Contacts of the helix formed by residues 13 - 18 (chain X) in PDB entry 2AT8
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 ASN 13 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9X GLN* 4.5 1.8 + - - -
11X GLY 3.3 5.0 + - - +
12X PHE* 1.3 76.0 - - - +
14X LYS* 1.3 62.5 + - - +
15X ASP* 3.4 9.2 + - - +
16X LYS* 3.2 49.8 + - + +
17X TYR* 3.2 20.8 + - - +
112X ALA* 6.0 0.2 - - - +
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Residues in contact with LYS 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X PHE* 3.6 31.2 + - + -
13X ASN* 1.3 70.2 + - - +
15X ASP* 1.3 78.8 + - - +
18X PHE* 2.9 40.8 + - + +
53X LEU* 6.4 0.2 - - + -
79X LEU* 4.1 19.3 - - + +
82X TYR* 4.3 6.5 - - - +
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Residues in contact with ASP 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X ASN* 3.4 6.9 + - - +
14X LYS* 1.3 98.1 - - - +
16X LYS* 1.3 62.4 + - + +
18X PHE* 3.5 20.3 - - - +
19X ASN* 3.6 7.8 + - - +
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Residues in contact with LYS 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X ASN* 3.2 42.5 + - + +
14X LYS 3.3 0.2 - - - -
15X ASP* 1.3 75.1 - - + +
17X TYR* 1.3 66.1 + - - +
19X ASN* 3.3 23.4 + - - +
23X TRP* 5.8 0.2 - - - -
113X ASP* 5.9 2.9 - - - +
114X ASP* 2.8 40.1 + - - +
139X ARG* 3.4 6.9 + - - -
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Residues in contact with TYR 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X PHE* 3.5 30.3 - + + -
13X ASN 3.2 4.7 + - - +
14X LYS 3.9 0.2 - - - +
16X LYS* 1.3 80.7 - - - +
18X PHE* 1.3 79.9 + + - +
19X ASN* 3.2 6.7 + - - +
23X TRP* 3.4 50.7 + + - -
44X LEU* 4.1 2.8 - - - +
46X ALA* 3.9 24.0 - - + +
55X GLU* 4.2 2.2 - - - -
107X PHE* 3.4 34.4 - + - -
109X VAL* 4.1 13.0 - - + -
112X ALA* 4.1 16.4 - - + -
117X ALA* 4.0 16.2 - - + -
119X ILE* 3.8 0.9 - - + +
137X LEU* 3.4 16.5 - - - +
139X ARG* 3.6 6.8 + - - +
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Residues in contact with PHE 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X PHE* 4.2 5.2 - + - -
14X LYS* 2.9 32.7 + - + +
15X ASP* 3.5 10.2 - - - +
17X TYR* 1.3 92.0 - + + +
19X ASN* 1.3 57.7 + - - +
20X GLY 3.4 3.1 - - - -
46X ALA* 3.5 22.0 - - + -
47X GLY* 3.5 19.4 - - - -
48X THR* 3.9 9.2 + - - +
53X LEU* 3.6 32.3 - - + -
54X LYS 4.1 1.6 - - - -
55X GLU* 3.9 14.8 - - + -
74X LEU* 3.8 25.8 - - + -
82X TYR* 3.6 40.8 - + - -
107X PHE* 5.2 1.1 - + - -
109X VAL* 5.5 0.2 - - + -
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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