Contacts of the strand formed by residues 210 - 216 (chain A) in PDB entry 3NN9
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 ARG 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A TRP* 3.2 7.7 - - - -
207A TYR 3.0 32.4 + - - +
208A ASN* 3.7 31.4 + - - +
209A ARG* 1.3 83.3 - - + +
211A PRO* 1.4 70.2 - - + +
212A VAL* 3.4 5.6 - - + +
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Residues in contact with PRO 211 (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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204A VAL* 3.9 20.9 - - + -
205A ILE 3.9 6.5 - - - +
206A TRP* 3.6 27.9 - - + -
210A ARG* 1.4 84.9 - - + +
212A VAL* 1.3 60.1 + - - +
214A GLU* 4.8 4.0 - - - +
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Residues in contact with VAL 212 (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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205A ILE 2.9 12.2 + - - +
207A TYR* 4.0 22.0 - - + +
210A ARG* 3.4 17.7 - - + +
211A PRO* 1.3 77.0 - - - +
213A THR* 1.3 65.5 + - - +
214A GLU* 3.3 12.3 + - - +
259A GLU 4.4 15.3 - - - +
260A GLY* 4.4 10.1 - - - -
261A LYS* 5.1 1.6 - - + +
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Residues in contact with THR 213 (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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204A VAL* 3.3 3.1 - - - +
205A ILE* 2.8 47.1 + - + +
212A VAL* 1.3 77.6 + - - +
214A GLU* 1.4 72.7 + - - +
215A ILE* 4.4 0.2 - - + -
257A PHE* 4.6 0.2 - - + -
260A GLY 2.8 26.7 + - - +
261A LYS* 3.9 7.1 - - - +
262A ILE* 3.8 35.0 - - + +
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Residues in contact with GLU 214 (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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202A SER* 5.8 2.5 - - - -
203A ALA 3.2 10.8 - - - +
204A VAL* 4.0 19.0 - - + +
205A ILE* 4.4 0.2 - - - -
211A PRO* 4.8 3.6 - - - +
212A VAL 3.3 18.9 + - - +
213A THR* 1.4 91.5 - - - +
215A ILE* 1.3 70.2 + - - +
262A ILE* 5.4 0.3 - - - +
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Residues in contact with ILE 215 (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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202A SER* 3.4 6.2 - - - -
203A ALA* 2.8 39.5 + - + +
205A ILE* 3.7 22.2 - - + -
213A THR* 4.4 0.4 - - + -
214A GLU* 1.3 84.0 - - - +
216A ASN* 1.3 74.7 + - - +
218A TRP* 3.9 21.3 - - + -
223A LEU* 4.4 2.6 - - + +
241A PHE* 5.0 8.3 - - + -
255A TYR* 3.7 26.9 - - + +
257A PHE* 4.1 7.9 - - + -
262A ILE* 3.7 29.4 - - + -
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Residues in contact with ASN 216 (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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200A ASN* 4.6 13.8 + - - +
201A ALA 3.4 16.1 + - - -
202A SER* 4.0 10.5 + - - -
215A ILE* 1.3 80.5 - - - +
217A THR* 1.3 87.6 + - - +
218A TRP* 3.3 18.0 + - - +
220A ARG* 5.7 0.3 + - - -
223A LEU* 4.0 4.0 - - - -
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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