Contacts of the strand formed by residues 217 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.1 30.5 - - + -
141A VAL* 3.6 11.0 - - + +
142A VAL 4.8 0.2 - - - -
143A ALA* 3.6 29.6 - - + +
211A LEU* 3.3 35.2 - - + +
214A ASP* 3.2 6.3 + - + +
215A ASP 3.9 4.2 - - - +
216A ARG* 1.3 74.8 - - - +
218A LYS* 1.3 59.8 + - - +
219A ALA 3.8 11.7 - - - +
220A VAL* 4.0 10.5 - - + -
241A LYS* 3.0 26.2 + - + +
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Residues in contact with LYS 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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50A GLN* 5.6 1.8 - - - +
139A MET* 3.6 44.8 + - + +
140A GLY* 5.1 0.9 - - - -
141A VAL 2.9 14.5 + - - +
215A ASP 3.1 25.6 - - - -
216A ARG* 3.1 24.2 + - - +
217A VAL* 1.3 73.9 - - - +
219A ALA* 1.3 62.4 + - - +
241A LYS* 3.7 14.1 - - - +
242A ARG* 3.5 14.0 + - - +
473A LYS* 5.9 3.7 - - - +
453B LYS* 5.8 6.5 - - - +
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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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139A MET* 4.7 7.6 - - + -
141A VAL 3.9 3.0 + - - -
142A VAL* 3.6 18.7 - - + +
143A ALA 2.9 26.0 + - - +
217A VAL* 3.6 2.8 - - - +
218A LYS* 1.3 80.5 - - - +
220A VAL* 1.3 66.5 + - - +
221A SER 4.3 0.4 - - - -
241A LYS* 4.4 0.4 - - - +
242A ARG* 3.5 29.2 - - + -
470A PHE* 4.0 14.6 - - + +
471A TYR* 5.3 0.2 - - + -
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Residues in contact with VAL 220 (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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143A ALA* 3.4 12.1 - - + +
145A ILE* 4.2 15.9 - - + -
211A LEU* 5.4 0.7 - - + +
212A LEU* 4.1 20.4 - - + +
217A VAL* 4.0 10.1 - - + -
219A ALA* 1.3 80.7 - - - +
221A SER* 1.3 65.1 + - - +
232A ILE* 4.0 26.0 - - + -
236A ALA* 4.7 0.7 - - + -
241A LYS* 3.9 26.9 - - + -
242A ARG 3.1 10.1 + - - +
243A CYS* 3.3 10.4 - - + -
244A GLN 3.1 26.2 + - - +
470A PHE* 3.6 3.0 - - - -
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Residues in contact with SER 221 (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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142A VAL* 5.3 0.4 - - - +
143A ALA 3.0 12.1 + - - -
144A GLY* 3.4 0.6 - - - -
145A ILE 2.9 26.3 + - - -
158A MET* 3.4 23.5 - - - +
169A PHE* 5.6 0.4 - - - -
219A ALA 4.3 0.4 - - - -
220A VAL* 1.3 70.4 - - - +
222A PHE* 1.3 59.5 + - - +
223A VAL* 6.1 0.2 - - - -
244A GLN* 2.6 32.7 + - - -
470A PHE* 3.4 3.3 - - - -
471A TYR* 2.6 31.3 + - - -
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Residues in contact with PHE 222 (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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145A ILE* 3.5 24.5 - - + -
220A VAL* 3.9 1.4 + - + -
221A SER* 1.3 73.1 - - - +
223A VAL* 1.3 72.0 + - - +
224A GLY* 3.3 32.8 - - - -
228A ILE* 3.5 25.8 - - + -
229A ALA* 3.4 36.8 - - + -
232A ILE* 3.7 33.2 - - + -
244A GLN* 2.8 15.0 + - - +
245A ALA* 4.1 4.0 - - + -
246A LEU* 2.9 28.4 + - - +
501A NAD 3.4 26.7 - - - -
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Residues in contact with VAL 223 (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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145A ILE 3.0 10.9 + - - +
146A THR 3.8 1.0 - - - -
147A PRO* 3.5 33.2 - - + +
154A VAL* 3.7 24.0 - - + -
157A TRP* 4.0 15.7 - - + -
158A MET* 3.5 19.3 - - + -
221A SER* 6.1 0.2 - - - -
222A PHE* 1.3 89.0 - - - +
224A GLY* 1.3 61.2 + - - +
246A LEU* 3.7 14.8 - - + -
462A ALA* 5.4 2.0 - - + -
501A NAD 3.7 32.6 - - + +
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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