Contacts of the helix formed by residues 240 - 252 (chain D) in PDB entry 4GKH
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 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D LEU 3.0 14.5 + - - +
237D GLY 4.0 3.5 + - - -
239D PHE* 1.3 80.8 - - - +
241D PRO* 1.3 73.4 - - - +
242D SER* 2.9 27.5 + - - -
243D LEU* 3.2 28.9 + - - +
244D GLN* 3.2 10.6 + - - +
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Residues in contact with PRO 241 (chain D).
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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237D GLY 4.8 7.4 - - - +
240D SER* 1.3 85.6 - - - +
242D SER* 1.3 64.4 + - - +
244D GLN* 3.3 21.9 + - - +
245D LYS* 3.2 20.8 + - - +
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Residues in contact with SER 242 (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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118D GLU* 5.3 4.5 + - - -
240D SER* 2.9 16.7 + - - -
241D PRO* 1.3 78.9 - - - +
243D LEU* 1.3 63.6 + - - +
245D LYS* 3.4 6.9 + - - +
246D ARG* 3.0 27.4 + - - +
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Residues in contact with LEU 243 (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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110D LEU* 4.4 7.9 - - + -
114D PRO 5.9 0.2 - - - +
117D GLY* 3.8 37.2 - - - +
118D GLU* 3.9 19.5 - - + +
121D VAL* 3.9 23.1 - - + +
236D LEU* 3.9 13.9 - - + +
239D PHE* 4.2 23.6 - - + -
240D SER* 3.2 21.8 + - - +
242D SER* 1.3 85.6 + - - +
244D GLN* 1.3 63.9 + - - +
246D ARG* 3.4 6.6 + - - +
247D LEU* 3.1 22.3 + - - +
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Residues in contact with GLN 244 (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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233D TRP* 2.9 88.9 + - - +
234D ASN* 4.4 2.2 + - - +
236D LEU* 3.9 8.7 - - + +
237D GLY* 3.3 26.5 - - - +
240D SER 3.2 12.2 + - - +
241D PRO* 3.3 21.8 + - - +
243D LEU* 1.3 76.6 - - - +
245D LYS* 1.3 62.3 + - - +
247D LEU* 3.3 17.8 + - - +
248D PHE* 3.6 4.9 + - - -
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Residues in contact with LYS 245 (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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233D TRP* 4.8 1.1 - - - +
241D PRO 3.2 9.3 + - - +
242D SER* 3.8 9.9 - - - +
243D LEU 3.3 0.2 - - - -
244D GLN* 1.3 78.8 - - - +
246D ARG* 1.3 62.9 + - - +
247D LEU 3.3 0.2 + - - -
248D PHE* 3.4 9.6 + - + +
249D GLN* 3.1 34.2 + - + +
254D ASP* 4.9 10.5 + - - +
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Residues in contact with ARG 246 (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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118D GLU* 3.5 52.8 + - - +
119D ASN* 5.7 0.6 + - - -
121D VAL* 4.1 8.5 - - + -
122D ASP* 2.5 45.2 + - - +
242D SER 3.0 17.0 + - - +
243D LEU* 3.7 8.7 - - - +
244D GLN 3.2 0.2 - - - -
245D LYS* 1.3 78.1 - - - +
247D LEU* 1.3 52.8 + - - +
249D GLN* 3.7 12.0 + - - +
250D LYS* 2.8 56.4 + - + +
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Residues in contact with LEU 247 (chain D).
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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121D VAL* 3.7 13.6 - - + +
124D LEU* 5.0 0.2 - - + -
125D ALA* 4.2 21.0 - - + +
128D LEU* 5.1 3.8 - - + -
229D LEU* 4.2 22.4 - - + +
232D LEU* 3.7 33.2 - - + -
233D TRP* 3.8 34.5 - - + +
236D LEU* 4.0 10.3 - - + -
243D LEU 3.1 12.9 + - - +
244D GLN 3.3 9.6 - - - +
246D ARG* 1.3 75.9 - - - +
248D PHE* 1.3 61.4 + - + +
250D LYS* 3.8 2.1 - - - +
251D TYR* 2.8 32.1 + - + +
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Residues in contact with PHE 248 (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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226D TYR* 3.6 34.5 - + - -
229D LEU* 3.9 31.0 - - + -
233D TRP* 3.2 44.2 - + + -
244D GLN 3.6 4.0 + - - -
245D LYS* 3.4 8.5 + - - +
247D LEU* 1.3 81.0 - - + +
249D GLN* 1.3 57.8 + - - +
251D TYR* 3.2 4.7 + - - +
252D GLY 2.9 10.9 + - - -
253D ILE* 2.8 57.0 + - + +
256D PRO* 3.6 31.4 - - + -
258D MSE 5.3 0.4 - - + -
261D LEU* 4.7 11.4 - - + -
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Residues in contact with GLN 249 (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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245D LYS* 3.1 31.8 + - + +
246D ARG* 3.7 12.6 + - - +
248D PHE* 1.3 76.7 - - - +
250D LYS* 1.3 92.3 + - - +
252D GLY* 3.3 13.0 + - - -
253D ILE 3.7 9.1 + - - -
254D ASP* 5.0 11.6 - - - +
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Residues in contact with LYS 250 (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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121D VAL* 5.2 0.4 - - + +
122D ASP* 3.4 27.5 + - + +
125D ALA* 3.6 21.7 - - + +
129D ARG* 3.7 13.3 + - - -
246D ARG* 2.8 55.3 + - + +
247D LEU* 5.0 0.2 - - - -
249D GLN* 1.3 95.5 + - - +
251D TYR* 1.3 65.6 + - - +
252D GLY* 3.4 0.7 + - - -
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Residues in contact with TYR 251 (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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125D ALA* 3.9 7.3 - - + +
128D LEU* 3.8 24.0 - - + -
129D ARG* 2.8 54.1 + - + +
132D HIS* 2.5 36.0 + - + +
225D ARG* 2.9 28.4 + - - -
229D LEU* 3.8 22.9 - - + -
247D LEU* 2.8 22.2 + - + +
248D PHE* 3.5 6.5 - - - +
250D LYS* 1.3 75.9 - - - +
252D GLY* 1.3 57.2 + - - +
253D ILE* 3.5 35.0 - - + -
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Residues in contact with GLY 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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129D ARG* 4.5 5.2 - - - -
248D PHE 2.9 2.0 + - - -
249D GLN 3.3 9.4 + - - -
250D LYS 3.2 3.1 - - - -
251D TYR* 1.3 81.1 - - - +
253D ILE* 1.3 64.8 + - - +
254D ASP* 3.9 9.0 + - - +
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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