Contacts of the strand formed by residues 222 - 226 (chain A) in PDB entry 4N9W
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 GLU 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TYR* 2.5 37.1 + - - -
186A ARG* 3.4 31.9 + - - +
189A ARG 3.0 9.2 + - - +
190A THR* 3.3 3.8 - - + +
191A VAL 2.9 26.9 + - - +
221A VAL* 1.3 75.1 - - - +
223A ILE* 1.3 79.2 + - - +
224A LEU* 3.6 14.0 - - - +
244A HIS 3.4 8.1 - - - +
246A ARG* 3.6 24.4 - - + +
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.3 29.8 - - + +
193A PHE* 4.8 1.6 - - + -
204A MET* 5.3 1.8 - - + -
207A LEU* 3.8 33.0 - - + -
211A LEU* 3.8 24.5 - - + -
214A LEU* 4.0 21.8 - - + -
221A VAL* 4.9 1.6 - - + -
222A GLU* 1.3 74.4 - - - +
224A LEU* 1.3 62.0 + - - +
225A ILE* 3.7 21.4 + - + +
244A HIS* 2.8 11.8 + - + +
245A LEU* 3.6 22.0 - - + -
246A ARG 2.9 26.9 + - - +
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Residues in contact with LEU 224 (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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181A LEU* 4.5 8.3 - - + -
184A TYR* 3.9 23.8 - - + +
190A THR* 3.7 19.5 - - + -
191A VAL 2.8 9.1 + - - +
192A LEU* 3.2 17.4 - - + +
193A PHE 2.9 25.1 + - - -
222A GLU* 3.6 17.3 - - - +
223A ILE* 1.3 69.8 - - - +
225A ILE* 1.3 61.4 + - - +
246A ARG* 3.6 19.3 - - - +
248A LEU* 3.8 29.2 - - + -
259A ALA* 4.2 30.5 - - + +
262A SER* 5.4 0.9 - - - -
263A ALA* 5.4 0.7 - - + -
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Residues in contact with ILE 225 (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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193A PHE* 3.5 16.2 - - + -
197A TYR* 3.7 33.4 - - + -
204A MET* 3.8 20.2 - - + -
223A ILE* 3.8 20.0 - - + +
224A LEU* 1.3 78.4 - - - +
226A VAL* 1.3 65.2 + - - +
227A GLY 4.9 0.7 - - - +
234A LEU* 3.8 7.4 - - + -
245A LEU* 4.0 20.6 - - + -
246A ARG 2.8 14.0 + - - +
247A PHE* 3.8 27.6 - - + +
248A LEU* 3.1 26.6 + - - +
249A GLY 4.1 1.9 + - - -
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Residues in contact with VAL 226 (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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192A LEU* 3.9 18.6 - - + -
193A PHE 2.8 14.6 + - - +
194A LEU* 3.2 23.8 - - + -
195A GLY 2.7 33.7 + - - +
224A LEU* 5.2 0.2 - - + -
225A ILE* 1.3 78.2 - - - +
227A GLY* 1.3 56.6 + - - +
248A LEU* 4.2 23.6 - - + -
249A GLY 3.9 3.8 - - - +
251A VAL* 3.9 21.3 - - + -
256A LYS* 4.9 2.7 - - + -
259A ALA* 4.3 10.5 - - + -
401A GDP 3.7 21.1 - - + +
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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