Contacts of the strand formed by residues 129 - 133 (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 ARG 129 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31P THR* 4.1 16.7 - - + +
32P VAL 3.0 18.8 - - - +
33P TYR* 4.0 19.2 + - + +
34P PHE* 4.4 4.9 - - - +
67P GLU 4.1 0.5 - - - +
69P ASN* 3.0 35.9 + - + +
70P THR* 4.8 0.2 - - - +
86P ARG* 5.0 2.5 - - - +
115P ALA* 3.4 30.0 - - - +
116P VAL* 5.3 3.3 - - - +
126P LYS* 3.3 24.2 + - - +
127P ASN 2.7 11.5 + - - +
128P ARG* 1.3 75.0 - - - +
130P ALA* 1.3 58.2 + - - +
131P VAL* 4.0 20.6 + - + +
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Residues in contact with ALA 130 (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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31P THR* 3.9 0.2 - - - -
32P VAL* 3.1 32.1 + - + +
34P PHE* 4.1 20.9 - - + -
66P VAL* 4.6 12.3 - - + -
67P GLU 2.8 15.3 - - - +
68P GLY* 3.9 11.0 - - - -
86P ARG* 6.0 3.1 - - + +
87P ALA* 6.1 4.0 - - + -
90P VAL* 6.1 2.7 - - + -
129P ARG* 1.3 72.3 - - - +
131P VAL* 1.3 63.7 + - - +
132P LEU* 3.5 5.7 + - + +
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Residues in contact with VAL 131 (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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30P ASN* 3.5 20.0 - - - +
31P THR* 3.2 34.3 - - + +
67P GLU* 2.7 38.4 + - + +
69P ASN* 5.3 6.7 - - - +
129P ARG* 4.0 22.9 - - + +
130P ALA* 1.3 71.4 - - - +
132P LEU* 1.3 61.8 - - - +
133P ALA* 2.8 12.3 + - + +
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Residues in contact with LEU 132 (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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30P ASN* 2.5 47.6 + - + +
32P VAL* 4.7 12.8 - - + -
48P ILE* 5.2 1.3 - - + -
49P LEU* 5.2 6.1 - - + -
52P HIS* 4.0 27.1 - - + +
64P VAL* 3.3 35.7 - - + -
65P LEU 4.1 1.6 - - - -
66P VAL* 3.6 28.7 - - + +
90P VAL* 4.7 11.9 - - + -
94P LEU* 5.0 6.7 - - + -
130P ALA* 4.1 9.0 - - + +
131P VAL* 1.3 68.5 - - - +
133P ALA* 1.3 60.9 + - - +
134P TYR* 3.9 6.3 + - + -
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Residues in contact with ALA 133 (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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64P VAL* 4.7 0.9 - - - -
65P LEU* 2.5 66.6 + - + +
67P GLU* 3.2 32.3 - - + +
131P VAL* 2.8 5.2 + - + +
132P LEU* 1.3 71.5 - - - +
134P TYR* 1.3 56.6 + - - +
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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