Contacts of the helix formed by residues 210 - 223 (chain A) in PDB entry 1EXD
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 MET 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR* 4.7 0.2 - - - -
189A VAL* 3.2 32.8 - - + +
190A LEU* 2.8 21.8 + - - +
191A TYR 4.2 0.2 - - - +
192A ARG* 3.4 39.5 - - + -
209A PRO* 1.3 73.6 - - - +
211A TYR* 1.3 62.2 + - - +
212A ASP* 3.5 9.0 - - + +
213A PHE* 3.3 4.6 + - - +
214A THR* 2.7 27.0 + - - -
973B G 4.2 2.9 - - + +
974B C 3.6 23.1 - - - +
975B C 3.5 27.8 - - + -
976B A 3.7 8.5 - - - +
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Residues in contact with TYR 211 (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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66A ASP* 3.7 9.0 - - - -
68A THR* 4.7 2.9 - - - -
210A MET* 1.3 73.7 - - - +
212A ASP* 1.3 89.0 + - - +
214A THR* 3.0 5.7 + - - -
215A HIS* 2.7 76.6 + + + +
229A CYS* 5.2 4.9 - - - +
233A PHE* 3.3 43.1 - + - +
236A ASN* 4.6 2.0 - - + -
240A TYR* 5.7 1.0 - + - -
255A GLN* 4.6 6.9 + - - -
976B A 3.0 76.0 + + + +
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Residues in contact with ASP 212 (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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184A VAL* 4.6 4.0 - - - +
188A PRO* 5.8 0.5 - - - +
189A VAL 6.2 0.2 - - - +
210A MET* 3.5 5.2 - - + +
211A TYR* 1.3 92.9 + - - +
213A PHE* 1.3 64.4 + - - +
215A HIS* 3.7 4.5 + - - +
216A CYS* 3.3 20.3 + - - +
236A ASN* 2.7 41.6 - - - +
239A LEU* 3.2 40.6 - - + +
240A TYR* 5.0 5.5 - - - +
243A VAL* 4.7 0.9 - - - +
976B A 4.8 5.9 + - - +
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Residues in contact with PHE 213 (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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106A LEU* 3.6 26.0 - - + -
109A TYR* 3.9 3.6 - - + -
110A ALA* 3.5 27.1 - - + -
113A LEU* 4.0 20.2 - - + -
190A LEU* 4.1 37.2 - - + +
191A TYR* 3.6 24.7 - + - -
209A PRO* 4.1 12.1 - - + -
210A MET* 3.3 9.8 + - + +
211A TYR 3.1 0.8 - - - -
212A ASP* 1.3 79.5 - - - +
214A THR* 1.3 62.3 + - - +
216A CYS* 3.5 4.2 - - - -
217A ILE* 3.4 46.0 - - + +
239A LEU* 5.3 0.6 - - - +
243A VAL* 3.9 22.7 - - + -
247A ILE* 5.6 0.7 - - + -
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Residues in contact with THR 214 (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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66A ASP* 4.6 3.4 - - - +
68A THR* 3.4 24.0 - - + +
99A SER* 3.8 11.9 - - - +
106A LEU* 3.3 31.0 - - + -
209A PRO* 3.3 20.6 - - - +
210A MET 2.7 16.7 + - - -
211A TYR* 3.0 4.8 + - - -
213A PHE* 1.3 76.1 - - - +
215A HIS* 1.3 62.7 + - - +
217A ILE* 3.6 0.7 + - - +
218A SER* 2.8 40.8 + - - +
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Residues in contact with HIS 215 (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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30A ARG* 2.6 35.5 + - - -
32A PRO* 3.7 15.0 - - + -
64A ARG* 3.5 12.8 + - - -
66A ASP* 3.0 24.3 + - - +
211A TYR* 2.7 51.6 + + + +
212A ASP* 4.4 2.7 - - - +
213A PHE 3.5 0.4 - - - -
214A THR* 1.3 71.2 - - - +
216A CYS* 1.3 66.1 + - - +
218A SER* 3.9 3.3 - - - -
219A ASP* 3.1 48.9 + - - +
227A SER* 3.8 2.8 + - - -
240A TYR* 3.9 13.9 - + + -
255A GLN* 5.2 1.1 - - - -
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Residues in contact with CYS 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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212A ASP 3.3 19.2 + - - -
213A PHE 3.5 8.1 - - - -
215A HIS* 1.3 79.1 - - - +
217A ILE* 1.3 65.8 + - - +
219A ASP* 3.3 2.1 + - - +
220A ALA* 2.9 29.8 + - - +
240A TYR* 3.6 49.6 - - + +
243A VAL* 3.5 33.7 - - - -
244A LEU* 3.7 12.6 - - + +
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Residues in contact with ILE 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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106A LEU* 3.3 29.6 - - + -
109A TYR* 3.9 32.8 - - + -
213A PHE* 3.4 52.0 - - + +
214A THR 3.6 1.0 + - - +
215A HIS 3.3 0.4 - - - -
216A CYS* 1.3 74.0 - - - +
218A SER* 1.3 59.7 + - - +
220A ALA* 3.2 6.9 + - - +
221A LEU* 2.9 41.3 + - + +
243A VAL* 4.1 14.1 - - + -
244A LEU* 4.4 2.2 - - + -
247A ILE* 4.1 10.8 - - + -
249A ILE* 4.7 2.5 - - + -
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Residues in contact with SER 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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64A ARG* 3.6 29.8 + - - -
66A ASP* 4.9 0.6 + - - -
99A SER* 4.4 1.9 + - - -
102A TYR* 3.2 33.8 - - - +
106A LEU* 5.2 0.2 - - - +
214A THR* 2.8 34.3 + - - +
215A HIS* 3.9 2.2 - - - -
217A ILE* 1.3 74.8 - - - +
219A ASP* 1.3 65.8 + - - +
221A LEU* 3.1 2.6 + - - +
222A GLU* 2.9 27.7 + - - +
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Residues in contact with ASP 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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30A ARG* 3.2 15.9 - - - -
64A ARG* 2.6 28.5 + - - +
215A HIS* 3.1 24.0 + - - +
216A CYS 3.4 4.5 - - - +
218A SER* 1.3 80.2 - - - +
220A ALA* 1.3 60.1 + - - +
222A GLU 3.5 0.7 + - - -
223A GLY 3.1 3.5 + - - -
224A ILE* 2.9 40.8 + - + +
227A SER* 2.8 19.2 + - - -
240A TYR* 2.8 26.3 + - - +
253A PRO* 3.8 7.4 - - + -
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Residues in contact with ALA 220 (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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216A CYS 2.9 17.2 + - - +
217A ILE 3.5 4.7 - - - +
218A SER 3.1 0.2 - - - -
219A ASP* 1.3 73.8 - - - +
221A LEU* 1.3 66.1 + - - +
223A GLY* 3.0 9.0 + - - -
244A LEU* 3.8 10.8 - - + -
249A ILE* 3.6 30.3 - - + -
251A VAL* 3.0 27.1 - - + +
253A PRO* 3.7 14.3 - - + +
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Residues in contact with LEU 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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102A TYR* 3.9 32.5 - - + -
105A GLN* 3.5 36.6 - - + +
109A TYR* 4.7 5.2 - - - +
217A ILE* 2.9 31.8 + - + +
218A SER 3.1 3.6 + - - +
220A ALA* 1.3 76.1 - - - +
222A GLU* 1.3 61.7 + - - +
223A GLY* 3.4 0.5 + - - -
249A ILE* 4.0 17.9 - - + -
250A PRO* 6.1 2.5 - - + -
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Residues in contact with GLU 222 (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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28A HIS* 3.9 15.9 + - - -
62A ASN* 2.8 37.6 + - - +
64A ARG* 2.8 45.5 + - - -
97A ARG* 3.7 14.6 - - - +
102A TYR* 2.6 31.6 + - + +
218A SER 2.9 13.4 + - - +
219A ASP 4.0 3.6 - - - +
221A LEU* 1.3 75.5 - - - +
223A GLY* 1.3 61.7 + - - +
224A ILE* 4.1 8.7 - - + +
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Residues in contact with GLY 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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28A HIS* 3.6 15.7 - - - +
219A ASP 3.1 0.4 + - - -
220A ALA 3.0 16.0 + - - -
221A LEU 3.2 1.3 - - - -
222A GLU* 1.3 80.4 - - - +
224A ILE* 1.3 66.4 + - - +
225A THR* 3.3 8.1 + - - +
251A VAL* 4.8 11.2 - - - -
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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