Contacts of the strand formed by residues 111 - 114 (chain O) in PDB entry 2JA7
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 THR 111 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O ALA* 5.7 4.5 - - + -
104O PHE 4.0 17.4 + - - +
105O GLY* 3.9 16.3 - - - -
106O GLU* 5.5 0.2 - - - +
107O SER* 2.7 27.4 + - - +
110O THR* 1.3 70.6 - - - +
112O ASN* 1.3 74.1 + - - +
146O LYS* 3.6 1.2 - - - -
147O LEU* 3.0 47.1 + - + +
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Residues in contact with ASN 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O THR* 3.6 25.5 + - - +
111O THR* 1.3 89.6 + - - +
113O VAL* 1.3 62.7 + - - +
114O TYR* 2.7 49.8 + - + -
117O ASP* 3.9 5.4 - - - +
143O LEU* 4.2 12.7 - - + +
145O CYS 4.0 3.4 - - - -
146O LYS* 4.3 11.6 - - - +
19V GLU* 3.2 14.2 - - - +
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Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O LEU* 4.0 36.8 - - + -
103O ALA* 3.8 22.4 - - + -
111O THR* 5.8 0.4 - - + -
112O ASN* 1.3 75.9 - - - +
114O TYR* 1.3 54.6 + - - +
117O ASP* 3.6 5.2 - - + +
143O LEU* 3.2 5.1 - - - +
144O ILE* 2.6 42.6 + - + +
145O CYS* 2.9 21.2 + - - +
147O LEU* 3.1 34.5 - - + -
153O LEU* 4.8 4.9 - - + -
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Residues in contact with TYR 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O LEU* 4.8 0.3 - - - +
112O ASN* 2.7 47.1 + - + -
113O VAL* 1.3 73.1 - - - +
115O SER* 1.3 53.6 + - - +
116O LYS* 4.0 11.0 - - + +
117O ASP* 2.7 45.0 + - - +
118O LEU 4.3 0.3 + - - -
136O ASP* 5.6 0.7 - - - -
140O ASN* 3.0 56.4 + - + +
141O GLY* 4.4 1.3 - - - -
142O VAL 3.4 5.8 - - - -
143O LEU* 4.2 21.5 - - + -
144O ILE* 4.6 7.3 - - - +
16V ASP* 6.3 0.9 - - - -
19V GLU* 2.6 34.5 + - - -
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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
------------------------------------------------------------
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