Contacts of the strand formed by residues 216 - 222 (chain A) in PDB entry 1SHZ
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA 4.6 3.1 - - - +
47A ARG* 3.9 29.2 - - + -
49A VAL* 4.2 23.8 - - + -
212A THR* 3.4 5.0 - - - +
213A PHE 3.1 29.4 + - - +
214A LYS 3.8 9.2 - - - +
215A ASP* 1.3 81.5 - - - +
217A HIS* 1.3 63.3 + - - +
218A PHE* 3.4 26.6 + - + -
362A THR* 4.4 6.5 - - + -
365A ILE* 5.1 6.3 - - + -
366A ILE* 3.9 30.1 - - + -
370A LEU* 4.9 11.4 - - + -
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Residues in contact with HIS 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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47A ARG* 3.2 37.2 + - + +
48A GLU* 3.8 14.7 - - - +
49A VAL* 3.0 25.6 + - - +
211A PHE 4.1 3.8 - - - -
212A THR* 3.4 26.4 + - + +
215A ASP 5.2 4.9 + - - -
216A LEU* 1.3 72.6 - - - +
218A PHE* 1.3 63.4 + - - +
219A LYS* 4.0 20.2 + - - +
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Residues in contact with PHE 218 (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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49A VAL* 3.6 26.2 - - + -
51A LEU* 4.6 13.9 - - + -
209A THR 3.6 0.5 - - - +
210A HIS* 3.4 8.7 - - - +
211A PHE* 3.0 67.4 + + + +
213A PHE* 3.8 31.9 - + + -
216A LEU* 3.6 26.9 - - + -
217A HIS* 1.3 71.6 - - - +
219A LYS* 1.3 64.0 + - - +
220A MET* 3.6 3.1 - - + +
358A PHE* 4.3 12.6 - + - -
362A THR* 4.0 26.7 - - + -
365A ILE* 4.1 16.8 - - + -
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Residues in contact with LYS 219 (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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48A GLU* 5.0 13.8 + - + +
49A VAL 2.6 20.3 + - - +
50A LYS* 3.7 7.5 - - + -
51A LEU* 3.2 18.0 + - - -
208A GLU* 4.5 3.8 - - - +
209A THR 3.6 3.8 - - - -
210A HIS* 3.3 43.1 + - + +
211A PHE 5.8 0.2 - - - +
217A HIS* 4.0 28.1 + - - +
218A PHE* 1.3 75.8 + - - +
220A MET* 1.3 58.7 + - - +
221A PHE* 3.2 28.7 - - + -
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Residues in contact with MET 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.8 44.6 - - + -
53A LEU* 4.4 11.2 - - + -
64A PHE* 6.1 0.4 - - + -
65A LEU* 3.5 29.8 - - + -
68A MET* 3.7 22.9 - - + -
208A GLU 3.4 1.2 - - - -
209A THR* 2.6 50.6 + - - +
211A PHE* 3.9 23.1 - - + -
218A PHE* 3.6 2.4 - - + -
219A LYS* 1.3 71.5 - - - +
221A PHE* 1.3 62.0 + - - +
222A ASP 4.3 0.2 + - - -
244A ILE* 4.8 4.7 - - + -
358A PHE* 3.9 21.3 - - + -
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Residues in contact with PHE 221 (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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50A LYS* 4.2 25.4 - - + -
51A LEU 3.2 9.4 + - - -
52A LEU* 3.9 20.3 - - + +
53A LEU* 3.0 32.0 + - - +
206A ILE* 3.8 26.2 - - + -
207A HIS 3.4 2.9 - - - -
208A GLU* 2.9 46.7 - - + -
219A LYS* 3.2 28.7 - - + -
220A MET* 1.3 76.2 - - - +
222A ASP* 1.3 60.5 + - - +
223A VAL* 4.7 1.9 - - + +
236A CYS* 4.5 11.2 - - + -
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Residues in contact with ASP 222 (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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53A LEU* 4.2 4.6 - - + +
61A LYS* 3.5 27.9 - - - +
62A SER* 2.7 25.8 + - - -
65A LEU* 3.3 37.3 - - + +
203A THR* 4.0 9.7 - - - +
205A GLY 3.8 1.2 - - - +
206A ILE* 3.5 1.7 - - - -
207A HIS* 2.7 48.1 + - + +
221A PHE* 1.3 73.1 - - - +
223A VAL* 1.3 70.3 + - - +
377A MG 4.0 2.0 - - - -
475A GDP 5.0 0.3 + - - -
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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