Contacts of the strand formed by residues 14 - 19 (chain z) in PDB entry 5Z58
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 14 (chain z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13z GLY* 1.3 76.8 - - - +
15z VAL* 1.3 70.6 + - - +
25z ASP* 3.7 32.8 + - - -
26z ILE 3.3 14.8 - - - +
27z GLU* 4.8 9.3 + - + +
28z LEU* 5.1 0.4 - - - +
134z THR* 4.9 7.6 - - - +
166z VAL* 3.7 0.5 - - - +
167z LEU* 2.8 57.8 + - + +
168z PHE* 2.9 21.8 + - + +
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Residues in contact with VAL 15 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14z LYS* 1.3 85.2 - - - +
16z LEU* 1.3 70.7 + - - +
17z LEU* 4.7 3.1 - - + -
24z ILE 3.7 0.5 - - - +
25z ASP* 3.7 1.7 - - - -
26z ILE* 2.9 39.2 + - + +
28z LEU* 3.9 17.9 - - + -
40z PHE* 3.6 39.7 - - + -
41z ILE* 4.4 5.4 - - + -
44z CYS* 4.1 11.9 - - + -
165z GLU 3.4 14.8 - - - +
166z VAL* 4.3 18.2 - - + -
167z LEU* 4.1 1.1 - - - +
168z PHE 5.1 0.2 - - - +
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Residues in contact with LEU 16 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15z VAL* 1.3 76.5 - - - +
17z LEU* 1.3 78.5 + - - +
18z LYS* 3.7 23.1 + - + -
23z ASP* 3.8 23.6 - - + +
24z ILE 3.5 6.3 - - - +
25z ASP* 3.2 22.9 - - - +
164z CYS* 3.5 4.2 - - - -
165z GLU* 2.5 69.9 + - + +
167z LEU* 4.1 18.0 - - + +
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Residues in contact with LEU 17 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15z VAL* 4.7 3.4 - - + -
16z LEU* 1.3 76.5 - - - +
18z LYS* 1.3 62.0 + - - +
19z THR* 3.7 11.1 + - + +
22z GLY 3.8 0.7 - - - +
23z ASP* 3.5 3.5 - - - -
24z ILE* 2.9 48.1 + - + +
26z ILE* 3.6 32.5 - - + -
40z PHE* 4.2 20.4 - - + -
44z CYS* 4.7 0.7 - - - -
49z TYR* 5.4 0.7 - - + -
113z PHE* 4.7 4.5 - - + -
115z PHE* 3.9 20.2 - - + -
161z ILE* 4.4 22.0 - - + -
163z SER 4.1 1.3 - - - +
164z CYS* 3.7 27.4 - - + -
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Residues in contact with LYS 18 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16z LEU* 3.7 23.3 - - + +
17z LEU* 1.3 71.4 - - - +
19z THR* 1.3 53.6 + - - +
23z ASP* 3.6 22.0 - - - +
161z ILE* 3.6 1.6 - - - -
162z LYS* 2.7 37.5 + - + +
163z SER* 3.3 35.4 + - - +
164z CYS* 5.9 0.2 - - - -
165z GLU* 2.8 31.8 + - + +
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Residues in contact with THR 19 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17z LEU* 4.3 14.8 - - + +
18z LYS* 1.3 78.7 - - - +
20z THR* 1.3 58.8 + - - +
21z ALA* 3.0 14.5 + - - +
22z GLY* 2.5 43.1 + - - +
24z ILE* 4.1 14.6 - - + +
54z PHE* 4.1 10.3 - - + -
144z LEU* 4.2 6.2 - - - +
160z LYS 3.2 16.8 - - - +
161z ILE* 3.7 22.4 - - + -
162z LYS* 4.2 4.7 - - - +
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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