Contacts of the strand formed by residues 217 - 223 (chain K) in PDB entry 4ZZ7
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 VAL 217 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K ILE* 4.2 29.2 - - + -
141K VAL* 3.4 15.3 - - + +
143K ALA* 3.5 18.4 - - + +
170K VAL* 6.0 0.4 - - + -
211K LEU* 3.3 33.7 - - + +
214K ASP* 3.3 6.6 + - + +
215K ASP 3.2 5.2 - - - +
216K ARG* 1.3 76.1 - - - +
218K LYS* 1.3 59.5 + - - +
219K ALA 3.5 22.7 - - - +
220K VAL* 4.0 8.5 - - + -
241K LYS* 2.9 25.5 + - - +
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Residues in contact with LYS 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453J LYS* 5.7 7.1 - - - +
50K GLN* 5.7 1.1 - - - +
139K MET* 3.6 43.1 + - + +
140K GLY* 5.3 0.4 - - - -
141K VAL 2.9 12.7 + - - +
215K ASP 3.0 26.0 - - - -
216K ARG* 3.5 16.4 - - - +
217K VAL* 1.3 74.1 - - - +
219K ALA* 1.3 61.2 + - - +
241K LYS* 3.5 19.0 - - - +
242K ARG* 3.5 12.6 + - - +
473K LYS* 5.8 3.8 - - - +
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Residues in contact with ALA 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K MET* 4.3 8.5 - - + -
141K VAL 4.0 2.4 + - - -
142K VAL* 4.4 19.5 - - + -
143K ALA 2.9 25.4 + - - -
217K VAL* 3.5 3.8 - - - +
218K LYS* 1.3 81.1 - - - +
220K VAL* 1.3 68.6 + - - +
221K SER 4.3 0.4 - - - -
241K LYS* 4.4 0.2 - - - +
242K ARG* 3.4 28.3 - - + -
470K PHE* 4.2 13.5 - - + +
471K TYR* 5.2 0.4 - - + -
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Residues in contact with VAL 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K ALA* 3.3 10.3 - - + +
145K ILE* 4.1 16.2 - - + -
212K LEU* 3.9 23.6 - - + +
217K VAL* 4.0 8.7 - - + -
219K ALA* 1.3 81.7 - - - +
221K SER* 1.3 63.8 + - - +
232K ILE* 3.9 28.5 - - + -
236K ALA* 4.7 0.9 - - + -
241K LYS* 3.9 22.4 - - + -
242K ARG 3.1 10.3 + - - +
243K CYS* 3.4 8.5 - - + -
244K GLN 3.2 26.7 + - - +
470K PHE* 4.1 3.9 - - - -
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Residues in contact with SER 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K VAL* 5.4 0.4 - - - +
143K ALA 2.7 13.0 + - - +
144K GLY* 3.5 1.7 - - - -
145K ILE* 2.9 28.1 + - - +
158K MET* 3.8 20.5 - - - +
169K PHE* 5.7 0.4 - - - -
219K ALA 4.3 0.4 - - - -
220K VAL* 1.3 74.2 - - - +
222K PHE* 1.3 59.3 + - - +
244K GLN* 2.6 30.7 + - - -
470K PHE* 3.4 10.8 - - - -
471K TYR* 2.8 24.6 + - - -
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Residues in contact with PHE 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K ILE* 3.4 35.7 - - + -
146K THR 6.3 0.2 - - - -
220K VAL* 3.7 0.6 + - + -
221K SER* 1.3 73.7 - - - +
223K VAL* 1.3 72.9 + - - +
224K GLY* 3.3 31.2 - - - -
225K SER 3.9 1.1 - - - -
228K ILE* 3.5 34.8 - - + -
229K ALA* 3.5 30.7 - - + -
232K ILE* 3.6 31.6 - - + -
244K GLN* 2.9 15.1 + - - +
245K ALA* 3.3 5.7 - - + -
246K LEU* 2.8 31.6 + - - +
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Residues in contact with VAL 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K ILE 3.0 11.1 + - - +
146K THR 3.9 1.2 - - - -
147K PRO* 3.5 35.2 - - + +
154K VAL* 3.8 22.0 - - + -
157K TRP* 4.1 22.0 - - + -
158K MET* 3.6 18.6 - - + -
222K PHE* 1.3 88.6 - - - +
224K GLY* 1.3 62.6 + - - +
246K LEU* 3.6 25.8 - - + -
247K GLY 5.9 0.4 - - - +
280K CYS* 5.5 9.9 - - + -
449K PHE* 6.3 0.4 - - + -
462K ALA* 5.4 1.3 - - + -
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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