Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 4H75
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 GLN 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY 5.2 2.7 - - - +
216A LYS* 1.3 81.3 - - - +
218A VAL* 1.3 66.5 + - - +
229A THR* 4.2 18.7 - - + +
230A GLY 3.3 10.5 - - - +
231A MET* 4.6 4.3 - - + +
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Residues in contact with VAL 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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216A LYS* 5.4 1.1 - - + -
217A GLN* 1.3 80.8 - - - +
219A GLU* 1.3 67.0 + - - +
220A TYR* 3.4 32.3 + - + -
229A THR* 3.3 6.6 - - - +
230A GLY 2.8 35.3 + - - +
232A VAL* 3.6 27.8 - - + +
245A ILE* 4.8 13.2 - - + -
247A PHE* 4.4 0.6 - - + -
258A LEU* 4.8 13.0 - - + -
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Residues in contact with GLU 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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218A VAL* 1.3 79.7 - - - +
220A TYR* 1.3 73.2 + - - +
227A LYS* 3.6 27.9 - - + +
228A ARG 3.2 15.9 + - - +
229A THR* 4.3 10.3 + - - +
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Residues in contact with TYR 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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218A VAL* 3.4 25.3 - - + -
219A GLU* 1.3 86.5 - - - +
221A ALA* 1.3 66.0 + - - +
222A LYS 3.3 2.1 + - - -
227A LYS* 3.4 2.6 - - - -
228A ARG* 2.8 46.7 + - + +
245A ILE* 5.9 1.3 - - + -
247A PHE* 4.0 27.0 - + + -
256A TYR* 3.5 60.0 - + - +
257A ASP 5.5 0.7 + - - -
258A LEU* 4.2 9.8 - - + +
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Residues in contact with ALA 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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219A GLU 4.3 0.2 + - - -
220A TYR* 1.3 75.5 - - - +
222A LYS* 1.3 65.8 + - - +
223A GLU 3.6 1.9 + - - -
226A SER 3.3 7.4 - - - +
227A LYS* 4.5 2.9 - - + +
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Residues in contact with LYS 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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220A TYR 3.3 5.2 + - - +
221A ALA* 1.3 73.7 - - - +
223A GLU* 1.3 77.4 + - - +
224A ASP* 3.0 32.1 + - - +
225A GLY* 3.1 12.5 + - - -
226A SER* 2.5 43.9 + - - +
227A LYS 4.5 6.0 + - - +
228A ARG* 3.7 40.0 - - + +
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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