Contacts of the strand formed by residues 217 - 223 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I ILE* 3.9 31.6 - - + -
141I VAL* 3.7 14.4 - - + +
143I ALA* 3.8 25.6 - - + +
211I LEU* 3.5 35.4 - - + +
214I ASP 3.2 6.1 + - - +
215I ASP 3.7 4.7 - - - +
216I ARG* 1.3 75.9 - - - +
218I LYS* 1.3 61.4 + - - +
219I ALA 3.8 12.6 - - - +
220I VAL* 4.1 9.0 - - + -
241I LYS* 3.1 25.3 + - + +
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Residues in contact with LYS 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I GLN* 5.7 0.9 - - - +
139I MET* 3.6 42.7 + - + +
140I GLY* 5.3 0.7 - - - -
141I VAL 3.0 15.1 + - - +
215I ASP 3.0 25.6 - - - -
216I ARG* 3.0 25.1 - - - +
217I VAL* 1.3 72.6 - - - +
219I ALA* 1.3 63.3 + - - +
241I LYS* 3.7 14.6 - - - +
242I ARG* 3.5 13.5 + - - +
473I LYS* 5.8 4.9 - - - +
453L LYS* 5.8 6.1 - - - +
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Residues in contact with ALA 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I MET* 4.5 4.9 - - + -
141I VAL 4.0 2.6 + - - -
142I VAL* 3.6 19.3 - - + +
143I ALA 2.8 32.2 + - - +
217I VAL* 3.6 2.4 + - - +
218I LYS* 1.3 82.7 - - - +
220I VAL* 1.3 61.1 + - - +
241I LYS* 4.7 0.2 - - - -
242I ARG* 3.5 29.6 - - + -
470I PHE* 4.0 16.4 - - + +
471I TYR* 5.3 0.4 - - + -
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Residues in contact with VAL 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ALA* 3.3 11.4 - - + +
145I ILE* 3.9 27.6 - - + -
211I LEU 5.0 1.3 - - - +
212I LEU* 4.0 23.1 - - + -
217I VAL* 4.1 8.7 - - + -
219I ALA* 1.3 80.4 - - - +
221I SER* 1.3 65.1 + - - +
232I ILE* 4.1 11.9 - - + -
236I ALA* 4.3 1.3 - - + -
241I LYS* 3.8 29.8 - - + -
242I ARG 3.2 7.7 + - - +
243I CYS* 3.3 9.6 - - - -
244I GLN 3.1 24.6 + - - +
470I PHE* 3.6 2.7 - - - -
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Residues in contact with SER 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I VAL* 5.3 0.6 - - - +
143I ALA 2.9 10.7 + - - -
144I GLY* 3.4 0.7 - - - -
145I ILE* 2.8 28.6 + - - +
158I MET* 3.5 21.9 - - - +
169I PHE* 5.8 0.2 - - - -
219I ALA 4.2 0.4 - - - -
220I VAL* 1.3 72.4 - - - +
222I PHE* 1.3 60.4 + - - +
244I GLN* 2.5 33.9 + - - +
470I PHE* 3.6 1.2 - - - -
471I TYR* 2.7 30.1 + - - -
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Residues in contact with PHE 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ILE* 3.5 22.7 - - + -
220I VAL* 4.0 0.4 + - + -
221I SER* 1.3 75.2 - - - +
223I VAL* 1.3 70.5 - - - +
224I GLY* 3.1 33.4 - - - -
228I ILE* 3.5 23.3 - - + -
229I ALA* 3.6 30.3 - - + -
232I ILE* 3.8 30.3 - - + -
244I GLN 2.8 15.0 + - - +
245I ALA* 3.4 6.8 - - + -
246I LEU* 2.9 32.5 + - - +
501I NAD 3.4 36.1 - - - -
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Residues in contact with VAL 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ILE 3.2 7.8 + - - +
147I PRO* 3.3 29.4 - - + +
154I VAL* 3.7 21.8 - - + -
157I TRP* 3.9 18.8 - - + -
158I MET* 3.7 16.6 - - + -
222I PHE* 1.3 83.5 - - - +
224I GLY* 1.3 57.6 + - - +
246I LEU* 3.6 15.5 - - + -
462I ALA* 5.5 0.7 - - + -
501I NAD 3.4 51.5 - - + +
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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