 3.2 9.1 + - - +
34A GLU* 2.9 49.4 + - - +
200A ASP* 3.0 30.8 + - - +
201A THR 2.9 37.4 + - - +
202A ALA* 4.6 2.4 - - - +
203A LEU 5.0 0.4 - - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.0 21.6 + - + +
28A TYR* 3.7 3.8 - - - +
30A ARG* 1.3 93.0 - - - +
32A ILE* 1.3 57.6 + - - +
34A GLU* 3.2 8.3 + - - +
35A LEU* 2.9 32.8 + - - +
195A TYR 5.5 0.6 + - - -
196A VAL* 4.1 16.6 - - + -
197A ASP* 2.6 50.6 + - - +
199A MET 2.7 21.7 + - - -
201A THR* 3.2 25.9 + - - -
202A ALA 4.9 1.2 + - - -
203A LEU* 3.7 28.5 - - + +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.4 7.4 - - + +
16A LEU* 3.9 11.6 - - + +
18A ILE* 3.7 46.2 - - + +
19A LEU* 3.7 22.9 - - + +
22A HIS* 3.4 34.5 - - + +
28A TYR* 2.8 24.6 + - + +
29A ARG 3.7 2.7 - - - +
31A LYS* 1.3 74.0 - - + +
33A GLU* 1.3 62.8 + - - +
35A LEU* 3.3 15.5 + - + +
36A SER* 3.1 21.3 + - - -
196A VAL* 5.5 3.4 - - + -
219A LEU* 6.0 0.2 - - + -
221A LYS* 5.0 6.3 - - + -
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 22.9 - - - +
19A LEU* 4.1 17.5 - - + +
29A ARG* 2.9 31.8 + - + +
30A ARG* 3.5 9.2 - - - +
32A ILE* 1.3 75.1 - - - +
34A GLU* 1.3 62.6 + - - +
36A SER* 2.3 27.8 + - - -
37A LYS* 3.6 20.1 + - - -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 2.9 37.1 + - - +
31A LYS* 3.2 9.1 + - - +
33A GLU* 1.3 74.0 - - - +
35A LEU* 1.3 65.0 + - - +
37A LYS* 3.1 30.3 + - + +
38A ARG* 4.3 7.3 + - - +
202A ALA* 5.5 1.2 - - - +
203A LEU* 3.9 33.2 + - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.9 14.6 - - + -
31A LYS 2.9 17.3 + - - +
32A ILE* 3.3 21.7 + - + +
34A GLU* 1.3 75.8 - - - +
36A SER* 1.3 57.4 + - - +
38A ARG* 2.9 28.8 + - - +
39A PHE* 2.9 27.8 + - + -
194A GLU* 3.9 31.0 - - + +
196A VAL* 4.2 9.4 - - + -
203A LEU* 3.8 19.7 - - + +
219A LEU* 3.8 31.4 - - + -
228A LEU* 5.0 4.3 - - + -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.7 22.0 - - - -
16A LEU* 3.9 16.6 - - - +
32A ILE 3.1 10.6 + - - -
33A GLU* 2.3 32.2 + - - -
35A LEU* 1.3 76.2 - - - +
37A LYS* 1.3 71.0 + - - +
38A ARG 3.2 0.4 - - - -
39A PHE 3.3 19.1 + - - +
40A THR* 5.3 2.6 - - - +
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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