Contacts of the helix formed by residues 215 - 226 (chain A) in PDB entry 4AFZ
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 TYR 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A HIS* 3.6 32.1 - + - -
88A HIS* 2.7 52.7 + - + -
90A ILE* 3.8 25.8 - - + -
164A LEU* 4.0 18.7 + - - +
210A THR* 3.4 27.1 - - + +
211A ARG 3.3 17.7 - - - -
212A ILE 2.8 9.7 + - - +
214A HIS* 1.3 96.3 - + - +
216A ARG* 1.3 53.9 + - - +
217A PRO* 3.3 3.4 - - - -
218A TRP* 2.8 31.5 + - + +
219A ILE* 2.9 15.9 + - + +
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Residues in contact with ARG 216 (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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36A ARG* 6.1 0.6 - - - +
110A PHE* 3.4 37.7 + - - -
111A PRO 3.2 35.9 + - - +
112A SER* 3.6 8.3 - - - +
113A GLN* 4.0 13.0 - - + +
212A ILE 3.4 4.6 + - - +
213A SER 3.3 13.4 + - - +
215A TYR* 1.3 76.8 - - - +
217A PRO* 1.3 71.6 - - + +
219A ILE* 3.3 6.1 + - - +
220A ASN* 3.0 53.4 + - - +
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Residues in contact with PRO 217 (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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113A GLN* 3.7 25.4 - - + +
214A HIS 3.6 13.9 - - - +
215A TYR* 3.5 3.8 - - - -
216A ARG* 1.3 95.4 - - + +
218A TRP* 1.3 60.4 + - - +
220A ASN* 3.4 13.4 + - + +
221A GLN* 3.2 31.6 + - - +
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Residues in contact with TRP 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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76A PHE 3.4 27.1 - - - -
77A ARG 4.1 2.5 - - - -
78A HIS* 3.7 43.3 - + + +
79A PRO* 3.6 21.3 - - + +
90A ILE* 4.0 35.0 - - + -
92A LEU* 3.9 28.9 - - + -
215A TYR* 2.8 17.4 + - + +
217A PRO* 1.3 78.1 - - - +
219A ILE* 1.3 85.1 + - + +
221A GLN* 3.4 14.7 + - + +
222A ILE* 3.2 48.1 + - + +
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Residues in contact with ILE 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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35A ILE* 4.2 9.9 - - + -
41A LEU* 4.2 17.7 - - + -
90A ILE* 4.5 6.5 - - + -
92A LEU* 4.1 12.6 - - + -
110A PHE* 3.6 37.9 - - + -
212A ILE* 4.0 26.5 - - + -
215A TYR 2.9 21.2 + - - +
216A ARG* 3.7 7.6 - - - +
218A TRP* 1.3 90.8 - - + +
220A ASN* 1.3 66.4 + - - +
222A ILE* 3.1 5.2 + - - +
223A LEU* 3.0 34.0 + - + +
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Residues in contact with ASN 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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110A PHE* 4.4 5.7 - - - -
216A ARG* 3.0 50.3 + - - +
217A PRO* 3.4 15.5 - - + +
219A ILE* 1.3 76.2 - - - +
221A GLN* 1.3 58.6 + - + +
223A LEU* 3.3 5.6 + - - +
224A GLN* 3.0 52.1 + - - +
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Residues in contact with GLN 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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217A PRO* 3.2 20.3 + - - +
218A TRP* 3.4 15.6 + - + +
219A ILE 3.2 0.4 - - - -
220A ASN* 1.3 80.3 - - + +
222A ILE* 1.3 65.9 + - + +
224A GLN* 4.2 8.8 - - - +
225A ALA* 3.3 24.4 + - - +
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Residues in contact with ILE 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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39A PHE* 4.2 7.0 - - + -
76A PHE* 3.7 46.9 - - + -
92A LEU* 3.6 29.2 - - + -
218A TRP* 3.2 46.1 + - + +
219A ILE 3.1 1.4 + - - +
221A GLN* 1.3 79.7 - - + +
223A LEU* 1.3 61.8 + - - +
225A ALA* 3.4 1.3 + - - -
226A ASN* 2.9 35.9 + - - +
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Residues in contact with LEU 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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35A ILE* 4.4 4.0 - - + -
36A ARG* 3.8 41.7 - - + +
39A PHE* 3.6 46.7 - - + -
92A LEU* 4.3 15.0 - - + -
110A PHE* 4.1 6.7 - - + -
219A ILE* 3.0 34.4 + - + +
220A ASN* 3.9 5.6 - - - +
222A ILE* 1.3 75.1 - - - +
224A GLN* 1.3 59.1 + - + +
226A ASN* 3.0 26.0 + - - +
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Residues in contact with GLN 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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220A ASN* 3.0 41.7 + - - +
221A GLN* 4.3 8.0 - - - +
223A LEU* 1.3 78.3 - - + +
225A ALA* 1.3 59.6 + - - +
226A ASN* 3.3 2.2 + - - +
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Residues in contact with ALA 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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221A GLN 3.3 18.7 + - - +
222A ILE* 4.9 0.2 - - - -
223A LEU 3.3 0.4 - - - -
224A GLN* 1.3 76.2 - - - +
226A ASN* 1.3 74.8 + - - +
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Residues in contact with ASN 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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38A ASN* 4.6 4.7 + - - +
39A PHE* 3.6 28.9 - - + -
74A LYS* 5.1 3.3 - - - +
76A PHE* 3.4 37.7 - - - -
94A LYS* 3.5 29.6 + - - +
222A ILE* 2.9 28.1 + - - +
223A LEU 3.0 16.3 + - - +
224A GLN 4.4 2.3 - - - +
225A ALA* 1.3 94.3 - - - +
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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