Contacts of the helix formed by residues 251 - 263 (chain D) in PDB entry 4ILW
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 SER 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D ASN* 4.8 4.9 - - - -
232D GLU* 3.7 22.8 + - - -
233D ALA* 3.5 8.4 - - - -
234D LEU 5.0 0.2 - - - +
249D ARG* 3.3 6.3 + - - +
250D LEU* 1.3 75.8 - - - +
252D GLN* 1.3 59.9 + - - +
253D ASP* 3.3 9.6 + - - +
254D ASP* 2.9 48.3 + - - +
255D VAL* 3.1 14.1 + - - +
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Residues in contact with GLN 252 (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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251D SER* 1.3 71.6 - - - +
253D ASP* 1.3 57.1 + - - +
255D VAL* 4.0 22.2 - - - +
256D ASN* 2.6 70.5 + - - +
259D GLN* 5.6 0.2 + - - -
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Residues in contact with ASP 253 (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* 4.2 6.8 + - - +
230D ASN* 3.3 33.0 - - - +
233D ALA* 4.6 7.2 - - + -
251D SER* 3.5 10.1 - - - +
252D GLN* 1.3 81.1 - - - +
254D ASP* 1.3 60.7 + - - +
256D ASN* 3.5 13.7 + - - +
257D GLY* 3.1 18.4 + - - -
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Residues in contact with ASP 254 (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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140D TRP* 4.1 10.1 - - + -
225D LEU* 4.5 5.3 - - - +
228D SER* 5.2 0.5 - - - -
233D ALA* 3.6 6.1 - - - +
234D LEU* 2.8 33.2 + - - +
235D MET* 3.2 33.1 + - - +
250D LEU* 3.8 17.2 - - + +
251D SER* 2.9 32.3 + - - +
253D ASP* 1.3 75.0 - - - +
255D VAL* 1.3 66.7 + - - +
257D GLY* 3.3 2.0 + - - -
258D ILE* 3.0 26.0 + - - +
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Residues in contact with VAL 255 (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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143D VAL* 4.4 13.5 - - + -
250D LEU* 4.0 25.1 - - + +
251D SER 3.1 14.8 + - - +
252D GLN* 3.6 26.9 - - - +
254D ASP* 1.3 74.3 - - - +
256D ASN* 1.3 66.3 + - - +
258D ILE* 3.3 6.9 + - - -
259D GLN* 2.9 55.6 + - + +
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Residues in contact with ASN 256 (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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252D GLN* 2.6 60.0 + - - +
253D ASP* 3.7 14.4 + - - +
255D VAL* 1.3 73.6 - - - +
257D GLY* 1.3 63.9 + - - +
259D GLN* 3.8 4.4 + - - +
260D SER* 2.9 26.2 + - - -
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Residues in contact with GLY 257 (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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225D LEU* 3.6 18.8 - - - +
253D ASP 3.1 12.9 + - - -
254D ASP 3.3 3.3 + - - -
255D VAL 3.2 0.2 - - - -
256D ASN* 1.3 79.0 - - - +
258D ILE* 1.3 60.5 + - - +
260D SER* 2.5 25.8 + - - -
261D LEU* 3.5 5.4 + - - +
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Residues in contact with ILE 258 (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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140D TRP* 3.8 19.5 - - + -
143D VAL* 3.7 28.0 - - + -
144D THR* 3.7 19.2 - - + +
223D LEU* 4.0 25.6 - - + -
225D LEU* 3.7 21.7 - - + +
254D ASP 3.0 16.3 + - - +
255D VAL* 3.4 11.9 - - - +
257D GLY* 1.3 76.3 - - - +
259D GLN* 1.3 63.2 + - + +
261D LEU* 3.3 2.4 + - + -
262D TYR* 3.1 53.4 + - + +
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Residues in contact with GLN 259 (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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143D VAL* 3.0 35.4 - - - +
252D GLN* 5.6 0.4 + - - -
255D VAL* 2.9 42.2 + - + +
256D ASN* 3.8 4.6 + - - +
258D ILE* 1.3 75.9 - - + +
260D SER* 1.3 59.8 + - - +
261D LEU 3.2 0.7 - - - -
263D GLY* 2.8 44.4 + - - +
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Residues in contact with SER 260 (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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256D ASN 2.9 16.1 + - - -
257D GLY* 2.5 23.1 + - - -
259D GLN* 1.3 77.2 - - - +
261D LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 261 (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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106D PRO* 3.9 24.7 - - + +
107D LYS* 2.8 44.7 + - + +
223D LEU 3.7 22.7 - - - +
224D GLY 3.9 22.2 - - - +
225D LEU* 3.9 17.3 - - + -
257D GLY 3.9 5.8 - - - +
258D ILE* 3.3 3.9 + - + +
259D GLN 3.2 0.2 - - - -
260D SER* 1.3 83.9 + - - +
262D TYR* 1.3 73.5 + - + +
263D GLY 3.7 0.7 - - - -
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Residues in contact with TYR 262 (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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107D LYS* 3.6 18.8 - - + +
108D TRP* 3.3 46.7 + + + -
110D LYS 4.9 1.6 - - - -
144D THR* 4.3 6.1 - - - -
145D PRO* 3.2 31.0 - - + +
146D LEU* 3.8 37.2 - - + -
223D LEU* 2.5 33.1 + - + -
258D ILE* 3.1 35.8 + - + +
261D LEU* 1.3 86.7 - - + +
263D GLY* 1.3 64.9 + - - +
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Residues in contact with GLY 263 (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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143D VAL 3.9 5.1 - - - +
144D THR* 4.1 1.2 - - - -
145D PRO* 3.7 14.8 - - - +
259D GLN* 2.8 47.7 + - - +
260D SER 4.8 0.2 - - - -
261D LEU 3.7 0.8 - - - -
262D TYR* 1.3 83.9 - - - +
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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