Contacts of the strand formed by residues 225 - 233 (chain A) in PDB entry 3NIA
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 VAL 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 4.0 27.6 - - + -
223A ASP 3.6 5.8 + - - +
224A TRP* 1.3 70.3 - - - +
226A VAL* 1.3 62.2 + - - +
243A PHE* 4.4 9.4 - - + -
244A PHE* 3.1 3.6 - - - -
245A LYS* 2.8 55.3 + - + +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.6 14.6 - - - +
216A LEU* 6.2 0.2 - - + -
217A ARG* 3.6 40.6 + - + +
220A PHE* 3.5 43.1 - - + -
221A PRO 5.5 0.2 - - - +
224A TRP* 3.4 21.3 + - + +
225A VAL* 1.3 81.3 - - - +
227A GLY* 1.3 68.7 + - - +
228A GLU* 4.5 6.7 - - + -
243A PHE* 3.3 14.6 - - - +
244A PHE* 3.5 9.6 - - + -
253A VAL* 6.3 0.9 - - + -
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.4 26.9 - - - -
207A ILE 3.7 2.5 - - - -
217A ARG* 4.8 0.7 - - - -
226A VAL* 1.3 74.7 - - - +
228A GLU* 1.3 65.6 + - - +
242A GLY* 3.3 0.9 - - - -
243A PHE* 2.9 46.8 + - - +
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.3 19.0 + - - +
209A ASN* 3.2 33.5 + - - +
212A GLY* 3.7 6.1 - - - -
216A LEU* 5.0 7.9 - - + -
217A ARG* 3.1 38.9 + - + -
226A VAL* 4.5 12.6 - - + -
227A GLY* 1.3 78.2 - - - +
229A LYS* 1.3 60.1 + - - +
230A THR* 3.5 13.7 - - - +
240A ASP* 2.5 38.3 - - - +
241A ILE 3.1 18.2 - - - +
242A GLY* 3.9 2.2 - - - -
253A VAL* 6.3 0.2 - - + -
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 3.3 25.8 - - - +
65A THR* 3.7 14.3 - - - +
67A LYS* 3.8 6.5 - - + -
68A PHE* 4.0 22.2 - - + +
121A ALA 3.5 21.8 - - - -
122A VAL* 3.4 28.5 + - + +
125A SER* 2.9 25.8 + - - -
206A LEU* 4.0 4.9 - - + +
209A ASN* 4.7 1.3 - - - +
211A THR* 4.4 2.6 + - - -
228A GLU* 1.3 73.7 - - - +
230A THR* 1.3 87.3 + - - +
240A ASP* 3.4 4.9 - - - -
241A ILE* 2.8 35.6 + - + +
289A TF7 3.2 7.3 + - - -
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 3.3 12.3 - - - -
65A THR* 4.0 2.7 - - - -
211A THR* 2.7 32.1 + - - +
212A GLY* 3.8 1.8 - - - -
215A THR* 3.4 26.0 - - - +
228A GLU* 3.5 14.8 - - - +
229A LYS* 1.3 96.4 + - - +
231A GLY* 1.3 59.6 + - - +
238A ARG* 3.7 15.5 - - - +
239A ASN 3.3 6.7 - - - +
240A ASP* 3.6 5.4 - - - +
289A TF7 2.7 25.3 + - - -
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER 3.9 9.2 - - - -
65A THR* 3.9 7.4 - - - +
230A THR* 1.3 76.3 - - - +
232A THR* 1.3 60.1 + - - -
238A ARG* 3.4 9.1 + - - -
239A ASN* 2.9 39.3 + - - -
288A TBE 3.4 8.7 - - - -
289A TF7 3.1 9.4 - - - -
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A CYS* 3.6 4.9 - - - +
165A ASN* 4.2 1.4 - - - +
231A GLY* 1.3 70.2 - - - -
233A CYS* 1.3 67.7 + - - +
237A GLY 3.4 11.9 - - - +
238A ARG* 3.0 22.5 + - - +
267A ARG* 6.3 2.9 - - - +
288A TBE 2.9 56.3 + - - +
289A TF7 2.8 25.8 + - + +
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Residues in contact with CYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.8 12.8 - - - -
63A CYS* 2.0 48.5 - - - -
165A ASN* 3.7 2.2 - - - -
167A ASN* 3.8 11.9 - - + +
232A THR* 1.3 78.9 - - - +
234A ALA* 1.3 72.9 + - - +
236A GLY* 3.6 2.8 + - - -
237A GLY* 3.0 32.2 + - - +
239A ASN* 3.6 20.4 - - - -
288A TBE 5.4 2.5 - - - -
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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