Contacts of the helix formed by residues 168 - 176 (chain F) 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 TRP 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234D PHE* 5.2 3.4 - - - -
60F MET* 4.8 1.9 - - - +
61F ALA* 4.3 19.1 - - + -
64F GLN* 3.5 32.5 - - + +
167F PRO* 1.3 79.6 - - + +
169F GLU* 1.3 57.5 + - - +
170F GLN* 3.1 3.6 - - - +
171F GLU* 3.5 19.1 + - - +
172F LEU* 2.9 29.4 + - - +
196F ARG* 5.3 1.6 - - - -
197F LEU* 3.7 51.4 + - + +
200F HIS* 3.4 54.1 - + + -
204F MET* 6.3 1.3 - - + -
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Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LYS* 5.5 13.5 - - + -
234D PHE* 5.9 0.8 - - + -
157F PHE* 5.4 0.3 - - - -
161F ARG* 2.8 47.7 + - - +
164F GLY* 5.7 5.2 - - - -
166F THR* 3.2 31.8 + - - +
167F PRO 2.7 7.8 + - - +
168F TRP* 1.3 74.3 - - - +
170F GLN* 1.3 57.0 + - - +
172F LEU* 3.3 19.8 - - - +
173F ALA* 3.1 35.8 + - + +
176F GLU* 4.5 2.4 - - - +
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Residues in contact with GLN 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LYS* 4.2 35.0 - - + +
168F TRP* 3.1 1.1 - - - -
169F GLU* 1.3 76.8 - - - +
171F GLU* 1.3 83.8 + - - +
173F ALA* 4.0 2.6 - - - +
174F GLN* 3.0 32.2 + - - +
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Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F TRP* 3.5 30.3 - - - +
170F GLN* 1.3 86.9 - - - +
172F LEU* 1.3 66.9 + - - +
174F GLN* 3.1 13.8 + - - +
175F LEU* 2.9 25.3 + - - +
193F VAL* 4.3 20.1 - - + +
196F ARG* 3.1 40.8 + - - +
197F LEU* 4.3 7.6 - - + -
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 4.1 16.4 - - + -
57F ALA* 4.1 11.9 - - + +
58F HIS* 3.4 54.9 - - + +
61F ALA* 4.4 13.5 - - + -
157F PHE* 5.5 0.2 - - + -
161F ARG* 4.2 6.3 - - - +
167F PRO 4.9 0.2 - - - +
168F TRP* 2.9 19.4 + - - +
169F GLU* 3.3 31.0 - - - +
171F GLU* 1.3 79.0 - - - +
173F ALA* 1.3 63.2 + - - +
175F LEU* 3.1 11.6 + - + +
176F GLU* 3.1 21.2 + - - +
193F VAL* 5.5 1.8 - - - +
197F LEU* 5.3 5.6 - - + +
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Residues in contact with ALA 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F GLU* 3.1 23.6 + - + +
170F GLN* 4.0 3.6 - - - +
172F LEU* 1.3 79.4 - - - +
174F GLN* 1.3 62.4 + - - +
176F GLU* 3.1 32.5 + - - +
177F ALA* 4.6 3.3 - - - +
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Residues in contact with GLN 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F GLN* 3.0 26.8 + - - +
171F GLU* 3.1 14.5 + - - +
173F ALA* 1.3 79.3 - - - +
175F LEU* 1.3 59.9 + - - +
177F ALA* 4.1 11.5 + - - +
178F TRP* 4.4 4.7 + - - +
189F ARG* 5.9 1.2 + - - +
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ALA* 4.0 16.4 - - + -
58F HIS* 5.7 4.0 - - - +
171F GLU 2.9 15.7 + - - +
172F LEU* 3.7 4.9 - - + +
174F GLN* 1.3 73.4 - - - +
176F GLU* 1.3 53.9 + - + +
177F ALA 2.7 17.4 + - - -
178F TRP* 3.3 11.2 + - + +
186F TYR* 3.4 32.6 + - + +
189F ARG* 3.5 40.2 - - + +
190F GLU* 3.7 21.5 - - + +
193F VAL* 3.6 30.1 - - + -
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Residues in contact with GLU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLN* 2.7 37.8 + - - +
58F HIS* 3.4 26.2 - - + +
161F ARG* 3.6 18.8 + - - -
169F GLU* 4.5 0.5 - - - +
172F LEU* 3.1 21.1 - - - +
173F ALA* 3.1 22.2 + - - +
175F LEU* 1.3 74.6 - - + +
177F ALA* 1.3 60.4 + - - +
186F TYR* 4.3 7.0 - - - +
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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