Contacts of the strand formed by residues 210 - 216 (chain S) in PDB entry 5M32
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 210 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47S VAL* 4.5 9.9 - - + -
48S ALA 3.4 7.9 - - - +
49S LEU* 4.9 2.2 - - + -
50S LYS* 4.5 1.1 - - - -
192S LEU* 4.6 10.1 - - + -
195S LEU* 4.7 4.3 - - + -
205S LEU* 3.8 34.8 - - + +
206S THR 3.5 13.3 + - - +
207S THR 3.9 4.0 - - - +
208S LYS 3.4 1.5 - - - +
209S ASN* 1.3 91.4 + - - +
211S SER* 1.3 61.1 + - - +
212S ILE* 3.9 15.3 - - + -
225S ASP 4.4 2.9 - - - +
226S ASP 5.1 0.2 + - - -
229S VAL* 3.5 41.6 - - + +
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Residues in contact with SER 211 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S ALA* 2.9 34.4 + - - +
50S LYS* 3.7 32.3 - - - -
61S LYS* 3.8 20.2 + - - -
62S LYS* 5.8 0.4 - - - -
63S ILE* 3.9 18.4 - - - +
209S ASN 3.7 1.0 + - - -
210S VAL* 1.3 73.2 - - - +
212S ILE* 1.3 61.4 + - - +
224S TYR 3.2 17.3 + - - -
225S ASP* 4.2 3.3 - - - -
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Residues in contact with ILE 212 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S LEU 3.3 11.4 - - - +
47S VAL* 3.8 30.1 - - + +
63S ILE* 3.7 9.3 - - - +
188S VAL* 3.7 10.8 - - + -
192S LEU* 4.2 4.7 - - + -
210S VAL* 3.9 13.9 - - + -
211S SER* 1.3 79.2 - - - +
213S GLY* 1.3 60.2 + - - +
214S ILE* 4.4 7.2 - - + -
223S ILE* 3.7 3.3 - - - -
224S TYR* 2.8 52.4 + - + +
229S VAL* 4.4 8.1 - - + -
232S PHE* 3.6 38.4 - - + -
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Residues in contact with GLY 213 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S VAL* 3.5 0.9 - - - -
46S LEU* 2.8 40.0 + - - +
63S ILE* 4.5 3.6 - - - +
212S ILE* 1.3 75.0 - - - +
214S ILE* 1.3 67.5 + - - +
215S VAL* 4.4 0.3 + - - +
221S PHE* 4.4 20.9 - - - -
222S THR 3.2 11.4 - - - -
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Residues in contact with ILE 214 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S HIS* 4.4 11.4 - - - +
44S ALA 4.1 1.3 - - - -
45S VAL* 3.7 21.1 - - + -
46S LEU 5.3 0.4 - - - +
184S LEU* 3.7 31.9 - - + -
188S VAL* 3.9 10.3 - - + -
212S ILE* 4.4 11.7 - - + -
213S GLY* 1.3 83.8 - - - +
215S VAL* 1.3 65.8 + - - +
219S LEU* 3.8 22.7 - - + -
220S GLU 3.4 3.5 - - - +
221S PHE* 3.2 3.8 - - - -
222S THR* 2.9 36.5 + - - +
224S TYR* 3.8 29.8 - - + +
232S PHE* 5.1 0.4 - - + -
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Residues in contact with VAL 215 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S HIS* 3.2 4.6 - - - +
44S ALA* 2.8 48.2 + - + +
46S LEU* 5.9 0.7 - - + -
69S HIS* 3.3 39.9 - - + +
135S ALA* 3.9 24.5 - - + +
136S GLY* 4.0 10.3 - - - +
137S TYR* 4.3 5.2 - - - +
142S PRO* 4.7 0.2 - - - +
213S GLY 5.8 0.2 - - - +
214S ILE* 1.3 77.0 - - - +
216S GLY* 1.3 62.7 + - - +
219S LEU* 3.7 9.2 - - - +
221S PHE* 3.6 26.2 - - + +
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Residues in contact with GLY 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S HIS* 3.6 13.0 - - - -
69S HIS* 5.8 1.0 - - - +
137S TYR* 3.5 32.2 - - - +
215S VAL* 1.3 81.1 - - - +
217S LYS* 1.3 66.3 + - - -
218S ASP 3.3 3.3 + - - -
219S LEU* 3.4 19.1 + - - +
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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