Contacts of the helix formed by residues 222 - 229 (chain A) in PDB entry 4IJ3
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
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Residue Dist Surf HB Arom Phob DC
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170A PRO* 5.5 4.0 - - + -
171A ALA 4.0 17.5 - - - +
172A LYS* 3.9 31.1 - - - +
173A LEU 4.3 0.3 + - - -
218A VAL* 4.1 10.1 - - + -
219A LEU* 3.0 29.5 + - + +
220A ASN 3.4 0.4 - - - -
221A THR* 1.3 72.2 + - - +
223A ALA* 1.3 65.4 + - - +
224A ASN* 3.4 21.7 + - - +
225A VAL* 2.9 16.4 + - + +
226A VAL* 3.1 12.4 + - - +
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Residues in contact with ALA 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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220A ASN 5.2 0.7 - - - -
221A THR 2.7 13.8 + - - +
222A GLU* 1.3 69.5 - - - +
224A ASN* 1.3 53.8 + - - +
226A VAL* 3.2 7.9 + - - +
227A ARG* 2.7 38.2 + - - +
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Residues in contact with ASN 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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173A LEU* 3.9 29.0 - - + +
174A GLU* 4.9 5.9 + - - -
222A GLU* 3.1 14.5 + - - +
223A ALA* 1.3 76.5 - - - +
225A VAL* 1.3 87.2 + - - +
227A ARG* 3.8 10.0 - - - +
228A LYS* 2.9 28.9 + - - +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 4.6 0.2 - - - +
172A LYS* 4.1 4.0 - - - -
173A LEU* 3.4 33.2 - - - +
176A ILE* 3.5 20.4 - - + -
192A PHE* 3.7 10.2 - - + -
218A VAL* 3.5 27.6 - - + -
222A GLU* 2.9 15.8 + - - +
224A ASN* 1.3 90.9 + - - +
226A VAL* 1.3 66.4 + - - +
228A LYS* 3.2 3.8 + - - -
229A PHE* 3.1 36.4 + - + +
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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 PHE* 4.2 16.4 - - + -
218A VAL* 4.9 0.2 - - + -
219A LEU 3.9 11.2 - - - +
220A ASN* 3.3 30.3 - - - +
222A GLU 3.1 11.0 + - - +
223A ALA* 3.6 8.7 - - - +
225A VAL* 1.3 75.5 - - - +
227A ARG* 1.3 58.9 + - - +
229A PHE 3.8 0.2 - - - -
230A GLY* 2.9 23.6 + - - -
231A VAL* 3.0 35.9 + - + +
234A PHE* 4.3 11.4 - - + -
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Residues in contact with ARG 227 (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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223A ALA 2.7 21.8 + - - +
224A ASN* 3.8 8.5 - - - +
226A VAL* 1.3 73.2 - - - +
228A LYS* 1.3 66.0 + - - +
230A GLY* 3.1 13.0 + - - -
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Residues in contact with LYS 228 (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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173A LEU* 3.4 26.7 - - + -
177A ASP* 3.1 23.7 + - - +
224A ASN 2.9 19.6 + - - +
225A VAL* 3.2 5.1 + - - +
227A ARG* 1.3 78.9 - - - +
229A PHE* 1.3 87.4 + - + +
230A GLY 3.5 0.2 + - - -
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Residues in contact with PHE 229 (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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173A LEU* 4.9 0.2 - - + -
176A ILE* 4.0 12.3 - - + -
190A LEU* 3.7 24.5 - - + -
192A PHE* 4.1 6.3 - + + -
225A VAL* 3.1 32.2 + - + +
228A LYS* 1.3 108.0 - - + +
230A GLY* 1.3 64.6 + - - +
231A VAL* 3.3 18.1 + - + +
238A TYR* 4.1 20.9 + + + -
240A LEU* 3.9 24.0 - - + -
246A VAL* 3.8 35.4 - - + -
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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