Contacts of the helix formed by residues 166 - 169 (chain b) in PDB entry 5W97
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 PRO 166 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366a VAL* 4.4 12.8 - - + +
433a LEU 6.2 0.4 - - - +
435a GLY* 4.8 17.7 - - - +
10b GLN* 3.8 29.2 - - + +
17b MET* 3.6 13.5 - - - +
164b ALA* 3.8 12.1 - - + -
165b VAL* 1.4 85.3 - - - +
167b SER* 1.3 63.3 + - - +
169b GLY* 3.0 16.6 + - - +
170b LEU 4.3 3.6 - - - +
171b LYS* 6.3 1.1 - - - +
193b TYR 3.8 13.7 - - - +
194b GLY* 3.9 6.3 - - - -
195b GLN 5.1 0.4 - - - +
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Residues in contact with SER 167 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1b FME 3.7 8.2 + - - -
10b GLN* 3.6 21.2 + - - -
11b ASP 3.5 14.8 - - - -
12b ALA* 3.6 5.5 - - - -
13b THR* 2.8 47.4 + - - -
14b SER 3.7 0.3 + - - -
17b MET* 3.6 6.6 - - - +
165b VAL* 3.2 5.0 + - - +
166b PRO* 1.3 78.6 - - - +
168b LEU* 1.3 57.4 + - - +
169b GLY 3.5 0.2 - - - -
192b TYR* 3.6 23.4 - - - +
193b TYR 5.0 1.0 + - - -
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Residues in contact with LEU 168 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13b THR* 3.8 24.9 - - + -
14b SER* 2.6 32.7 + - - +
16b ILE* 3.7 7.6 - - - +
17b MET* 3.9 1.3 - - - -
165b VAL* 3.0 20.1 + - + +
167b SER* 1.3 78.7 + - - +
169b GLY* 1.3 62.2 + - - +
170b LEU* 3.8 16.5 - - + +
184b LEU* 4.4 13.0 - - + -
185b MET 3.5 27.4 - - - +
186b SER* 4.0 9.9 - - - +
192b TYR* 4.9 6.5 - - + -
211b LEU* 3.3 33.9 - - + -
213b LEU* 5.3 1.8 - - + -
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Residues in contact with GLY 169 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365a ILE* 3.5 14.7 - - - +
366a VAL* 3.6 20.3 - - - +
16b ILE* 4.7 3.8 - - - +
17b MET* 3.8 13.4 - - - +
20b LEU* 4.8 2.9 - - - -
87b MET* 4.4 10.6 - - - +
166b PRO 3.0 14.6 + - - -
167b SER 3.5 0.4 - - - -
168b LEU* 1.3 79.7 - - - +
170b LEU* 1.3 64.8 + - - +
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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