Contacts of the helix formed by residues 101 - 106 (chain J) in PDB entry 2AAZ
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 TRP 101 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79J GLU* 2.9 23.9 + - - -
82J TRP* 3.8 15.3 - + - -
83J PHE* 4.7 0.2 - - - -
90J ALA* 4.0 21.8 - - + +
93J LEU* 3.7 21.1 - - + +
98J VAL 5.1 0.8 + - - -
99J GLY* 3.1 1.0 - - - -
100J ILE* 1.3 100.4 - - + +
102J ASP* 1.3 65.0 + - - +
103J GLY 3.2 2.9 - - - -
104J ASN* 3.6 26.7 + - + +
105J GLY* 3.1 21.5 + - - -
123J LEU* 4.0 22.4 - - + +
126J VAL* 6.2 4.5 - - + -
127J TYR* 3.6 34.8 - + - -
183J ALA* 6.1 0.4 - - + -
184J LEU* 4.0 36.1 - - + -
185J PRO 6.2 0.2 - - - -
400J UMP 4.8 11.7 - + - -
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Residues in contact with ASP 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ALA* 4.6 7.4 - - - +
94J SER* 3.5 25.2 - - - -
98J VAL 4.3 1.0 - - - +
99J GLY* 3.0 33.6 + - - +
101J TRP* 1.3 80.4 - - - +
103J GLY* 1.3 58.8 + - - +
105J GLY* 3.7 1.5 - - - +
106J SER* 3.0 31.9 + - - +
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Residues in contact with GLY 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J GLY 4.4 1.8 + - - -
100J ILE 4.7 2.4 + - - -
101J TRP* 3.2 1.4 - - - +
102J ASP* 1.3 78.7 - - - +
104J ASN* 1.3 59.3 + - - +
106J SER* 3.2 21.7 + - - -
109J PHE* 3.5 9.2 - - - +
315J MET* 4.6 15.0 - - - +
317J ALA* 4.8 8.2 - - - +
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Residues in contact with ASN 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ARG* 5.0 0.2 - - - +
100J ILE 5.1 1.6 - - - +
101J TRP* 3.6 27.3 + - + -
102J ASP 3.4 0.2 - - - -
103J GLY* 1.3 76.3 - - - +
105J GLY* 1.3 59.5 + - - +
106J SER 3.5 0.2 - - - -
109J PHE* 3.2 48.8 - - + -
110J LEU* 3.8 3.6 - - - +
123J LEU* 3.9 4.0 - - + -
183J ALA* 3.5 18.0 - - + +
184J LEU* 3.8 28.2 - - + +
315J MET* 3.4 23.3 - - - +
317J ALA* 3.6 15.8 + - - +
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Residues in contact with GLY 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ALA* 5.1 1.1 - - - -
101J TRP 3.1 14.6 + - - -
102J ASP* 3.7 2.5 - - - -
104J ASN* 1.3 77.5 - - - +
106J SER* 1.3 66.7 + - - +
110J LEU* 3.5 8.6 - - - +
120J GLU* 3.4 3.3 - - - +
121J GLY* 2.8 33.4 + - - -
123J LEU* 3.5 18.2 - - - -
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Residues in contact with SER 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J ASP 3.0 15.9 + - - -
103J GLY* 3.2 13.4 + - - -
104J ASN 3.5 0.2 - - - -
105J GLY* 1.3 81.3 - - - +
107J LYS* 1.3 64.6 + - - +
108J GLU* 3.7 8.8 + - - +
109J PHE* 3.1 16.5 + - - +
110J LEU* 3.0 21.8 + - - +
120J GLU* 3.8 11.7 - - - -
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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