Contacts of the strand formed by residues 237 - 246 (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 GLY 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASN* 4.4 4.7 - - - -
232A THR* 3.4 9.4 - - - +
233A CYS* 3.0 48.4 + - - +
234A ALA 3.6 1.6 + - - -
235A ASN 3.5 2.8 + - - -
236A GLY* 1.3 76.9 - - - +
238A ARG* 1.3 61.9 + - - +
239A ASN* 4.4 2.2 - - - -
257A THR 3.3 9.6 - - - -
258A THR* 4.4 3.1 - - - -
267A ARG* 4.8 2.1 - - - -
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Residues in contact with ARG 238 (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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211A THR 4.4 10.7 + - - -
214A ALA* 5.9 0.8 - - - +
215A THR* 3.6 16.9 - - + +
230A THR* 3.7 14.3 - - - +
231A GLY 3.4 10.7 + - - -
232A THR* 3.0 29.2 + - - +
236A GLY 3.7 0.6 + - - -
237A GLY* 1.3 74.8 - - - -
239A ASN* 1.3 62.6 + - - +
257A THR* 2.7 48.8 + - - +
264A ALA 5.2 0.8 + - - -
267A ARG* 4.0 30.3 - - + +
268A ASP* 2.8 31.2 + - - +
271A VAL* 3.8 20.2 - - + +
289A TF7 3.1 23.5 + - - +
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Residues in contact with ASN 239 (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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60A PHE* 5.3 1.2 - - - +
61A ALA 3.1 23.9 + - - +
62A MET 3.4 11.9 + - - -
63A CYS* 4.4 1.8 - - - +
65A THR* 3.6 12.8 - - + -
215A THR* 5.5 1.0 - - - +
230A THR* 3.3 5.9 - - - +
231A GLY 2.9 29.7 + - - +
233A CYS* 3.6 17.0 - - - -
237A GLY* 4.4 0.7 - - - -
238A ARG* 1.3 87.1 + - - +
240A ASP* 1.3 64.9 + - - +
255A VAL 3.3 10.8 - - - +
256A TYR* 3.1 19.5 - - + +
257A THR 3.2 19.1 + - - +
271A VAL* 5.2 3.1 - - - -
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Residues in contact with ASP 240 (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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215A THR* 2.7 24.2 + - - +
216A LEU* 3.0 38.7 + - + +
228A GLU* 2.5 36.6 - - - +
229A LYS 3.3 14.6 - - - +
230A THR* 3.7 8.3 - - - -
239A ASN* 1.3 74.6 - - - +
241A ILE* 1.3 61.5 + - - +
254A ALA 3.9 0.2 - - - -
255A VAL* 2.8 34.3 + - - +
271A VAL* 4.1 11.4 - - + -
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Residues in contact with ILE 241 (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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65A THR* 3.6 36.8 - - + +
68A PHE* 3.9 23.2 - - + -
69A PRO* 4.4 1.6 - - + -
181A MET* 3.7 27.1 - - + -
185A VAL* 4.1 5.2 - - + -
216A LEU* 5.6 0.4 - - - -
228A GLU* 3.1 5.6 - - - -
229A LYS* 2.8 36.5 + - + +
240A ASP* 1.3 79.8 - - - +
242A GLY* 1.3 59.7 + - - +
253A VAL* 3.4 10.3 - - - +
254A ALA* 3.8 11.0 - - + -
255A VAL 4.6 0.4 - - - +
256A TYR* 3.4 34.8 - - + +
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Residues in contact with GLY 242 (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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68A PHE* 4.5 9.2 - - - -
185A VAL* 3.4 19.6 - - - +
206A LEU* 5.4 0.2 - - - -
227A GLY 3.3 10.8 - - - -
228A GLU* 3.9 2.5 - - - -
241A ILE* 1.3 78.1 - - - +
243A PHE* 1.3 62.6 + - - -
252A ALA* 3.5 0.2 - - - -
253A VAL* 2.9 38.1 + - - +
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Residues in contact with PHE 243 (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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189A LEU* 3.4 26.2 - - + -
190A TYR* 3.5 17.3 - + + +
203A GLU* 3.9 27.1 - - + -
206A LEU* 3.9 22.7 - - + -
207A ILE* 3.8 21.8 - - + -
225A VAL* 4.4 16.2 - - + -
226A VAL* 3.3 5.3 - - - +
227A GLY* 2.9 58.5 + - - +
242A GLY* 1.3 75.0 - - - +
244A PHE* 1.3 73.1 + - - +
245A LYS* 6.0 1.6 - - + -
251A TYR 3.2 15.0 - - - +
252A ALA* 4.4 1.6 - - - +
253A VAL* 4.3 1.3 - - - +
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Residues in contact with PHE 244 (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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43A ILE* 4.4 5.4 - - + -
190A TYR* 4.3 0.8 + - - -
220A PHE* 3.8 22.2 - + - -
224A TRP* 3.4 33.0 - + + -
225A VAL 3.1 6.1 - - - -
226A VAL* 3.5 23.3 - - + -
243A PHE* 1.3 82.2 - - - +
245A LYS* 1.3 61.1 + - - +
246A ALA* 4.1 4.5 - - + -
249A ARG 3.8 0.5 - - - +
250A ASP* 3.6 1.2 - - - -
251A TYR* 2.9 69.6 + + + -
253A VAL* 4.0 27.1 - - + -
278A ILE* 4.1 11.7 - - + -
282A ILE* 4.0 19.1 - - + -
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Residues in contact with LYS 245 (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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224A TRP* 3.6 9.5 - - - +
225A VAL* 2.8 46.9 + - + +
243A PHE* 5.0 2.2 - - + -
244A PHE* 1.3 72.8 - - - +
246A ALA* 1.3 61.6 + - - +
248A GLU* 4.3 26.4 + - - +
249A ARG 3.2 11.7 - - - +
250A ASP* 2.7 42.8 + - - +
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Residues in contact with ALA 246 (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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224A TRP* 3.3 44.6 - - + +
244A PHE* 4.1 7.8 - - + -
245A LYS* 1.3 73.7 - - - +
247A GLN* 1.3 75.6 + - + +
248A GLU 3.1 0.9 - - - -
249A ARG* 2.9 23.3 + - - +
251A TYR* 4.2 4.0 + - + -
282A ILE* 4.0 15.9 - - + +
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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