Contacts of the strand formed by residues 233 - 236 (chain E) in PDB entry 1NJI
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 233 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E THR* 3.5 26.3 + - - +
136E VAL* 5.4 0.8 - - - +
137E PRO* 4.0 3.5 - - - +
138E VAL* 3.3 25.3 + - - +
192E ILE* 4.5 0.4 - - - -
193E LEU* 3.4 27.5 - - + +
195E VAL* 3.8 18.2 - - + -
223E LEU* 4.7 1.1 - - + +
231E ARG* 2.6 23.1 + - - +
232E LEU* 1.3 77.7 - - - +
234E VAL* 1.3 75.3 + - - +
235E PHE* 3.3 26.7 - - + -
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Residues in contact with VAL 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 3.0 20.6 - - + +
140E VAL* 4.2 16.8 - - + -
144E PHE* 5.3 9.2 - - + -
157E LEU* 5.2 5.8 - - + -
160E LEU* 6.1 1.1 - - + -
162E VAL* 6.4 0.4 - - + -
192E ILE* 3.2 30.3 - - + -
193E LEU 3.1 2.6 + - - +
194E PHE* 3.4 29.9 - - + +
195E VAL 3.0 22.5 + - - +
233E THR* 1.3 78.3 - - - +
235E PHE* 1.3 71.3 + - - +
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Residues in contact with PHE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E PHE* 3.6 22.9 - + - -
115E LEU* 3.9 13.2 - - + -
118E THR* 3.8 7.2 - - + -
137E PRO* 3.6 32.3 - - + -
138E VAL 2.8 9.5 + - - +
139E VAL* 4.9 2.9 - - + -
140E VAL* 3.2 22.3 + - - +
144E PHE* 6.0 1.4 - - - -
195E VAL* 3.5 26.5 - - + -
218E VAL* 6.0 0.7 - - + -
223E LEU* 5.1 2.0 - - + -
233E THR* 3.3 28.0 - - + -
234E VAL* 1.3 82.0 - - - +
236E THR* 1.3 64.2 + - - +
240E LEU* 4.1 34.8 - - + +
243E VAL* 3.6 27.8 - - + -
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Residues in contact with THR 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E VAL* 4.6 1.1 - - - -
140E VAL 3.5 4.0 + - - -
141E SER 4.2 2.9 + - - -
142E ASP* 3.3 22.0 + - - +
144E PHE* 4.4 9.9 - - - +
145E GLU* 4.4 11.3 - - - +
195E VAL 3.2 10.7 + - - -
196E THR* 4.0 8.4 - - - +
197E SER* 4.2 11.2 - - - +
235E PHE* 1.3 76.7 - - - +
237E GLU* 1.3 68.4 + - - +
238E SER* 3.2 13.5 - - - +
239E ALA* 2.7 31.6 + - + +
240E LEU* 2.6 25.5 + - - +
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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
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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