Contacts of the strand formed by residues 156 - 159 (chain D) in PDB entry 3FZ7
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 ASN 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D LYS 4.2 1.8 + - - -
155D PRO* 1.3 74.5 - - - +
157D LEU* 1.3 59.9 + - - +
158D VAL* 3.9 2.1 - - - +
175D VAL* 3.6 3.8 - - - -
176D GLU* 3.1 21.7 + - + +
178D ARG* 3.1 45.7 - - - +
199D ASP* 3.1 23.8 + - - -
201D ASN* 2.9 18.4 + - - +
202D THR* 2.9 28.8 + - - +
203D ILE* 2.6 35.0 + - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D MET* 3.9 13.2 - - + -
156D ASN* 1.3 74.3 - - - +
158D VAL* 1.3 60.7 + - - +
159D CYS* 4.0 11.2 + - + -
166D TRP* 4.3 14.4 - - + +
169D PHE* 4.7 11.2 - - + -
170D ALA* 5.9 1.1 - - + -
175D VAL* 3.8 13.5 - - + -
176D GLU 2.8 9.6 + - - +
177D LEU* 3.7 25.9 - - + +
178D ARG* 2.8 28.7 + - - +
203D ILE* 3.9 19.5 - - + -
204D GLY 3.5 17.0 - - - +
206D VAL* 3.8 30.5 - - + -
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ASN* 3.9 5.8 - - - +
157D LEU* 1.3 70.5 - - - +
159D CYS* 1.3 64.2 + - - +
178D ARG* 3.6 7.0 - - + -
180D ILE* 3.8 18.8 - - + -
189D MET* 4.0 2.0 - - - -
194D MET* 3.8 35.2 - - + +
197D ALA* 3.4 34.5 - - + +
198D CYS* 4.1 3.1 - - - -
202D THR* 3.7 18.1 - - + +
204D GLY 3.2 6.7 + - - +
205D VAL* 3.2 14.9 - - + +
206D VAL* 2.9 25.3 + - - +
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Residues in contact with CYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 4.3 7.9 - - + -
158D VAL* 1.3 77.2 - - - +
160D GLY* 1.3 70.9 + - - +
162D VAL* 3.5 26.9 - - + -
177D LEU* 3.5 31.2 - - - -
178D ARG 3.3 2.8 + - - -
179D GLU* 3.6 13.8 - - - -
180D ILE* 2.8 31.4 + - - +
189D MET* 3.7 10.3 - - - -
206D VAL* 3.7 13.2 - - + +
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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