Contacts of the strand formed by residues 215 - 220 (chain S) in PDB entry 5A0Q
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 215 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S VAL 3.5 16.8 - - - +
52S LYS* 3.8 6.2 + - - +
199S LEU* 3.7 27.1 - - + -
202S LEU* 3.4 26.5 - - + -
210S LEU* 4.2 14.8 - - + -
211S ASN 3.7 12.6 - - - +
212S ALA* 3.0 30.1 - - - +
213S THR 3.5 0.4 - - - -
214S ASN* 1.4 78.7 + - - +
216S GLU* 1.3 78.2 + - - +
217S LEU* 4.0 18.4 - - + -
228S MET* 5.6 0.3 - - - +
231S LYS* 4.9 0.9 - - - -
234S LEU* 3.8 19.1 - - + +
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Residues in contact with GLU 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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49S ALA* 4.3 0.3 - - - -
50S VAL* 3.2 37.4 + - + +
52S LYS* 3.2 34.8 + - + +
62S SER* 5.2 2.1 - - - -
64S ILE 2.9 22.1 - - - +
65S GLU* 3.5 40.7 - - - +
66S LYS* 3.7 15.9 + - + +
67S ILE* 4.3 4.5 - - + +
215S ILE* 1.3 81.6 - - - +
217S LEU* 1.3 61.5 + - - +
218S ALA 4.2 0.2 + - - -
228S MET* 4.4 22.2 - - + +
231S LYS* 5.6 0.2 - - - -
234S LEU* 5.3 0.4 - - - -
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Residues in contact with LEU 217 (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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47S CYS* 3.8 4.7 - - - -
48S LEU 3.8 5.2 - - - +
49S ALA* 3.4 29.6 - - + -
67S ILE* 5.1 0.2 - - - -
195S ILE* 3.8 21.5 - - + -
198S SER* 3.8 14.1 - - - +
199S LEU* 4.7 3.1 - - + -
215S ILE* 4.0 15.6 - - + +
216S GLU* 1.3 73.2 - - - +
218S ALA* 1.4 62.4 + - - +
219S THR* 3.7 23.8 - - + -
228S MET* 3.3 10.6 - - - +
229S PHE* 3.0 31.3 + - + +
234S LEU* 3.6 38.8 - - + +
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Residues in contact with ALA 218 (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 VAL* 5.3 0.5 - - - +
48S LEU* 2.8 34.8 + - - +
67S ILE* 3.8 17.7 - - + +
216S GLU 4.2 0.6 + - - -
217S LEU* 1.4 75.9 - - - +
219S THR* 1.3 63.4 + - - +
226S PHE* 2.7 42.5 - - + -
227S HIS 3.4 9.0 - - - +
228S MET* 4.0 4.7 - - - -
229S PHE 4.2 0.9 - - - +
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Residues in contact with THR 219 (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 VAL 3.4 8.7 - - - -
47S CYS* 4.1 8.5 - - - -
191S LEU* 5.7 4.2 - - - +
195S ILE* 4.0 22.9 - - + +
217S LEU* 3.7 27.8 - - + -
218S ALA* 1.3 80.2 - - - +
220S VAL* 1.4 63.3 + - - +
227S HIS* 1.6 89.8 + - - +
229S PHE* 3.7 4.1 - - + -
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Residues in contact with VAL 220 (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 GLY* 3.2 3.6 - - - -
46S VAL* 3.0 47.2 + - + -
72S ALA 5.1 1.1 - - - +
73S HIS* 4.9 10.8 - - - +
75S GLY* 5.2 0.7 - - - +
144S GLY 5.0 8.3 - - - +
146S VAL* 3.7 22.7 - - + +
191S LEU* 4.6 0.9 - - - -
219S THR* 1.4 69.5 - - - +
221S GLN* 1.3 67.1 + - - +
224S GLN* 3.3 26.7 - - + +
225S ASN* 4.5 0.2 - - - -
226S PHE* 3.3 47.6 - - + +
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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