Contacts of the helix formed by residues 226 - 240 (chain D) in PDB entry 4GAW
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 LYS 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D ILE* 5.0 0.5 - - - +
177D ARG 3.1 24.3 + - - -
178D ALA* 3.2 26.9 + - - +
179D THR 2.6 15.8 + - - +
180D GLU 3.3 12.6 - - - +
181D ILE* 3.3 31.9 - - + -
208D GLN 3.9 4.3 - - - -
224D TYR 3.6 2.0 + - - -
225D ILE* 1.3 73.0 - - - +
227D VAL* 1.3 61.9 + - - +
228D SER* 4.1 14.4 + - - +
229D HIS* 3.8 11.6 - - + +
230D PHE* 3.1 26.3 - - - -
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 4.9 1.8 - - + -
104D ILE* 5.2 2.2 - - + -
124D LEU* 4.6 6.3 - - + -
125D PRO* 4.5 7.4 - - + -
207D ALA* 3.9 17.3 - - + +
208D GLN* 2.9 32.2 + - - +
209D GLY* 3.7 7.0 - - - +
210D ILE* 3.7 29.6 - - + -
225D ILE 3.9 1.3 - - - +
226D LYS* 1.3 70.2 - - - +
228D SER* 1.3 57.4 + - - +
229D HIS 2.8 4.5 - - - -
230D PHE* 2.6 28.1 + - - -
231D LEU* 3.0 33.7 + - + -
234D ILE* 4.0 12.1 - - + -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 5.6 2.9 - - - +
128D LYS* 4.8 21.1 - - - -
129D ALA 5.2 2.0 - - - -
130D GLN* 6.0 1.8 - - - -
208D GLN* 4.3 13.9 + - - +
226D LYS* 4.1 18.2 + - - +
227D VAL* 1.3 78.4 - - - +
229D HIS* 1.3 65.7 + - - +
231D LEU* 3.7 24.8 + - - +
232D PRO* 4.1 2.6 - - - +
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Residues in contact with HIS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN* 5.7 0.2 - - - -
178D ALA* 2.9 33.7 + - + +
179D THR* 3.9 16.0 - - + +
226D LYS* 3.8 12.5 + - + +
227D VAL 2.7 0.6 + - - -
228D SER* 1.3 87.0 + - - +
230D PHE* 1.3 90.6 + + + +
231D LEU 3.2 0.4 - - - -
232D PRO* 3.2 16.1 - - - +
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 3.0 42.2 - + - -
102D ASN* 3.7 33.7 - - + -
104D ILE* 3.6 26.7 - - + -
179D THR* 4.2 11.2 - - - -
225D ILE* 3.6 20.2 - - + -
226D LYS 3.1 22.2 - - - +
227D VAL 2.6 12.0 + - - +
229D HIS* 1.3 98.1 - + + +
231D LEU* 1.3 62.8 + - - -
232D PRO* 3.3 2.7 - - - -
233D TRP* 3.0 12.2 + + + +
234D ILE* 3.0 29.3 + - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.6 34.5 - - + -
125D PRO* 4.0 35.4 - - + +
128D LYS* 5.7 12.8 - - + +
227D VAL* 3.0 19.6 + - + +
228D SER* 3.8 20.4 - - - +
230D PHE* 1.3 77.8 - - - +
232D PRO* 1.3 75.2 - - + +
234D ILE* 3.1 5.5 + - + +
235D LYS* 2.9 45.0 + - + +
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Residues in contact with PRO 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D SER 4.1 3.1 - - - +
229D HIS 3.2 16.2 - - - +
230D PHE 3.5 1.6 - - - -
231D LEU* 1.3 94.4 - - + +
233D TRP* 1.3 61.5 + - - +
235D LYS* 3.9 6.0 - - + +
236D ARG* 2.9 39.2 + - - +
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Residues in contact with TRP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.7 0.4 - - + -
90D ILE* 3.2 28.5 - - + +
91D PRO 3.0 29.2 - - - -
92D HIS* 3.7 26.2 - + - +
93D PRO* 3.4 24.1 - - + +
104D ILE* 4.1 23.1 - - + -
106D LEU* 3.7 27.8 - - + -
230D PHE* 3.0 17.1 + + - +
232D PRO* 1.3 78.8 - - - +
234D ILE* 1.3 73.5 + - + +
236D ARG* 3.5 22.4 - - - +
237D THR* 2.6 56.5 + - + +
240D ARG* 5.7 2.2 - - - +
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 5.1 1.8 - - + -
55D LEU* 3.8 31.2 - - + -
104D ILE* 5.2 1.8 - - + -
106D LEU* 4.0 24.2 - - + -
124D LEU* 3.9 13.5 - - + -
227D VAL* 4.0 11.0 - - + -
230D PHE* 3.0 21.9 + - + +
231D LEU* 3.3 28.3 - - + +
233D TRP* 1.3 87.1 - - + +
235D LYS* 1.3 65.2 + - + +
237D THR* 3.3 2.3 + - - -
238D MET* 3.0 48.7 + - + +
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Residues in contact with LYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 5.7 8.1 - - + +
125D PRO 5.3 5.9 + - - -
128D LYS* 5.7 5.1 - - - +
231D LEU* 2.9 44.4 + - + +
232D PRO* 3.9 5.8 - - + +
234D ILE* 1.3 76.0 - - + +
236D ARG* 1.3 63.8 + - + +
238D MET* 3.9 12.6 - - + +
239D LYS* 3.5 43.0 + - - +
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Residues in contact with ARG 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PRO* 2.9 19.9 + - - +
233D TRP* 3.5 35.5 + - - +
235D LYS* 1.3 74.6 - - - +
237D THR* 1.3 73.2 + - - +
238D MET 3.0 1.9 + - - -
239D LYS* 3.3 2.4 + - - +
240D ARG* 2.8 44.4 + - + +
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Residues in contact with THR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 3.7 35.2 - - + -
106D LEU* 3.5 21.8 - - + -
233D TRP* 2.6 50.9 + - - +
236D ARG* 1.3 74.5 + - - +
238D MET* 1.3 65.7 + - - +
240D ARG* 3.8 24.4 + - - +
241D LEU* 3.6 23.0 + - + +
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Residues in contact with MET 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 4.4 11.9 - - + +
50D ARG* 3.8 44.0 + - + +
53D PHE* 3.7 53.1 - - + -
106D LEU* 4.0 8.7 - - + -
124D LEU* 5.1 5.4 - - + -
234D ILE* 3.0 40.9 + - + +
235D LYS* 3.9 14.1 - - + +
236D ARG 3.0 0.6 + - - -
237D THR* 1.3 80.1 - - - +
239D LYS* 1.3 65.8 + - - +
241D LEU* 3.2 22.5 - - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ARG* 3.5 33.8 - - - +
235D LYS* 3.5 35.3 + - - +
236D ARG* 3.3 2.9 + - - +
238D MET* 1.3 81.3 - - - +
240D ARG* 1.3 67.9 + - - +
241D LEU* 5.1 0.4 - - - +
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Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 5.5 2.6 - - - +
233D TRP* 5.7 1.6 - - - +
236D ARG* 2.8 33.3 + - + +
237D THR* 3.8 32.9 + - - +
238D MET 3.2 1.2 - - - -
239D LYS* 1.3 83.3 - - - +
241D LEU* 1.3 93.5 + - - +
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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