Contacts of the helix formed by residues 214 - 229 (chain A) in PDB entry 4XQ2
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 ASP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PHE* 4.1 2.5 - - - -
168A ARG* 5.9 1.1 - - - +
189A ASP* 5.7 0.9 - - - +
212A TYR* 3.9 5.9 - - - +
213A ARG* 1.3 88.2 - - + +
215A ALA* 1.3 60.6 + - - +
216A ASP* 4.9 6.9 + - - +
217A LEU* 3.2 23.2 + - + +
218A HIS* 2.9 25.8 + - - +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.6 28.0 - - + -
213A ARG 4.0 1.4 + - - -
214A ASP* 1.3 72.4 - - - +
216A ASP* 1.3 62.5 + - - +
218A HIS* 3.3 4.5 - - - +
219A ALA* 3.1 24.1 + - - +
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Residues in contact with ASP 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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214A ASP* 3.3 7.4 + - - +
215A ALA* 1.3 79.3 - - - +
217A LEU* 1.3 66.0 + - - +
218A HIS 3.2 0.2 - - - -
219A ALA* 3.5 7.2 + - - +
220A ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 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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83A LEU* 4.4 6.5 - - + -
86A LEU* 3.7 27.1 - - + -
168A ARG* 3.8 30.9 - - - +
189A ASP* 4.6 3.1 - - + +
190A VAL* 3.7 28.5 - - + -
212A TYR* 3.7 27.1 - - + -
214A ASP* 3.2 23.5 + - + +
216A ASP* 1.3 79.0 - - - +
218A HIS* 1.3 63.5 + - - +
220A ALA* 3.3 4.1 + - - -
221A VAL* 3.0 31.1 + - + +
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Residues in contact with HIS 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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69A PHE* 3.5 40.9 - + + +
70A ALA 4.1 0.9 - - - -
71A THR* 3.9 0.2 - - - -
212A TYR* 2.6 41.2 + - + -
214A ASP 2.9 13.9 + - - +
215A ALA* 3.3 15.9 - - - +
216A ASP 3.2 0.2 - - - -
217A LEU* 1.3 77.6 - - - +
219A ALA* 1.3 64.0 + - - +
221A VAL* 3.2 1.7 + - - +
222A ARG* 3.0 69.0 + - + +
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Residues in contact with ALA 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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215A ALA 3.1 13.2 + - - +
216A ASP* 3.9 8.7 - - - +
217A LEU 3.3 0.4 - - - -
218A HIS* 1.3 82.6 - - - +
220A ALA* 1.3 57.1 + - - +
222A ARG* 3.4 4.5 + - - +
223A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 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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86A LEU* 4.1 30.6 - - + +
216A ASP 3.2 15.0 + - - +
217A LEU* 3.8 4.5 - - - +
219A ALA* 1.3 77.4 - - - +
221A VAL* 1.3 63.1 + - - +
223A ALA* 3.8 6.3 - - - +
224A TYR* 3.1 24.8 + - - +
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Residues in contact with VAL 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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71A THR* 3.5 37.0 - - + +
73A PHE* 3.8 12.8 - - + -
82A THR* 4.0 18.8 - - + +
83A LEU* 5.3 3.4 - - + -
86A LEU* 4.6 6.5 - - + -
210A LEU* 4.2 14.1 - - + -
212A TYR* 3.8 10.1 - - + +
217A LEU* 3.0 37.4 + - + +
218A HIS 3.7 2.9 - - - +
220A ALA* 1.3 76.4 - - - +
222A ARG* 1.3 57.7 + - - +
224A TYR* 3.4 2.9 + - - +
225A ARG* 3.0 26.9 + - - +
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Residues in contact with ARG 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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49A GLY 5.5 1.8 + - - -
54A ARG* 5.5 1.4 - - - +
55A GLU* 5.8 4.2 - - - +
58A GLU* 3.4 21.8 + - - +
70A ALA 2.7 25.9 + - - -
71A THR* 2.8 28.2 + - - +
218A HIS* 3.0 46.7 + - + +
219A ALA* 4.0 4.7 - - - +
221A VAL* 1.3 72.9 - - - +
223A ALA* 1.3 55.4 + - - +
225A ARG* 3.6 27.3 + - - +
226A THR* 2.6 40.8 + - + +
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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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219A ALA 2.9 17.6 + - - +
220A ALA* 3.8 7.2 - - - +
221A VAL 3.3 0.2 - - - -
222A ARG* 1.3 76.2 - - - +
224A TYR* 1.3 59.2 + - - +
226A THR* 2.7 18.3 + - - -
227A THR* 2.9 20.9 + - - +
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Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ALA* 4.4 9.7 + - + +
82A THR* 3.4 44.0 - - + -
85A SER* 3.6 32.4 - - - +
86A LEU* 5.4 3.4 - - + -
220A ALA 3.1 17.2 + - - +
221A VAL 3.8 3.1 - - - +
223A ALA* 1.3 76.0 - - - +
225A ARG* 1.3 56.7 + - - +
227A THR* 4.7 2.2 - - - -
228A ALA* 2.7 62.8 + - + +
230A ASN* 3.8 7.4 - - - -
109B LEU* 4.2 24.5 - - + -
224B TYR* 4.7 9.9 + - - -
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Residues in contact with ARG 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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48A ARG 4.8 3.0 + - - -
49A GLY* 4.3 4.0 + - - -
54A ARG* 3.1 42.7 - - - +
58A GLU* 2.7 26.1 + - - -
71A THR* 3.3 15.5 - - - +
72A VAL 3.0 26.0 + - - -
73A PHE* 3.9 11.9 - - + -
221A VAL 3.0 17.9 + - - +
222A ARG* 3.6 29.8 + - - +
224A TYR* 1.3 77.9 - - - +
226A THR* 1.3 62.2 + - - +
229A GLY* 2.8 29.6 + - - -
230A ASN* 3.2 26.0 + - - +
231A VAL* 3.6 23.4 - - + +
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Residues in contact with THR 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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48A ARG* 3.1 48.9 + - + +
49A GLY* 4.0 27.8 - - - +
222A ARG* 2.6 27.6 + - + +
223A ALA* 2.7 17.5 + - - -
225A ARG* 1.3 79.7 - - + +
227A THR* 1.3 57.6 + - - +
77B GLN* 4.1 0.5 - - - +
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Residues in contact with THR 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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48A ARG* 5.3 0.2 - - - +
223A ALA* 2.9 17.3 + - - +
224A TYR 3.2 3.4 + - - -
226A THR* 1.3 77.3 + - - +
228A ALA* 1.3 63.5 + - - +
229A GLY 3.2 1.1 - - - -
77B GLN* 2.8 31.7 + - - +
102B GLY* 4.5 1.1 - - - +
105B GLY* 3.9 22.2 - - - -
106B LEU* 3.9 19.6 - - + +
109B LEU* 3.8 28.4 - - + +
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Residues in contact with ALA 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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224A TYR* 2.7 53.7 + - + +
227A THR* 1.3 75.0 - - - +
229A GLY* 1.3 64.0 + - - +
230A ASN* 3.2 12.7 + - + +
77B GLN 3.5 0.7 - - - +
78B ALA* 3.1 26.6 - - - +
81B ALA* 4.2 15.0 - - + +
106B LEU* 4.9 2.2 - - + +
109B LEU* 5.4 0.4 - - + +
230B ASN* 5.2 1.2 + - - -
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Residues in contact with GLY 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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48A ARG* 3.7 17.7 - - - -
225A ARG 2.8 16.1 + - - -
226A THR 4.0 0.2 - - - -
227A THR 3.2 2.4 - - - -
228A ALA* 1.3 78.3 - - - +
230A ASN* 1.3 57.2 + - - +
231A VAL* 2.9 11.6 + - - +
74B SER* 2.8 18.3 + - - -
75B SER* 2.8 27.6 + - - -
77B GLN* 4.0 1.6 - - - -
78B ALA* 3.8 0.2 - - - +
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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