Contacts of the helix formed by residues 26 - 35 (chain F) in PDB entry 4N3E
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 GLU 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F LYS* 2.8 48.9 + - - +
22F ALA 4.1 1.1 - - - -
25F LEU* 1.3 77.5 - - - +
27F ARG* 1.3 63.9 + - - +
28F HIS* 3.1 12.6 - - + +
29F GLN* 3.1 31.6 + - + +
30F VAL* 3.0 28.3 + - + +
158F PHE* 3.8 19.5 - - + -
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Residues in contact with ARG 27 (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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22F ALA 3.6 11.3 + - - -
23F LEU* 3.2 34.6 + - - +
24F VAL* 3.4 18.1 + - - +
26F GLU* 1.3 76.7 - - - +
28F HIS* 1.3 57.5 + - - +
30F VAL* 4.5 0.9 - - - -
31F LEU* 2.8 52.8 + - + +
70F HIS* 6.1 2.4 + - - -
72F PHE* 6.2 3.6 - - + -
84F TYR* 4.0 19.0 + - - -
101F TYR* 6.2 0.6 - - - -
140F ALA* 4.1 20.2 + - - +
143F PHE* 3.4 37.8 - - + -
144F TYR* 5.9 0.2 - - - +
201F 2AN 3.7 31.6 - - - -
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU 4.1 15.8 + - - -
26F GLU* 3.1 14.4 - - + -
27F ARG* 1.3 77.7 - - - +
29F GLN* 1.3 95.6 + - + +
31F LEU* 4.9 0.2 - - - -
32F VAL* 3.4 22.7 + - - +
42F GLY* 3.5 35.4 - - - -
43F GLU* 4.1 8.7 - - - +
44F ILE* 3.6 31.2 + - + +
55F THR* 3.9 27.3 - - + +
57F ILE* 3.7 16.2 - - + +
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Residues in contact with GLN 29 (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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26F GLU* 3.1 27.5 + - + +
28F HIS* 1.3 104.9 + - + +
30F VAL* 1.3 65.5 + - + +
31F LEU 3.1 2.2 - - - -
32F VAL* 2.9 21.7 + - - +
33F LYS* 3.1 41.1 + - - +
42F GLY 4.9 3.8 - - - +
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Residues in contact with VAL 30 (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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22F ALA* 3.5 26.7 - - - +
26F GLU* 3.0 20.2 + - + +
27F ARG 4.2 0.9 - - - +
29F GLN* 1.3 78.3 - - + +
31F LEU* 1.3 58.3 + - - +
33F LYS* 4.2 16.2 - - + +
34F ALA* 3.0 30.2 + - + +
143F PHE* 3.6 17.3 - - + -
147F VAL* 3.7 25.8 - - + -
158F PHE* 4.3 20.2 - - + -
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ARG* 2.8 36.0 + - + +
28F HIS 4.3 0.4 - - - +
30F VAL* 1.3 78.6 - - - +
32F VAL* 1.3 56.2 + - - +
33F LYS 3.2 0.4 - - - -
35F GLN* 3.1 36.8 + - - +
39F PHE* 3.6 32.9 - - + -
57F ILE* 3.6 33.0 - - + -
68F MET* 4.6 10.1 - - + -
70F HIS* 6.3 1.1 - - + -
143F PHE* 3.7 37.9 - - + -
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Residues in contact with VAL 32 (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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28F HIS 3.4 19.7 - - - +
29F GLN* 2.9 14.1 + - - +
31F LEU* 1.3 78.7 - - + +
33F LYS* 1.3 61.6 + - - +
35F GLN 4.5 3.1 - - - +
36F PRO* 4.7 12.2 - - + +
39F PHE* 3.8 29.6 - - + +
40F LYS 3.6 23.1 - - - +
41F SER* 3.8 20.4 - - - +
42F GLY 3.9 0.9 - - - +
57F ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 33 (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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29F GLN* 3.1 44.1 + - - +
30F VAL* 3.3 16.5 + - + +
31F LEU 3.2 0.6 - - - -
32F VAL* 1.3 80.3 - - - +
34F ALA* 1.3 67.3 + - - +
35F GLN 3.2 0.7 - - - -
36F PRO* 3.6 12.7 - - - +
158F PHE* 5.4 8.1 - - - -
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Residues in contact with ALA 34 (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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30F VAL* 3.0 17.4 + - + +
33F LYS* 1.3 80.0 - - - +
35F GLN* 1.3 61.7 + - + +
36F PRO* 3.5 4.7 - - - +
37F HIS* 4.6 3.8 - - - -
143F PHE* 3.6 18.8 - - + -
146F GLN* 3.5 32.9 + - + +
147F VAL* 4.3 9.2 - - + -
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Residues in contact with GLN 35 (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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31F LEU* 3.1 28.8 + - - +
33F LYS 3.2 0.2 - - - -
34F ALA* 1.3 86.8 - - + +
36F PRO* 1.4 57.9 - - - +
37F HIS* 3.0 24.8 + - + -
38F VAL* 3.0 22.9 + - + +
39F PHE* 3.0 32.6 + - + -
139F LYS 4.8 3.8 + - - -
142F GLU* 4.8 12.0 + - - +
143F PHE* 3.6 27.6 - - + +
146F GLN* 3.4 25.7 + - - +
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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