Contacts of the helix formed by residues 120 - 128 (chain P) in PDB entry 2AIZ
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 ASP 120 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118P GLY* 3.9 4.9 - - - -
119P HIS* 1.3 95.0 + - - +
121P GLU* 1.3 52.0 + - - +
122P ALA* 2.6 17.8 + - + +
123P ALA* 2.8 9.6 + - + +
124P TYR* 2.6 39.1 + - - +
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Residues in contact with GLU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P ASP* 1.3 72.6 - - - +
122P ALA* 1.3 51.7 + - - +
124P TYR* 4.2 5.5 - - - +
125P SER* 2.5 61.2 + - - +
128P ARG* 3.1 25.0 + - - -
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Residues in contact with ALA 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P ASP* 2.6 13.3 + - + +
121P GLU* 1.3 73.8 - - - +
123P ALA* 1.3 62.1 + - - +
125P SER* 3.8 2.3 - - - -
126P LYS* 3.1 41.3 + - - +
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Residues in contact with ALA 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P VAL* 3.5 36.9 - - + +
117P LEU 3.7 16.4 - - - +
118P GLY* 4.2 13.7 - - - -
120P ASP* 2.8 13.3 + - + +
122P ALA* 1.3 75.0 - - - +
124P TYR* 1.3 67.2 + - - +
126P LYS* 3.2 8.2 + - - +
127P ASN* 3.0 19.9 + - - +
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Residues in contact with TYR 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P ASP* 3.6 29.1 - - + +
72P GLU* 3.1 14.6 + - + -
73P ARG* 2.7 30.6 - - + +
118P GLY 3.6 9.2 - - - -
119P HIS* 3.4 41.7 - - + +
120P ASP* 2.6 23.7 + - - +
121P GLU* 4.2 3.4 - - - +
123P ALA* 1.3 73.6 - - - +
125P SER* 1.3 61.4 + - - +
127P ASN* 3.0 18.8 + - - +
128P ARG* 3.0 32.5 + - - +
5U 6CL 4.8 1.8 - - - -
7U DAL 3.3 33.0 + - + -
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Residues in contact with SER 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P TYR* 3.5 21.2 - - - -
34P PHE 4.7 1.0 - - - +
121P GLU* 2.5 51.7 + - - +
122P ALA* 3.8 3.1 - - - -
124P TYR* 1.3 76.7 - - - +
126P LYS* 1.3 63.8 + - - +
127P ASN 3.3 0.5 + - - -
128P ARG* 2.9 30.0 + - - +
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Residues in contact with LYS 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P TYR* 4.0 16.5 - - + +
116P VAL* 3.3 41.7 - - + +
122P ALA* 3.1 32.3 + - - +
123P ALA* 3.2 6.4 + - - +
125P SER* 1.3 78.1 - - - +
127P ASN* 1.3 56.0 + - - +
129P ARG* 3.3 34.0 + - - +
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Residues in contact with ASN 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P ASN* 2.2 33.8 - - - +
70P THR* 4.2 6.6 + - - +
71P ASP* 4.2 22.5 - - - +
72P GLU* 4.7 5.3 - - - +
114P PRO* 4.7 7.9 - - - +
115P ALA* 2.9 22.3 - - - +
116P VAL* 2.7 46.3 + - - +
118P GLY 5.1 1.2 + - - -
123P ALA 3.0 9.4 + - - +
124P TYR* 3.0 16.2 + - - +
126P LYS* 1.3 77.4 - - - +
128P ARG* 1.3 52.1 + - - +
129P ARG* 2.7 11.0 + - - +
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Residues in contact with ARG 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P TYR* 3.4 4.3 - - - -
34P PHE* 2.8 43.8 + - + +
35P GLY* 3.4 34.3 - - - +
36P PHE* 3.9 14.7 - - - +
69P ASN 3.9 2.5 - - - -
70P THR* 4.2 7.4 - - - +
71P ASP* 4.4 17.9 - - - +
86P ARG* 4.7 4.3 - - - +
121P GLU* 3.1 30.9 + - - -
124P TYR* 3.0 29.3 + - - +
125P SER* 2.9 42.8 + - - +
127P ASN* 1.3 71.4 - - - +
129P ARG* 1.3 61.1 + - - +
5U 6CL 4.9 5.4 - - - +
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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