Contacts of the helix formed by residues 16 - 26 (chain F) in PDB entry 3A68
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 16 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F ILE* 3.4 32.3 + - + +
15F PHE* 1.3 77.2 - - - +
17F PRO* 1.3 68.4 - - + +
18F PHE 3.4 1.3 - - - +
19F GLU* 3.1 32.8 + - + +
20F GLU* 3.0 29.4 + - - +
115G VAL* 3.9 15.7 - - + +
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Residues in contact with PRO 17 (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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15F PHE* 3.7 34.0 - - + +
16F GLU* 1.3 83.6 - - - +
18F PHE* 1.3 65.0 + - + +
20F GLU* 3.3 2.1 + - - +
21F VAL* 2.8 40.4 + - - +
58G ASN* 4.1 10.3 - - + +
59G VAL* 6.2 0.2 - - + -
62G VAL* 4.1 24.7 - - + -
115G VAL* 3.7 19.5 - - + -
117G PRO* 6.0 0.9 - - + -
139G LEU* 4.1 19.1 - - + -
142G LEU* 4.1 3.7 - - + +
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Residues in contact with PHE 18 (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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16F GLU* 3.4 0.6 - - - +
17F PRO* 1.3 88.0 - - + +
19F GLU* 1.3 63.5 + - + +
21F VAL* 3.4 14.6 - - + +
22F LYS* 3.0 31.1 + - - +
62G VAL* 3.8 30.7 - - + -
66G MET* 5.2 1.8 - - + -
115G VAL* 6.1 0.2 - - + -
116G MET 5.0 2.7 - - - -
117G PRO* 3.6 16.2 - - + -
118G LEU* 3.0 69.3 - - + -
121G PHE* 4.2 13.2 - + - -
135G LEU* 4.9 11.7 - - + -
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Residues in contact with GLU 19 (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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16F GLU* 3.1 37.2 + - + +
17F PRO 3.3 0.4 - - - -
18F PHE* 1.3 80.3 - - + +
20F GLU* 1.3 61.9 + - - +
21F VAL 3.2 1.1 + - - -
22F LYS* 3.6 22.3 + - - +
23F LYS* 4.6 2.1 + - - +
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Residues in contact with GLU 20 (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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15F PHE* 3.1 24.1 - - - -
16F GLU 3.0 18.8 + - - +
17F PRO 3.6 0.2 - - - -
19F GLU* 1.3 76.4 - - - +
21F VAL* 1.3 58.4 + - - +
22F LYS 3.5 0.2 - - - -
23F LYS* 4.2 18.0 + - - +
24F GLU* 4.3 4.2 + - - +
142G LEU* 3.9 27.4 - - + +
146G LYS* 2.8 28.3 + - - -
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Residues in contact with VAL 21 (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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17F PRO 2.8 18.6 + - - +
18F PHE* 3.4 26.5 - - + +
19F GLU 3.2 0.4 - - - -
20F GLU* 1.3 77.7 - - - +
22F LYS* 1.3 69.4 + - + +
23F LYS 3.0 2.7 - - - -
24F GLU* 2.9 16.0 + - + +
25F LEU* 2.9 15.0 + - + +
135G LEU* 4.6 16.2 - - + +
138G SER* 3.5 41.1 - - - +
139G LEU* 3.9 13.2 - - + +
142G LEU* 4.8 5.4 - - + -
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Residues in contact with LYS 22 (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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18F PHE 3.0 21.9 + - - +
19F GLU* 3.6 20.2 - - - +
20F GLU 3.5 0.4 - - - -
21F VAL* 1.3 83.0 - - + +
23F LYS* 1.3 60.7 + - - +
25F LEU* 3.9 10.8 + - - +
26F ASP* 3.8 13.2 + - - +
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Residues in contact with LYS 23 (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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19F GLU 4.6 1.0 + - - +
20F GLU* 4.2 13.3 + - + +
21F VAL* 3.0 0.8 - - - +
22F LYS* 1.3 78.7 - - - +
24F GLU* 1.3 76.7 + - - +
26F ASP* 2.7 37.7 - - - +
27F LEU* 3.6 18.0 - - + +
142G LEU* 6.0 1.0 - - - +
145G GLU* 3.5 27.8 + - - -
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Residues in contact with GLU 24 (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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20F GLU 4.7 2.6 - - - +
21F VAL* 2.9 15.8 + - + +
23F LYS* 1.3 95.4 + - - +
25F LEU* 1.3 61.6 + - - +
27F LEU* 3.1 34.8 + - - +
28F VAL* 3.7 4.7 + - - +
39F GLN* 4.5 3.1 + - - +
138G SER* 3.4 39.1 + - - +
141G LYS* 3.9 26.9 - - + +
142G LEU* 4.5 7.8 + - + +
145G GLU* 3.0 27.2 - - - +
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Residues in contact with LEU 25 (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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21F VAL 2.9 15.3 + - - +
22F LYS* 4.2 7.4 - - - +
23F LYS 3.2 0.2 - - - -
24F GLU* 1.3 77.9 - - - +
26F ASP* 1.3 56.7 + - - +
27F LEU 3.2 0.7 - - - -
28F VAL* 2.9 29.5 - - + +
126G LYS* 5.8 5.8 - - - -
131G HIS* 4.3 15.5 - - + +
134G GLU* 3.9 37.7 - - + +
135G LEU* 3.4 26.7 - - + -
138G SER* 3.2 18.8 + - - +
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Residues in contact with ASP 26 (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 LYS 3.8 6.8 + - - +
23F LYS* 2.7 34.2 + - - +
25F LEU* 1.3 76.6 - - - +
27F LEU* 1.3 76.8 + - - +
28F VAL* 3.4 3.9 - - - +
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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