Contacts of the helix formed by residues 45 - 56 (chain E) in PDB entry 7KHE
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 LYS 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384D LYS* 6.0 5.4 - - - +
414D GLU 2.9 19.8 + - - -
415D VAL* 2.5 36.0 + - - +
417D ARG* 3.4 3.2 - - + +
418D GLU* 3.2 42.7 - - + +
419D HIS* 4.5 8.7 - - + +
477D GLN* 5.2 9.4 - - - +
43E ASN 5.6 1.1 - - - +
44E ASP* 1.3 74.1 - - - +
46E THR* 1.3 68.0 + - + +
47E THR* 3.2 10.7 + - + +
48E VAL* 3.5 5.1 - - - +
49E ILE* 3.0 24.9 + - - +
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Residues in contact with THR 46 (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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474D LEU* 3.9 8.5 - - + -
27E ALA* 3.0 37.8 + - + +
30E MET* 3.5 23.3 - - - -
31E GLN* 3.5 28.7 - - + +
45E LYS* 1.3 72.6 - - + +
47E THR* 1.3 69.0 + - + +
49E ILE* 3.7 12.3 - - - +
50E ALA* 2.9 22.2 + - - +
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Residues in contact with THR 47 (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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418D GLU* 4.6 7.4 + - - +
474D LEU* 3.9 20.6 - - + -
477D GLN* 3.2 36.8 - - + +
478D LEU* 4.1 19.3 - - + -
481D ARG* 4.0 18.2 + - - -
27E ALA* 4.5 3.8 - - - -
45E LYS* 4.5 8.4 + - + +
46E THR* 1.3 76.8 - - + +
48E VAL* 1.3 74.2 + - - +
50E ALA* 3.0 5.9 + - - +
51E LEU* 3.0 29.0 + - - +
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Residues in contact with VAL 48 (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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418D GLU* 4.1 18.2 - - + -
481D ARG* 4.8 8.3 - - - +
2E ALA* 3.7 28.3 - - - +
3E ARG* 4.1 21.3 - - + +
44E ASP* 3.4 39.7 - - + +
45E LYS 3.5 4.7 - - - +
47E THR* 1.3 85.1 + - - +
49E ILE* 1.3 59.0 + - - +
51E LEU* 4.1 9.9 - - + -
52E ARG* 2.9 30.9 + - + +
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Residues in contact with ILE 49 (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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30E MET* 3.8 30.1 - - + -
37E PRO* 4.4 8.5 - - + -
39E VAL* 5.0 9.9 - - + +
41E GLU* 4.3 25.4 - - + +
44E ASP* 3.4 25.1 - - + +
45E LYS 3.0 29.5 + - - +
46E THR* 3.7 10.5 - - - +
47E THR 3.1 0.6 - - - -
48E VAL* 1.3 76.8 - - - +
50E ALA* 1.3 57.6 + - - +
52E ARG* 3.2 11.4 + - - +
53E GLU* 2.9 40.8 + - + +
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Residues in contact with ALA 50 (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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23E ALA* 3.5 32.5 - - + +
26E ARG* 4.0 17.9 - - + +
27E ALA* 4.1 2.9 - - + -
30E MET* 5.4 0.7 - - - -
46E THR* 2.9 18.5 + - - +
47E THR* 3.0 4.5 + - - +
49E ILE* 1.3 76.7 - - - +
51E LEU* 1.3 63.0 + - - +
53E GLU* 3.2 12.1 + - - +
54E ILE* 2.9 30.7 + - - +
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Residues in contact with LEU 51 (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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478D LEU* 3.3 29.2 - - + -
481D ARG* 5.0 15.7 - - + -
482D ALA* 5.4 4.9 - - + -
2E ALA* 5.1 4.5 - - + +
6E VAL* 3.6 31.0 - - + -
9E ALA* 4.7 4.5 - - + -
19E LEU* 4.2 17.3 - - + -
23E ALA* 3.9 7.6 - - + -
47E THR* 3.0 32.1 + - - +
48E VAL* 3.7 14.6 - - + +
49E ILE 3.2 0.2 - - - -
50E ALA* 1.3 76.0 - - - +
52E ARG* 1.3 56.6 + - - +
54E ILE* 3.1 7.5 + - + +
55E GLU* 2.9 45.2 + - - +
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Residues in contact with ARG 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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2004D G4P 4.0 9.7 + - - -
2E ALA* 3.9 29.0 - - + +
39E VAL* 4.0 32.0 - - + +
40E PRO* 4.8 7.0 + - - +
42E GLU* 4.7 16.9 + - - +
44E ASP* 4.2 12.6 + - - -
48E VAL* 2.9 36.0 + - - +
49E ILE* 3.6 10.5 - - - +
51E LEU* 1.3 74.8 - - - +
53E GLU* 1.3 62.4 + - - +
55E GLU* 4.2 7.6 - - - +
56E GLU* 3.5 41.7 + - - +
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Residues in contact with GLU 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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26E ARG* 2.7 42.2 + - + +
30E MET* 4.4 1.2 - - - +
37E PRO* 3.9 1.2 - - - +
38E LEU* 2.9 40.8 + - + +
39E VAL* 3.6 22.1 + - + -
49E ILE* 2.9 30.6 + - + +
50E ALA 3.6 4.3 - - - +
51E LEU 3.2 0.2 - - - -
52E ARG* 1.3 75.3 - - - +
54E ILE* 1.3 65.1 + - - +
56E GLU* 3.8 2.8 + - - -
58E LEU* 3.6 11.9 + - - +
59E ILE* 3.3 35.6 + - + +
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Residues in contact with ILE 54 (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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9E ALA* 4.2 14.4 - - + -
12E LYS* 3.9 8.5 - - - +
13E ILE* 3.3 31.8 - - + +
19E LEU* 4.4 9.6 - - + +
22E VAL* 4.2 15.5 - - + -
23E ALA* 3.5 41.5 - - + +
26E ARG* 5.7 1.6 - - + -
50E ALA* 2.9 26.1 + - + +
51E LEU* 3.1 10.5 + - + +
53E GLU* 1.3 78.0 - - + +
55E GLU* 1.3 62.4 + - - +
57E GLY* 3.2 12.3 + - - -
59E ILE* 3.4 23.6 - - + +
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Residues in contact with GLU 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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2004D G4P 5.0 0.9 + - - -
2E ALA* 2.9 38.9 - - - +
5E THR 4.9 5.1 - - - +
6E VAL* 4.8 3.1 - - - +
8E ASP* 3.4 30.4 - - - +
9E ALA* 3.5 28.4 - - + +
12E LYS* 3.0 29.5 - - - -
51E LEU* 2.9 37.8 + - - +
52E ARG* 3.6 5.5 + - - +
53E GLU 3.4 0.2 - - - -
54E ILE* 1.3 77.1 - - - +
56E GLU* 1.3 58.4 + - + +
57E GLY 3.3 0.4 - - - -
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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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8E ASP* 6.1 0.2 - - - +
12E LYS* 4.3 5.5 + - - +
39E VAL* 4.4 16.8 - - - +
52E ARG* 3.5 32.6 + - - +
53E GLU* 3.8 1.0 + - - +
54E ILE 3.3 1.0 - - - -
55E GLU* 1.3 78.9 - - + +
57E GLY* 1.3 55.5 + - - +
58E LEU* 3.2 33.9 - - + +
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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