Contacts of the strand formed by residues 217 - 223 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.9 32.3 - - + -
141B VAL* 3.5 13.0 - - + -
142B VAL 5.4 0.2 - - - -
143B ALA* 3.7 26.5 - - + +
170B VAL* 5.8 0.2 - - + -
211B LEU* 3.5 36.3 - - + +
214B ASP 3.0 6.4 + - - +
215B ASP 3.8 4.5 - - - +
216B ARG* 1.3 76.3 - - - +
218B LYS* 1.3 62.5 + - - +
219B ALA 4.0 9.9 - - - +
220B VAL* 4.2 2.9 - - + -
241B LYS* 2.8 37.2 + - + +
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN* 5.6 2.5 - - - +
139B MET* 3.5 52.1 - - + +
140B GLY* 4.9 0.7 - - - -
141B VAL 2.9 16.8 + - - +
215B ASP* 2.5 30.5 + - - +
216B ARG* 3.3 20.9 + - - +
217B VAL* 1.3 72.3 - - - +
219B ALA* 1.3 63.6 + - - +
241B LYS* 3.9 15.1 - - - +
242B ARG* 3.6 8.3 + - - +
473B LYS* 5.8 5.4 - - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MET* 4.6 5.8 - - + -
141B VAL 4.1 1.8 + - - -
142B VAL* 3.7 19.2 - - + +
143B ALA* 3.0 26.3 + - - +
217B VAL* 3.7 2.3 - - - +
218B LYS* 1.3 81.3 - - - +
220B VAL* 1.3 64.2 + - - +
221B SER 4.2 0.2 - - - -
241B LYS* 4.5 0.6 - - - +
242B ARG* 3.5 29.2 - - + -
470B PHE* 4.0 15.3 - - + +
471B TYR* 5.3 0.4 - - + -
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ALA* 3.5 10.3 - - + +
145B ILE* 4.2 13.0 - - + -
212B LEU* 4.0 22.2 - - + -
217B VAL* 4.2 9.6 - - + -
219B ALA* 1.3 79.0 - - - +
221B SER* 1.3 70.1 + - - +
232B ILE* 3.9 26.0 - - + -
236B ALA* 4.4 1.8 - - + -
241B LYS* 4.0 24.2 - - + -
242B ARG 3.1 7.4 + - - +
243B CYS* 3.4 14.9 - - - -
244B GLN 3.0 24.8 + - - -
470B PHE* 3.6 2.6 - - - -
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 5.5 0.2 - - - +
143B ALA 3.1 10.3 + - - +
144B GLY* 3.5 1.7 - - - -
145B ILE* 3.0 25.8 + - - +
158B MET* 3.6 25.9 - - - +
169B PHE* 5.8 0.2 - - - -
219B ALA 4.2 0.2 - - - -
220B VAL* 1.3 74.1 - - - +
222B PHE* 1.3 60.6 + - - +
244B GLN* 2.6 33.5 + - - -
470B PHE* 3.3 12.3 - - - -
471B TYR* 3.1 17.0 + - - -
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Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE* 3.4 35.0 - - + -
146B THR 6.1 0.2 - - - -
220B VAL* 4.9 0.4 - - + -
221B SER* 1.3 74.1 - - - +
223B VAL* 1.3 71.8 - - - +
224B GLY* 3.2 33.0 - - - -
225B SER 3.9 1.3 - - - -
228B ILE* 3.5 35.0 - - + -
229B ALA* 3.4 34.5 - - + -
232B ILE* 3.7 31.9 - - + -
244B GLN* 2.8 13.6 + - - +
245B ALA* 4.1 4.0 - - + -
246B LEU* 3.0 27.1 + - - +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE 3.0 8.2 + - - +
146B THR 3.7 3.1 - - - -
147B PRO* 3.2 31.9 - - + +
154B VAL* 3.7 26.9 - - + -
157B TRP* 4.2 23.1 - - + -
158B MET* 3.7 19.1 - - + -
222B PHE* 1.3 87.1 - - - +
224B GLY* 1.3 62.7 + - - +
246B LEU* 3.8 26.0 - - + -
247B GLY 6.1 0.4 - - - +
280B CYS* 5.4 10.1 - - + -
462B ALA* 5.4 1.6 - - + -
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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