Contacts of the strand formed by residues 207 - 213 (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 HIS 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.9 5.4 - - + -
203A THR* 4.0 19.1 - - + +
204A LYS 3.2 26.7 - - - -
205A GLY* 3.7 4.8 + - - -
206A ILE* 1.3 84.7 + - - +
208A GLU* 1.3 62.7 + - - +
209A THR* 4.0 2.9 + - - +
220A MET 3.7 0.7 - - - +
221A PHE* 3.4 2.7 - - - -
222A ASP* 2.7 53.9 + - + +
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Residues in contact with GLU 208 (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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206A ILE* 4.2 1.6 + - + +
207A HIS* 1.3 71.3 - - - +
209A THR* 1.3 72.8 + - - +
210A HIS* 3.3 31.2 + - + +
219A LYS* 4.5 4.5 - - - +
220A MET 3.5 3.1 - - - -
221A PHE* 2.9 48.2 - - + -
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Residues in contact with THR 209 (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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65A LEU* 3.6 27.7 - - + +
68A MET* 6.3 2.7 - - + -
69A ARG* 6.2 4.7 - - + -
207A HIS* 4.5 0.5 - - - +
208A GLU* 1.3 80.6 + - - +
210A HIS* 1.3 80.1 + - - +
211A PHE* 4.6 8.2 - - + -
218A PHE 3.6 0.2 - - - +
219A LYS 3.6 0.2 - - - -
220A MET* 2.6 54.1 + - - +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 3.3 33.5 + - + -
209A THR* 1.3 91.6 - - - +
211A PHE* 1.3 72.5 + - - +
218A PHE 3.4 4.9 - - - +
219A LYS* 3.3 40.6 + - + +
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Residues in contact with PHE 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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68A MET* 4.2 15.7 - - + -
72A HIS* 3.6 42.6 - + + -
73A GLY* 4.9 9.9 - - - +
209A THR* 4.7 8.5 - - + -
210A HIS* 1.3 86.6 - - - +
212A THR* 1.3 64.1 + - - +
213A PHE* 4.5 4.9 - - + -
216A LEU 3.7 0.3 - - - +
217A HIS* 4.0 0.4 - - - -
218A PHE* 3.0 60.1 + + + +
219A LYS* 5.8 0.2 - - - +
220A MET* 3.9 44.2 - - + -
358A PHE* 4.2 10.5 - + - -
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Residues in contact with THR 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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72A HIS* 5.3 5.2 - - - +
211A PHE* 1.3 77.2 + - - +
213A PHE* 1.3 65.4 + - - +
215A ASP* 4.3 13.2 - - - +
216A LEU 3.4 18.8 - - - +
217A HIS* 3.4 26.8 + - + +
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Residues in contact with PHE 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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72A HIS* 3.9 32.3 - + + +
211A PHE* 4.1 2.8 + - + -
212A THR* 1.3 75.6 - - - +
214A LYS* 1.3 111.5 + - + +
215A ASP 3.2 0.9 - - - -
216A LEU* 3.1 22.8 + - - +
218A PHE* 3.8 16.1 - + + -
358A PHE* 3.6 31.2 - + - -
359A ASP* 3.8 18.2 - - - -
362A THR* 3.3 24.9 - - + -
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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