Contacts of the strand formed by residues 212 - 217 (chain A) in PDB entry 6N8P
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 LEU 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 5.0 1.1 - - + -
175A LEU* 4.3 7.0 - - + -
178A LEU* 3.7 27.1 - - + -
182A ALA 4.8 0.9 - - - +
189A GLU* 4.1 4.0 - - - +
208A TYR* 2.8 63.4 + - + -
210A ARG* 3.4 33.8 - - - +
211A GLY* 1.3 77.0 - - - +
213A VAL* 1.3 65.3 + - - +
214A VAL* 3.8 20.2 - - + -
226A HIS* 4.2 9.4 - - - +
227A PHE 3.7 6.5 - - - +
228A LEU* 3.7 21.0 - - + +
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Residues in contact with VAL 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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205A LEU* 3.7 30.1 - - + -
206A ILE 3.4 6.7 - - - +
207A GLY* 4.5 0.9 - - - -
211A GLY 4.1 3.8 - - - +
212A LEU* 1.3 79.2 - - - +
214A VAL* 1.3 66.0 + - - +
225A TYR* 5.0 1.5 - - + -
226A HIS* 3.1 5.5 - - - -
227A PHE* 3.1 72.5 + - + -
229A SER* 4.6 0.2 - - - +
233A LEU* 3.7 30.1 - - + -
236A ILE* 3.9 8.7 - - + -
245A LEU* 4.4 1.1 - - + -
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 4.1 18.2 - - + -
178A LEU* 4.1 10.5 - - + -
204A ILE 3.9 0.5 - - - +
205A LEU* 3.3 2.6 - - - +
206A ILE* 2.7 47.2 + - + +
208A TYR* 5.0 2.5 - - + -
212A LEU* 3.8 19.9 - - + -
213A VAL* 1.3 81.1 - - - +
215A ILE* 1.3 72.0 + - - +
216A TRP* 4.0 7.8 + - + +
223A VAL* 3.6 27.6 - - + -
225A TYR 3.3 3.4 - - - -
226A HIS* 3.6 17.7 - - + -
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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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203A GLN* 3.5 35.0 - - + +
204A ILE 3.3 8.5 - - - +
205A LEU* 4.5 9.2 - - + -
214A VAL* 1.3 76.0 - - - +
216A TRP* 1.3 61.2 + - - +
223A VAL* 3.6 5.0 - - - -
224A LEU* 3.0 32.9 + - + -
225A TYR* 3.0 44.5 + - + +
238A TRP* 3.7 32.1 - - + -
245A LEU* 4.8 1.3 - - + -
259A VAL* 3.8 22.0 - - + -
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Residues in contact with TRP 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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169A ILE* 3.6 41.1 - - + +
173A ALA* 4.0 18.8 - - + -
174A VAL* 3.7 32.8 - - + -
177A ARG* 4.1 11.4 - - - -
203A GLN* 3.3 8.5 - - - -
204A ILE* 2.7 42.8 + - + +
206A ILE* 4.4 10.3 - - + -
214A VAL* 4.0 3.3 + - + -
215A ILE* 1.3 75.6 - - - +
217A ASP* 1.3 84.1 + - - +
218A LEU* 3.5 15.5 + - + +
221A SER* 3.5 37.8 + - - +
222A ARG 3.9 5.2 - - - -
223A VAL* 3.7 30.5 - - + -
224A LEU* 4.8 2.0 - - - -
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Residues in contact with ASP 217 (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 ASN* 3.1 23.6 + - - -
203A GLN* 5.1 1.0 - - - +
216A TRP* 1.3 77.8 + - - +
218A LEU* 1.3 61.6 + - - +
219A GLN 2.9 34.1 - - - +
220A GLY* 3.3 6.1 - - - -
221A SER* 2.8 27.2 + - - -
222A ARG* 2.9 49.1 + - + +
224A LEU* 4.0 22.2 - - + +
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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