Contacts of the helix formed by residues 15 - 19 (chain E) in PDB entry 4KZX
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 PRO 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E LEU* 4.6 5.6 - - + -
13E ALA 4.6 1.8 - - - +
14E ALA* 1.4 88.4 - - + +
16E LYS* 1.3 67.9 + - - +
17E HIS* 3.0 29.5 + - + +
18E TRP* 3.2 41.5 + - + +
19E MET 4.4 0.2 + - - -
20E LEU 5.6 0.3 + - - -
38E LEU* 4.4 5.4 - - + -
39E ARG* 3.9 38.6 - - + +
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Residues in contact with LYS 16 (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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14E ALA 3.6 3.3 + - - -
15E PRO* 1.3 71.9 - - - +
17E HIS* 1.3 55.1 + - + +
18E TRP 3.0 0.2 - - - -
19E MET* 2.7 53.4 + - - +
20E LEU 4.3 16.2 + - - +
22E LYS* 5.4 9.3 - - - +
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Residues in contact with HIS 17 (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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15E PRO* 3.0 23.8 + - + +
16E LYS* 1.3 77.9 + - - +
18E TRP* 1.3 75.9 + + - +
19E MET* 3.2 1.3 - - - -
39E ARG* 3.0 29.9 + - + -
40E GLU* 4.8 2.6 - - - -
41E CYS 4.0 4.8 + - - -
42E LEU* 4.4 10.1 - - + +
51E LYS* 4.4 4.9 + - - -
103E TYR* 5.5 5.5 - + - -
107E GLY 3.3 26.7 - - - +
108E ARG* 3.5 28.5 - - + +
109E PHE* 4.5 13.6 + + - +
189E LEU* 6.0 2.7 - - + -
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Residues in contact with TRP 18 (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 LEU* 4.6 1.1 - - + -
14E ALA* 4.5 8.1 - - + -
15E PRO* 3.8 31.4 - - + +
16E LYS 2.9 1.0 + - - -
17E HIS* 1.3 95.8 + + - +
19E MET* 1.3 73.7 + - - +
20E LEU* 4.2 23.5 - - + +
29E PRO* 4.1 13.5 - - + -
30E ARG 4.3 5.4 - - - -
31E PRO* 3.5 38.4 - - + -
38E LEU 4.0 8.3 - - - -
41E CYS 2.7 28.9 + - - -
42E LEU* 3.4 18.8 - - + +
43E PRO* 3.7 13.0 - - + -
46E ILE* 2.8 43.1 - - + +
50E ASN* 5.5 1.4 - - - +
51E LYS* 3.6 16.7 + - - +
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Residues in contact with MET 19 (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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15E PRO 4.4 0.2 + - - -
16E LYS* 2.7 42.9 + - - +
17E HIS* 5.1 0.2 - - - -
18E TRP* 1.3 82.6 - - - +
20E LEU* 1.3 65.4 + - - +
21E ASP 4.1 0.5 + - - -
50E ASN* 5.7 1.6 - - - +
51E LYS* 4.2 8.2 + - - +
108E ARG* 3.5 46.2 - - - +
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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