Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 3N4L
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 ILE 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A VAL* 5.0 0.7 - - + -
208A ILE* 1.3 71.5 - - - +
210A VAL* 1.3 63.3 + - - +
211A ARG 4.0 3.6 - - - +
212A VAL* 3.9 22.7 - - + -
223A CYS* 4.0 2.4 - - - +
226A TYR* 3.7 25.5 - - + +
227A ASN* 2.6 29.3 + - - +
231A SER* 3.7 23.8 - - - +
242A LEU* 6.0 0.2 - - + -
291A LEU* 4.4 17.3 - - + -
292A TYR 3.5 10.5 - - - +
293A LEU* 3.8 20.0 - - + -
337A THR* 3.8 23.8 - - + +
339A MET* 4.4 12.3 - - - -
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Residues in contact with VAL 210 (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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208A ILE* 3.7 22.0 - - + +
209A ILE* 1.3 78.0 - - - +
211A ARG* 1.3 58.7 + - + +
223A CYS* 3.4 19.9 - - - +
226A TYR* 4.0 2.2 - - - -
292A TYR* 2.6 34.6 + - + +
293A LEU 4.5 0.2 - - - -
294A MET* 3.9 18.8 - - + +
301A SER* 4.0 18.4 - - - -
382A THR* 4.1 23.8 - - + +
385A MET* 4.3 12.1 - - + +
388A CYS* 4.1 17.1 - - - -
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Residues in contact with ARG 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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209A ILE* 3.7 1.7 - - - +
210A VAL* 1.3 83.2 - - + +
212A VAL* 1.3 68.1 + - - +
213A GLU* 2.8 24.9 + - + +
218A ASP* 2.7 42.3 + - - +
226A TYR* 3.9 6.7 - - - -
291A LEU* 3.9 0.2 - - - -
292A TYR* 3.0 60.2 + - + +
381A VAL 5.7 1.6 - - - -
382A THR* 4.7 17.9 - - - -
303C ARG* 3.1 17.8 - - - +
377C GLU* 5.4 2.6 - - - +
380C PHE* 3.7 23.6 - - - -
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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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209A ILE* 3.9 7.0 - - + -
211A ARG* 1.3 81.4 - - - +
213A GLU* 1.3 67.5 + - - +
214A ILE* 4.9 2.5 - - + -
218A ASP* 3.2 4.6 + - - +
219A LEU* 3.1 51.2 + - + +
226A TYR* 3.7 31.8 + - + -
242A LEU* 6.5 0.4 - - + -
246A VAL* 5.4 3.4 - - + -
289A ILE* 4.1 18.6 - - + -
290A SER 3.5 10.5 - - - +
291A LEU* 3.8 20.9 - - + -
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Residues in contact with GLU 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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211A ARG* 2.8 34.6 + - + +
212A VAL* 1.3 75.5 - - - +
214A ILE* 1.3 62.3 + - - +
215A ASN 4.0 0.6 + - - -
216A GLY* 3.9 18.4 + - - +
217A GLN 3.3 6.1 - - - +
218A ASP* 3.6 21.1 - - + +
288A VAL* 4.0 0.5 - - - +
289A ILE* 3.5 3.3 - - - +
290A SER* 2.8 47.4 + - - +
292A TYR* 2.7 32.7 + - + -
303A ARG* 4.1 6.6 + - - -
213C GLU* 5.4 1.2 - - - +
216C GLY 5.6 0.7 - - - +
303C ARG* 3.3 19.3 + - - -
380C PHE* 5.2 0.7 - - - -
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Residues in contact with ILE 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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212A VAL* 4.9 2.5 - - + -
213A GLU* 1.3 74.9 - - - +
215A ASN* 1.3 73.2 + - + +
217A GLN* 3.0 24.3 + - + +
219A LEU* 4.2 15.5 - - + -
250A ALA* 4.0 37.9 - - + +
253A SER* 3.7 25.3 + - - +
254A ILE* 4.1 12.1 - - + -
257A ALA* 5.9 0.7 - - + -
287A PRO* 3.7 29.2 - - + -
288A VAL 3.5 4.7 - - - +
289A ILE* 4.5 17.9 - - + -
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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