Contacts of the helix formed by residues 240 - 252 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B LEU 3.1 11.6 + - - +
237B GLY* 4.3 4.7 + - - -
239B PHE* 1.3 82.4 - - - +
241B PRO* 1.3 73.9 - - - +
242B SER* 3.0 10.5 + - - -
243B LEU* 2.9 29.7 + - - +
244B GLN* 3.2 18.2 + - - +
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Residues in contact with PRO 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLY 5.9 0.2 - - - +
240B SER* 1.3 86.2 - - - +
242B SER* 1.3 59.4 + - - +
244B GLN* 3.3 21.7 + - - +
245B LYS* 3.0 43.3 + - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 5.0 8.0 + - - +
240B SER* 3.0 9.0 + - - -
241B PRO* 1.3 80.7 - - - +
243B LEU* 1.3 61.3 + - - +
245B LYS* 3.3 8.6 + - - +
246B ARG* 2.9 28.9 + - - +
249B GLN* 5.2 0.3 - - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.8 6.5 - - + -
117B GLY* 3.8 39.9 - - - +
118B GLU* 3.8 21.1 - - + +
121B VAL* 3.9 16.7 - - + +
236B LEU* 3.7 19.2 - - + +
239B PHE* 3.9 25.4 - - + -
240B SER* 2.9 23.7 + - - +
242B SER* 1.3 77.2 - - - +
244B GLN* 1.3 65.4 + - - +
246B ARG* 3.6 7.7 - - - +
247B LEU 3.1 18.4 + - - -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B TRP* 2.9 87.9 + - + +
234B ASN* 4.4 2.0 + - - +
236B LEU* 3.7 7.6 - - - -
237B GLY* 3.4 28.9 - - - +
240B SER 3.2 10.3 + - - +
241B PRO* 3.4 25.6 - - - +
242B SER 3.2 0.2 - - - -
243B LEU* 1.3 79.1 - - - +
245B LYS* 1.3 64.1 + - + +
247B LEU* 3.4 11.8 + - - +
248B PHE* 3.7 3.3 + - - -
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B TRP* 5.3 2.9 - - - +
241B PRO* 3.0 30.5 + - - +
242B SER* 3.3 7.8 + - - +
244B GLN* 1.3 77.7 - - + +
246B ARG* 1.3 62.9 + - - +
248B PHE* 3.1 11.0 + - - +
249B GLN* 3.0 38.2 + - + +
256B PRO* 6.4 1.6 - - + -
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 3.4 56.2 + - - +
119B ASN* 5.5 1.0 + - - -
121B VAL* 4.0 8.7 - - + -
122B ASP* 2.8 36.7 + - - +
242B SER* 2.9 19.7 + - - +
243B LEU* 3.6 9.9 - - - +
244B GLN 3.2 0.2 - - - -
245B LYS* 1.3 74.3 - - - +
247B LEU* 1.3 66.1 + - - +
249B GLN* 3.4 18.1 + - - +
250B LYS* 2.9 51.7 + - + +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 3.6 10.9 - - + +
124B LEU* 5.2 0.2 - - + -
125B ALA* 4.0 24.1 - - + +
128B LEU* 5.0 4.0 - - + -
229B LEU* 3.9 28.3 - - + +
232B LEU* 3.8 31.2 - - + -
233B TRP* 3.7 36.6 - - + +
236B LEU* 3.8 15.7 - - + -
243B LEU 3.1 7.1 + - - -
244B GLN 3.5 9.6 - - - +
245B LYS 3.2 0.2 - - - -
246B ARG* 1.3 75.8 - - - +
248B PHE* 1.3 63.8 + - + +
250B LYS 4.0 0.2 - - - -
251B TYR* 3.0 26.1 + - + +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR* 3.7 33.9 - + - -
229B LEU* 3.8 30.3 - - + -
233B TRP* 3.2 40.4 - + + -
244B GLN 4.0 4.0 - - - -
245B LYS* 3.1 9.8 + - - +
247B LEU* 1.3 78.0 - - + +
249B GLN* 1.3 68.3 + - + +
251B TYR* 3.3 3.8 + + - +
252B GLY 2.9 6.1 + - - -
253B ILE* 2.9 50.4 + - + +
256B PRO* 3.6 33.9 - - + -
261B LEU* 4.4 14.6 - - + -
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Residues in contact with GLN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B SER 5.2 0.3 - - - +
245B LYS* 3.0 31.0 + - + +
246B ARG* 3.2 26.9 + - - +
248B PHE* 1.3 79.0 - - + +
250B LYS* 1.3 70.0 + - + +
252B GLY* 3.2 12.6 + - - -
253B ILE 4.0 8.0 + - - +
254B ASP* 5.6 7.2 - - - +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 5.2 0.4 - - + +
122B ASP* 3.1 36.8 + - + +
125B ALA* 3.7 19.5 - - + +
126B VAL* 6.1 1.1 - - + +
129B ARG* 3.8 12.8 + - - -
246B ARG* 2.9 46.5 + - + +
247B LEU* 5.1 0.2 - - - -
249B GLN* 1.3 76.3 - - + +
251B TYR* 1.3 64.2 + - - +
252B GLY* 3.1 2.8 + - - -
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ALA* 3.8 10.5 - - + +
128B LEU* 3.9 20.9 - - + -
129B ARG* 2.8 53.8 + - + +
132B HIS* 2.6 37.3 + + + +
225B ARG* 2.8 30.9 + - - -
229B LEU* 3.9 22.2 - - + -
247B LEU* 3.0 21.3 + - + +
248B PHE* 3.3 4.7 + - - +
250B LYS* 1.3 77.3 - - - +
252B GLY* 1.3 57.1 + - - +
253B ILE* 3.9 34.3 - - + -
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Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 4.4 6.3 - - - -
248B PHE 2.9 2.8 + - - -
249B GLN 3.2 9.6 + - - -
250B LYS 3.1 2.9 - - - -
251B TYR* 1.3 81.7 - - - +
253B ILE* 1.3 65.4 - - - +
254B ASP* 3.8 2.3 + - - -
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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