Contacts of the helix formed by residues 16 - 21 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE* 1.3 80.3 - - - +
17H PRO* 1.3 61.8 - - - +
18H PHE 3.3 1.8 - - - +
19H GLU* 2.9 54.4 + - + +
20H GLU* 3.1 20.1 + - - +
115X VAL* 4.1 23.6 - - + +
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Residues in contact with PRO 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE* 3.4 43.3 - - + +
16H GLU* 1.3 84.2 - - - +
18H PHE* 1.3 62.5 + - + +
20H GLU 3.8 0.2 - - - -
21H VAL* 2.8 36.3 + - - +
58X ASN* 4.0 15.0 - - + +
59X VAL* 5.4 2.5 - - + +
62X VAL* 4.4 21.5 - - + -
115X VAL* 4.0 16.2 - - + -
139X LEU* 4.6 13.9 - - + -
142X LEU* 4.3 5.5 - - + +
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Residues in contact with PHE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H GLU* 3.3 1.2 - - - +
17H PRO* 1.3 84.4 - - + +
19H GLU* 1.3 65.5 + - + +
21H VAL* 3.8 13.8 - - + +
22H LYS* 3.7 24.3 + - + +
62X VAL* 3.7 31.6 - - + -
115X VAL* 6.0 2.2 - - + -
116X MET 4.9 2.5 - - - -
117X PRO* 3.6 17.3 - - + -
118X LEU* 3.1 64.8 - - + -
121X PHE* 4.4 5.4 - + - -
135X LEU* 3.6 25.8 - - + -
139X LEU* 5.5 2.2 - - + -
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Residues in contact with GLU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H GLU* 2.9 46.9 + - + +
18H PHE* 1.3 81.6 - - + +
20H GLU* 1.3 63.8 + - + +
21H VAL 3.1 4.3 + - - -
22H LYS* 3.8 11.7 + - - +
23H LYS* 4.7 10.6 + - - +
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Residues in contact with GLU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE* 3.0 43.0 - - - -
16H GLU 3.1 18.8 + - - +
19H GLU* 1.3 78.8 - - + +
21H VAL* 1.3 59.5 + - - +
22H LYS 3.7 0.2 - - - -
23H LYS* 4.5 4.2 + - - +
24H GLU* 4.1 12.3 + - - +
142X LEU* 3.4 23.9 - - + +
146X LYS* 3.1 23.8 + - - -
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Residues in contact with VAL 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H PRO 2.8 23.0 + - - +
18H PHE* 3.8 13.9 - - + +
19H GLU 3.1 0.2 - - - -
20H GLU* 1.3 78.2 - - - +
22H LYS* 1.3 61.7 + - + +
23H LYS 3.1 2.9 - - - -
24H GLU* 2.7 9.3 + - + +
25H LEU* 2.6 35.0 + - + +
135X LEU* 3.8 22.0 - - + -
138X SER* 3.4 35.9 - - - +
139X LEU* 3.4 23.8 - - + -
142X LEU* 4.7 5.2 - - + -
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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