Contacts of the helix formed by residues 16 - 21 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C VAL* 4.0 27.9 - - + +
116C MET 5.6 1.0 - - - +
14S ILE* 3.6 14.3 + - + +
15S PHE* 1.3 76.2 - - - +
17S PRO* 1.3 69.4 - - + +
18S PHE* 3.3 3.4 + - - +
19S GLU* 3.2 37.9 + - + +
20S GLU* 3.0 24.9 + - - +
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Residues in contact with PRO 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASN* 2.8 44.9 - - - +
59C VAL* 6.1 0.7 - - + -
62C VAL* 4.0 20.0 - - + -
115C VAL* 3.9 10.1 - - + -
117C PRO* 6.1 0.2 - - + -
139C LEU* 5.1 12.6 - - + -
142C LEU* 4.0 2.4 - - + +
15S PHE* 3.3 23.3 - - + +
16S GLU* 1.3 83.3 - - - +
18S PHE* 1.3 68.5 + - + +
20S GLU 3.6 0.7 - - - -
21S VAL* 2.8 35.9 + - - +
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Residues in contact with PHE 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.7 30.3 - - + -
115C VAL* 6.2 0.9 - - + -
116C MET 5.0 2.9 - - - -
117C PRO* 3.6 17.0 - - + -
118C LEU* 3.1 66.2 - - + -
121C PHE* 4.4 4.0 - + - -
135C LEU* 3.5 36.8 - - + -
139C LEU* 5.1 1.8 - - + -
16S GLU* 3.3 3.0 - - - +
17S PRO* 1.3 86.2 - - + +
19S GLU* 1.3 63.3 + - + +
21S VAL* 3.6 6.1 - - + +
22S LYS* 3.1 30.6 + - - +
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Residues in contact with GLU 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S GLU* 3.2 44.4 + - + +
18S PHE* 1.3 79.7 - - + +
20S GLU* 1.3 60.8 + - - +
21S VAL 3.2 2.0 + - - -
22S LYS* 3.5 37.2 + - - +
23S LYS* 4.7 0.9 + - - +
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Residues in contact with GLU 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 3.8 28.2 - - + +
145C GLU* 6.2 0.2 - - - +
146C LYS* 3.1 39.6 + - - -
15S PHE* 3.4 14.8 - - + -
16S GLU 3.0 16.2 + - - +
19S GLU* 1.3 76.9 - - + +
21S VAL* 1.3 56.8 + - - +
22S LYS 3.5 0.4 - - - -
23S LYS* 3.3 29.8 + - - +
24S GLU* 4.5 1.7 + - - +
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Residues in contact with VAL 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.9 20.9 - - + -
138C SER* 3.5 32.3 - - - +
139C LEU* 3.5 25.8 - - + -
142C LEU* 4.4 6.5 - - + -
17S PRO 2.8 21.4 + - - +
18S PHE* 3.6 17.5 - - + +
20S GLU* 1.3 77.2 - - - +
22S LYS* 1.3 70.8 + - - +
23S LYS 3.2 2.7 - - - -
24S GLU* 3.2 5.1 + - + -
25S LEU* 2.9 25.5 + - + +
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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