Contacts of the strand formed by residues 215 - 219 (chain A) in PDB entry 1Z8G
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 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.6 38.4 - - + -
181A ARG 3.2 32.1 - - - -
182A TYR* 3.3 23.1 - + - -
187A LEU* 4.1 20.0 - - + -
188A CYS* 5.4 0.2 - - + -
204A CYS* 3.3 31.9 - - + -
205A PHE* 3.6 26.0 - + - -
209A ASN* 2.8 32.3 + - + -
210A ARG* 4.6 0.2 - - - +
211A VAL 3.8 8.3 - - - -
212A LEU* 3.1 30.6 + - + +
214A ARG* 1.3 80.0 - - - +
216A ARG* 1.3 81.5 + - - +
217A VAL* 6.4 0.2 - - + -
233A GLY* 4.2 7.8 - - - -
234A VAL* 3.9 19.0 - - + +
237A VAL* 5.6 0.2 - - + -
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Residues in contact with ARG 216 (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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179A SER 3.6 1.4 - - - +
180A LEU* 3.6 3.3 - - - +
181A ARG* 2.9 39.1 + - + +
212A LEU 4.8 0.2 + - - -
213A SER* 2.8 29.9 + - - +
214A ARG 4.3 3.6 - - - +
215A TRP* 1.3 97.1 + - - +
217A VAL* 1.3 64.1 + - - +
218A PHE 4.0 0.2 - - - -
231A GLN* 3.6 35.3 + - + +
232A LEU* 3.5 22.2 - - - +
233A GLY* 4.1 8.2 - - - +
234A VAL* 5.0 0.2 - - - -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.8 35.7 - - + -
179A SER 3.4 2.5 - - - -
180A LEU* 3.6 19.7 - - + -
198A VAL* 4.4 5.4 - - + -
215A TRP* 6.4 0.2 - - + -
216A ARG* 1.3 75.2 - - - +
218A PHE* 1.3 61.4 + - - +
219A ALA* 3.9 1.4 + - - +
230A LEU 3.6 2.4 - - - +
231A GLN* 3.1 5.3 - - - -
232A LEU* 2.9 33.1 + - - +
234A VAL* 3.9 16.6 - - + -
261A VAL* 4.4 3.6 - - + -
263A LEU* 3.4 41.4 - - + +
267A LEU* 5.3 4.8 - - + +
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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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177A GLN 4.5 0.2 - - - +
178A VAL* 3.3 7.1 - - - -
179A SER* 2.9 45.6 + - - +
181A ARG* 3.4 41.3 - - - +
216A ARG 4.0 0.8 - - - -
217A VAL* 1.3 70.4 - - - +
219A ALA* 1.3 61.6 + - - +
221A ALA* 3.6 37.9 - - + -
223A ALA 3.5 23.6 - - - -
224A GLN* 3.8 8.3 - - - -
226A SER 3.7 19.1 - - - -
229A GLY* 4.5 11.4 - - - -
230A LEU 3.5 9.2 - - - -
231A GLN* 3.6 21.5 - - + +
296A TRP* 4.4 7.4 - + - -
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Residues in contact with ALA 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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175A PRO 5.9 0.4 - - - +
177A GLN 4.6 2.5 - - - +
178A VAL* 3.8 16.6 - - + -
192A LEU* 4.7 0.7 - - + -
217A VAL 3.9 0.9 + - - +
218A PHE* 1.3 75.9 - - - +
220A GLY* 1.3 64.6 + - - +
221A ALA* 3.3 5.3 + - - +
229A GLY* 3.4 2.8 - - - -
230A LEU* 2.8 36.9 + - - +
267A LEU* 3.7 31.4 - - + -
273A ILE* 4.2 13.9 - - + -
296A TRP* 6.3 0.2 - - - -
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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