Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 1XXE
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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176A LEU 4.8 0.2 - - - +
177A ALA* 3.4 11.0 - - - +
178A ARG* 2.7 51.1 + - - +
204A LEU* 3.3 27.0 - - + +
217A LEU* 4.7 2.7 - - + -
218A ARG* 2.9 27.5 + - - +
219A TYR* 2.5 35.9 + - + +
221A ASN* 1.3 69.6 - - - +
223A PRO* 1.3 76.6 - - + +
225A ARG* 2.9 17.4 + - - +
226A HIS* 3.0 11.1 + - - +
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Residues in contact with PRO 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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155A PHE* 4.7 9.6 - - + -
159A LEU* 4.2 25.4 - - + -
180A PHE* 3.0 62.6 - - + -
204A LEU* 5.3 0.7 - - + -
206A LEU* 4.4 5.2 - - + -
217A LEU* 4.8 12.6 - - + -
219A TYR 4.4 1.6 - - - +
220A GLU 5.2 0.9 - - - +
221A ASN* 3.6 3.4 - - - -
222A GLU* 1.3 103.5 - - + +
224A VAL* 1.3 61.4 + - + +
226A HIS* 3.5 1.6 + - + +
227A LYS* 3.2 13.7 + - - +
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Residues in contact with VAL 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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151A TYR* 3.7 24.9 - - + -
155A PHE* 3.5 30.7 - - + -
162A GLN* 3.6 28.3 - - + +
164A PHE* 3.9 15.9 - - + +
221A ASN* 2.9 41.7 - - + +
223A PRO* 1.3 75.8 - - + +
225A ARG* 1.3 65.8 + - - +
227A LYS* 3.2 1.4 + - - +
228A VAL* 3.0 29.0 + - - +
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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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164A PHE* 2.6 62.6 - - + -
173A GLU* 3.2 44.1 + - - +
174A ILE* 3.8 5.2 - - + +
177A ALA* 3.5 10.5 - - + -
219A TYR* 3.2 33.3 - - - +
220A GLU* 4.7 3.8 + - - -
221A ASN* 2.4 51.5 + - - +
222A GLU 3.2 7.9 - - - +
224A VAL* 1.3 79.1 - - - +
226A HIS* 1.3 57.9 + - - +
228A VAL* 3.3 2.8 + - - +
229A PHE* 2.9 26.9 + - - +
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Residues in contact with HIS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 3.3 21.8 - + - -
101A GLY 3.4 4.3 - - - -
102A SER* 5.1 0.7 - - - -
177A ALA* 2.7 33.3 + - + +
178A ARG 3.8 8.7 - - - +
179A THR* 2.9 32.7 + - - -
180A PHE* 4.7 2.9 - - + -
222A GLU 3.0 7.1 + - - +
223A PRO 3.7 8.7 - - - +
225A ARG* 1.3 76.0 - - - +
227A LYS* 1.3 63.1 + - + +
229A PHE* 3.0 12.0 + + - +
230A ASP* 2.7 46.8 + - - -
319A ZN 2.5 29.5 - - - -
320A TUX 5.2 8.3 - - - -
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Residues in contact with LYS 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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151A TYR* 3.5 48.0 - - + +
180A PHE* 5.2 0.4 - - + -
223A PRO 3.2 9.2 + - - +
224A VAL 3.2 4.2 + - - +
226A HIS* 1.3 80.7 - - - +
228A VAL* 1.3 58.2 + - - +
230A ASP* 3.0 15.1 + - - +
231A LEU* 2.8 29.0 + - + +
251A GLY 4.3 17.4 + - - +
252A GLY* 5.2 4.1 - - - -
253A HIS* 4.0 15.5 + - - -
256A ASN* 5.3 8.1 - - - +
320A TUX 2.7 56.1 + - - +
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Residues in contact with VAL 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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149A VAL* 3.9 22.0 - - + +
151A TYR* 3.5 26.5 - - + -
164A PHE* 3.9 21.3 - - + +
166A PHE* 3.7 31.2 - - + -
174A ILE* 4.4 7.4 - - + -
224A VAL 3.0 16.5 + - - +
225A ARG 3.6 5.8 - - - +
227A LYS* 1.3 74.6 - - - +
229A PHE* 1.3 64.4 + - - +
231A LEU* 3.1 15.8 + - - +
232A ILE* 3.1 17.5 + - + +
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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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74A HIS* 3.7 19.1 - + + -
77A SER* 2.6 55.2 + - - -
78A VAL* 3.7 23.1 - - + -
81A LEU* 3.8 13.2 - - + -
102A SER 5.2 0.7 - - - -
103A GLY* 4.3 17.5 - - - -
174A ILE* 2.6 35.4 - - + +
175A VAL* 3.8 18.8 - - + -
177A ALA 5.2 2.9 - - - +
225A ARG 2.9 11.7 + - - +
226A HIS* 3.0 19.3 + + - +
228A VAL* 1.3 77.9 - - - +
230A ASP* 1.3 73.4 + - - +
232A ILE* 3.5 7.7 + - + +
233A GLY 3.2 9.0 + - - -
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Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 2.3 29.5 - - - +
74A HIS* 3.3 8.2 + - - -
77A SER* 5.2 0.7 - - - -
226A HIS* 2.7 42.6 + - - +
227A LYS* 3.4 15.9 - - - +
229A PHE* 1.3 75.5 - - - +
231A LEU* 1.3 62.0 + - - +
232A ILE 3.1 1.6 - - - -
233A GLY* 3.0 3.4 + - - +
234A ASP* 2.3 33.4 + - - +
253A HIS* 3.5 12.6 + - + -
256A ASN* 5.4 0.7 - - - +
319A ZN 2.5 22.0 - - - -
320A TUX 5.1 0.5 - - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 5.1 3.1 - - + -
149A VAL* 3.2 31.9 - - + -
150A THR 5.1 0.2 - - - +
151A TYR* 5.7 2.2 - - + -
227A LYS* 2.8 17.7 + - + +
228A VAL* 3.1 12.1 + - - +
230A ASP* 1.3 73.5 - - - +
232A ILE* 1.3 62.5 + - - +
234A ASP* 3.3 3.6 + - - +
235A LEU* 3.1 35.5 + - + +
246A PHE* 5.3 5.4 - - + -
248A SER* 3.7 28.0 - - - +
256A ASN* 3.3 42.8 - - + +
259A LEU* 5.7 3.8 - - + -
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Residues in contact with ILE 232 (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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77A SER* 4.4 4.3 - - - +
80A HIS* 2.8 48.0 + - + +
81A LEU* 4.0 12.8 - - + -
147A LEU* 5.2 4.0 - - + -
149A VAL* 4.6 18.2 - - + -
166A PHE* 3.9 21.5 - - + -
174A ILE* 3.8 28.5 - - + -
228A VAL* 3.1 16.2 + - + +
229A PHE* 3.7 8.3 - - - +
230A ASP 3.1 0.4 - - - -
231A LEU* 1.3 74.0 - - - +
233A GLY* 1.3 59.6 + - - +
234A ASP 2.9 1.8 - - - -
235A LEU* 2.7 27.6 + - + +
236A TYR 2.8 11.4 + - - -
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Residues in contact with GLY 233 (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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73A GLU* 3.5 27.1 - - - +
76A LEU* 3.8 18.5 - - - +
77A SER* 3.5 16.8 - - - -
229A PHE 3.2 5.7 + - - -
230A ASP 3.0 7.6 + - - -
232A ILE* 1.3 79.0 - - - +
234A ASP* 1.3 62.1 + - - +
236A TYR* 3.7 6.6 + - - +
237A LEU* 4.1 7.3 + - - +
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Residues in contact with ASP 234 (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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60A THR* 3.4 16.6 + - - +
73A GLU* 3.7 12.1 - - - +
230A ASP 2.3 30.6 + - - +
231A LEU* 3.7 7.2 - - + +
232A ILE 2.9 0.8 - - - -
233A GLY* 1.3 78.1 - - - +
235A LEU* 1.3 64.4 + - - +
237A LEU* 3.2 33.9 - - + +
253A HIS* 2.9 36.5 + - - +
256A ASN* 4.2 20.0 - - + -
257A VAL* 4.5 5.6 - - + +
260A VAL* 3.5 9.0 - - - +
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Residues in contact with LEU 235 (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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80A HIS* 4.6 3.1 - - + -
147A LEU* 5.9 1.1 - - + -
149A VAL* 4.6 8.1 - - + -
231A LEU* 3.1 33.6 + - + +
232A ILE* 2.7 17.6 + - + +
234A ASP* 1.3 69.4 - - - +
236A TYR* 1.3 59.7 + - - +
237A LEU 3.0 6.8 + - - -
238A LEU* 3.4 16.3 + - + +
242A VAL* 3.3 41.1 - - + +
246A PHE* 4.4 32.3 - - + -
256A ASN 5.9 0.4 - - - +
259A LEU* 4.2 17.9 - - + -
260A VAL* 3.5 22.4 - - + -
263A LEU* 4.5 6.5 - - + -
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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