Contacts of the helix formed by residues 215 - 227 (chain A) in PDB entry 6DXW
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 PRO 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A PRO* 5.4 1.1 - - + -
118A LEU* 4.0 19.5 - - + -
121A GLU* 3.4 21.1 - - + +
209A LEU* 4.3 11.0 - - + -
214A ILE* 1.3 90.0 - - + +
216A VAL* 1.3 66.0 + - - +
218A TRP* 3.1 54.8 + - + +
219A LEU* 3.1 18.9 + - - +
243A ILE* 3.7 16.6 - - + -
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Residues in contact with VAL 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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121A GLU* 3.0 20.1 + - + +
181A TRP* 3.4 32.8 - - + -
201A TRP* 6.5 0.2 - - + -
215A PRO* 1.3 72.8 - - + +
217A SER* 1.3 63.0 + - - +
219A LEU 3.5 0.3 + - - -
220A ILE* 3.3 18.5 + - - +
242A LEU* 3.8 11.0 - - + -
243A ILE* 4.7 1.3 - - + +
244A ALA* 3.6 36.1 - - + +
245A ASP 4.4 2.2 - - - +
246A VAL* 3.9 24.9 - - + -
248A TYR* 2.8 28.1 + - + +
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Residues in contact with SER 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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121A GLU* 2.3 29.3 + - - -
177A TYR* 3.0 11.3 + - - -
179A GLY* 3.5 4.7 - - - -
180A LEU 3.1 49.8 + - - +
181A TRP* 4.2 11.7 - - - -
216A VAL* 1.3 80.1 - - - +
218A TRP* 1.3 75.7 + - - +
220A ILE* 3.9 3.1 - - - -
221A ARG* 3.4 9.0 + - - +
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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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91A LEU* 5.0 10.3 - - + -
92A PRO* 4.0 21.5 - - + -
95A PHE* 3.2 62.7 - + + -
96A THR* 4.9 0.7 - - + -
99A ILE* 3.7 29.2 - - + -
114A LEU* 4.4 14.6 - - + -
117A ASN* 4.5 16.2 + - + -
118A LEU* 5.1 2.7 - - + -
121A GLU* 4.5 2.6 + - - -
177A TYR* 5.2 0.6 + - - -
178A VAL* 3.8 15.5 - - + +
179A GLY* 3.6 13.7 - - - +
209A LEU* 6.4 0.2 - - + -
214A ILE* 4.4 5.8 - - + -
215A PRO* 3.1 46.0 + - + +
217A SER* 1.3 90.7 + - - +
219A LEU* 1.3 60.2 + - - +
221A ARG 3.3 1.0 + - - -
222A ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 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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214A ILE* 3.6 18.3 - - + +
215A PRO 3.1 8.7 + - - +
216A VAL 3.8 0.4 - - - +
217A SER 3.3 0.4 - - - -
218A TRP* 1.3 74.7 - - - +
220A ILE* 1.3 59.4 + - - +
222A ALA* 3.3 2.6 + - + -
223A THR* 2.8 43.0 + - - +
236A LYS* 4.0 22.9 - - + +
237A LEU* 4.0 12.8 - - + +
240A THR* 3.7 42.4 - - + +
242A LEU* 3.5 22.2 - - + -
248A TYR* 3.6 28.0 - - + +
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Residues in contact with ILE 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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180A LEU* 3.2 28.9 - - + +
181A TRP* 3.9 13.2 - - + +
182A THR 4.9 1.1 - - - +
191A VAL* 3.9 24.8 - - + +
193A GLY* 3.9 27.1 - - - +
216A VAL 3.3 7.3 + - - +
217A SER* 3.7 3.4 - - - +
218A TRP 3.3 0.4 - - - -
219A LEU* 1.3 77.1 - - - +
221A ARG* 1.3 57.0 + - - +
223A THR* 3.2 3.5 + - - -
224A LEU* 2.9 44.7 + - + +
237A LEU* 4.2 7.4 - - + -
248A TYR* 3.4 34.8 - - + -
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Residues in contact with ARG 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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38A VAL* 5.8 0.2 - - - +
40A LEU* 3.8 23.4 - - - +
47A ARG* 3.8 3.2 - - - +
48A TRP* 4.3 4.2 - - - -
94A PRO* 4.4 7.8 - - - +
95A PHE* 4.0 18.2 - - + -
98A GLU* 2.6 44.9 + - - -
161A PHE* 3.8 21.3 - - - -
169A PHE* 4.0 13.1 - - + -
178A VAL* 3.0 28.5 + - - +
180A LEU* 3.6 34.3 - - + +
217A SER 3.4 9.4 + - - +
218A TRP 3.3 7.5 + - - +
219A LEU 3.2 0.4 - - - -
220A ILE* 1.3 78.8 - - - +
222A ALA* 1.3 63.6 + - - +
224A LEU* 3.2 4.8 + - - +
225A SER* 3.0 23.6 + - - -
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Residues in contact with ALA 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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95A PHE* 4.5 12.9 - - + -
214A ILE* 5.2 4.3 - - + -
218A TRP 2.9 16.8 + - - +
219A LEU* 3.7 9.4 - - + +
221A ARG* 1.3 77.3 - - - +
223A THR* 1.3 56.9 + - - +
225A SER* 3.4 5.1 + - - -
226A GLU* 3.0 48.8 + - - +
236A LYS* 3.9 12.8 - - - +
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Residues in contact with THR 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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189A PHE* 3.4 10.6 - - + -
191A VAL* 5.1 0.9 - - + -
219A LEU* 2.8 21.4 + - - +
220A ILE* 3.5 4.3 - - - -
222A ALA* 1.3 73.4 - - - +
224A LEU* 1.3 66.4 + - - +
225A SER 3.1 1.6 - - - -
227A SER* 2.9 30.4 + - - +
233A ALA* 3.6 35.7 - - + +
236A LYS* 3.4 22.8 - - + +
237A LEU* 3.5 28.5 - - + +
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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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168A ALA 4.4 1.7 - - - +
169A PHE* 3.8 24.2 - - + +
170A THR 4.3 2.5 - - - +
180A LEU* 3.9 23.1 - - + -
183A GLY* 3.6 29.2 - - - +
184A GLN* 3.6 33.2 - - - +
185A SER* 3.6 19.4 + - - +
189A PHE* 3.7 20.4 - - + -
191A VAL* 4.0 7.2 - - + -
220A ILE* 2.9 30.4 + - + +
221A ARG 3.2 5.4 + - - +
223A THR* 1.3 77.2 - - - +
225A SER* 1.3 60.0 + - - +
227A SER 4.9 1.6 + - - +
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Residues in contact with SER 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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40A LEU* 5.0 1.7 - - - +
163A LYS* 3.4 30.9 + - - +
168A ALA* 5.9 0.2 - - - +
169A PHE* 3.7 23.6 - - - -
221A ARG* 3.0 16.9 + - - -
222A ALA* 3.7 7.6 - - - -
223A THR 3.1 0.2 - - - -
224A LEU* 1.3 79.7 - - - +
226A GLU* 1.3 66.1 + - - +
227A SER 5.4 0.2 - - - -
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Residues in contact with GLU 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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222A ALA* 3.0 29.0 + - - +
225A SER* 1.3 88.0 - - - +
227A SER* 1.3 67.0 + - - +
228A GLU* 3.4 8.1 + - - +
236A LYS* 3.2 25.3 + - + +
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Residues in contact with SER 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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185A SER* 4.7 1.7 + - - -
188A LYS* 3.8 7.3 - - - +
189A PHE* 3.5 20.3 - - - -
223A THR* 2.9 22.0 + - - +
224A LEU 4.9 1.7 - - - +
225A SER 5.4 0.2 - - - -
226A GLU* 1.3 76.7 - - - +
228A GLU* 1.3 62.9 + - - +
229A ASN 3.4 0.2 - - - -
232A ALA* 3.7 8.1 + - - +
233A ALA* 3.5 36.6 + - - -
236A LYS* 3.7 15.1 - - - +
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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