Contacts of the strand formed by residues 222 - 228 (chain A) in PDB entry 3NT2
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 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU 3.1 8.2 + - - +
150A MET* 3.3 5.4 - - - +
151A ILE 2.9 24.2 + - - +
152A HIS* 5.9 0.2 - - - -
214A VAL* 4.3 17.3 - - + -
215A ILE 3.7 3.1 - - - +
216A GLU* 4.3 13.5 - - + +
220A GLY 3.7 4.7 - - - +
221A ILE* 1.3 72.5 - - - +
223A ILE* 1.3 70.7 + - - +
224A ASN* 4.1 0.6 + - + -
195B ILE* 4.2 19.3 - - + -
196B TYR 4.5 1.1 - - - +
197B PRO* 3.5 37.0 - - + -
212B ILE* 3.7 27.9 - - + +
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Residues in contact with ILE 223 (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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151A ILE* 3.4 26.5 - - + +
153A CYS* 4.5 6.5 - - - -
181A LEU* 3.6 36.3 - - + -
185A VAL* 6.1 1.1 - - + -
189A TYR* 3.7 31.0 - - + -
213A VAL 3.7 0.6 - - - +
214A VAL* 3.2 6.4 - - - +
215A ILE* 2.7 61.6 + - + +
217A THR* 4.5 7.9 - - + -
221A ILE* 4.6 6.7 - - + +
222A VAL* 1.3 78.1 - - - +
224A ASN* 1.3 70.1 + - - +
225A ALA* 4.2 5.8 - - + +
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Residues in contact with ASN 224 (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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151A ILE 3.0 5.9 + - - +
152A HIS* 2.8 33.8 + - - +
153A CYS 3.3 19.6 + - - +
212A ILE* 4.8 5.8 - - + +
213A VAL 3.4 3.1 - - - +
214A VAL* 4.2 19.3 - - + -
222A VAL* 4.1 2.8 + - + +
223A ILE* 1.3 77.0 - - - +
225A ALA* 1.3 60.4 + - - +
226A GLU 4.1 0.3 + - - -
152B HIS* 4.9 3.6 + - - -
212B ILE* 5.3 9.5 - - + +
224B ASN* 3.3 40.8 + - - +
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Residues in contact with ALA 225 (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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153A CYS* 3.3 24.2 - - - -
174A LEU* 4.0 26.0 - - + -
177A GLU* 5.5 0.4 - - + -
181A LEU* 6.0 0.2 - - + -
211A GLN 3.9 0.2 - - - +
212A ILE* 3.5 4.7 - - - +
213A VAL* 2.8 46.3 + - + +
215A ILE* 6.1 2.0 - - + -
223A ILE* 4.2 6.7 - - + -
224A ASN* 1.3 73.4 - - - +
226A GLU* 1.3 63.0 + - - +
227A ILE* 3.8 3.2 + - - +
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Residues in contact with GLU 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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153A CYS 2.8 15.6 + - - +
154A ALA* 3.2 4.5 - - + +
155A HIS* 2.8 27.7 + - - +
156A ARG* 2.7 44.0 + - - -
211A GLN 3.7 4.5 - - - +
212A ILE* 4.7 4.5 - - + +
224A ASN 4.1 0.6 + - - -
225A ALA* 1.3 73.3 - - - +
227A ILE* 1.3 69.5 + - - +
228A TYR* 3.9 4.9 - - + +
150B MET* 3.3 39.4 - - + +
152B HIS* 2.8 34.4 + - + -
242B VAL* 3.7 6.0 - - - +
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Residues in contact with ILE 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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155A HIS* 3.6 12.3 - - + +
169A ALA* 3.8 24.5 - - + +
170A VAL* 4.8 1.6 - - + -
173A THR* 4.1 12.8 - - + -
174A LEU* 3.6 48.2 - - + -
209A ASP* 3.6 2.5 - - - +
210A PRO* 3.3 4.6 - - - +
211A GLN* 2.9 47.3 + - + +
213A VAL* 4.1 12.6 - - + -
225A ALA* 4.3 6.3 - - + +
226A GLU* 1.3 77.8 - - - +
228A TYR* 1.3 62.0 + - - +
229A VAL* 4.0 20.9 - - + -
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Residues in contact with TYR 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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155A HIS 3.2 8.5 + - - -
156A ARG* 3.2 10.8 - - + +
157A ASN 3.0 23.1 + - - +
200A SER* 2.8 33.0 + - - -
209A ASP* 3.1 22.2 - - - -
210A PRO* 4.0 11.0 - - + -
226A GLU* 3.9 15.4 - - - +
227A ILE* 1.3 75.1 - - - +
229A VAL* 1.3 58.4 + - - +
230A ASN 3.1 24.0 + - - -
231A CYS* 3.5 20.7 - - + +
149B LEU* 3.9 8.1 - - + -
150B MET* 4.4 3.8 - - + -
242B VAL* 4.1 17.9 - - + -
243B GLY 3.5 19.3 - - - -
244B GLU* 2.7 25.9 + - - -
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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