Contacts of the helix formed by residues 241 - 252 (chain D) in PDB entry 3GBA
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 GLY 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D LEU 3.8 0.2 - - - -
238D GLN 3.1 14.6 + - - -
239D GLU 3.2 2.4 + - - -
240D GLU* 1.3 77.2 - - - +
242D LYS* 1.3 58.0 + - - +
243D LEU 3.4 2.5 - - - -
244D HIS* 3.4 13.9 + - - +
245D MET* 3.1 34.4 + - - +
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Residues in contact with LYS 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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42D GLU* 4.3 16.4 + - - +
237D LEU* 2.9 38.3 + - + +
240D GLU* 3.7 33.0 - - + +
241D GLY* 1.3 76.6 - - - +
243D LEU* 1.3 60.3 + - - +
245D MET* 3.7 19.4 - - + +
246D MET* 2.9 40.2 + - + +
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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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35D TYR* 3.9 17.3 + - - +
39D LEU* 4.1 22.0 - - + -
105D PHE* 3.7 35.9 - - + +
234D ILE* 4.0 10.3 - - + +
237D LEU* 3.4 24.3 + - + -
238D GLN* 3.8 36.6 - - + +
241D GLY 3.4 0.4 - - - -
242D LYS* 1.3 77.7 - - - +
244D HIS* 1.3 62.6 + - - +
246D MET* 3.3 11.6 + - - +
247D LYS* 3.0 24.3 + - - +
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Residues in contact with HIS 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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238D GLN 5.9 0.2 + - - -
241D GLY* 3.4 15.1 + - - +
242D LYS 3.3 0.2 - - - -
243D LEU* 1.3 79.6 - - - +
245D MET* 1.3 67.7 + - + +
247D LYS* 3.4 6.7 + - - +
248D GLU* 3.0 27.7 + - + +
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Residues in contact with MET 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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240D GLU 5.1 3.6 - - - +
241D GLY 3.1 26.6 + - - +
242D LYS* 3.7 20.2 - - + +
244D HIS* 1.3 81.0 - - + +
246D MET* 1.3 58.0 + - + +
248D GLU* 3.3 8.1 + - - +
249D LYS* 2.9 29.5 + - - +
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Residues in contact with MET 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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35D TYR* 3.5 36.0 - - + +
38D ASP* 3.9 16.8 - - + +
39D LEU* 3.4 43.5 - - + +
42D GLU* 4.6 14.6 - - - +
237D LEU* 5.4 1.1 - - - -
242D LYS* 2.9 28.8 + - + +
243D LEU* 3.3 10.5 + - - +
245D MET* 1.3 75.0 - - + +
247D LYS* 1.3 64.2 + - - +
249D LYS* 3.3 7.2 + - + -
250D TRP* 3.2 32.6 + - + -
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Residues in contact with LYS 247 (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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35D TYR* 3.6 12.2 - - + -
106D MET* 4.1 25.7 - - + +
107D THR 5.3 1.4 + - - -
192D THR* 4.5 13.4 - - - +
195D GLU* 3.5 26.0 + - - -
243D LEU 3.0 15.9 + - - +
244D HIS* 3.8 6.1 - - - +
246D MET* 1.3 75.8 - - - +
248D GLU* 1.3 64.9 + - - +
250D TRP 3.2 0.3 + - - -
251D TRP* 2.9 63.5 + - + +
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Residues in contact with GLU 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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244D HIS* 3.0 26.7 + - + +
245D MET* 3.7 7.2 - - - +
247D LYS* 1.3 76.0 - - - +
249D LYS* 1.3 69.8 + - - +
251D TRP* 5.0 2.2 - - - -
252D ARG* 2.9 68.2 + - + +
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Residues in contact with LYS 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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38D ASP* 2.8 34.9 + - - +
245D MET 2.9 18.2 + - - +
246D MET* 3.5 9.9 - - + +
247D LYS 3.2 0.2 - - - -
248D GLU* 1.3 85.8 + - - +
250D TRP* 1.3 84.8 + - + +
252D ARG* 4.0 11.5 + - - +
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Residues in contact with TRP 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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15D PRO* 3.9 10.3 - - + +
18D MET* 3.5 31.6 - - + -
33D GLU* 4.2 20.6 - - + -
34D GLY* 3.4 29.4 - - - -
35D TYR* 3.5 24.0 - + + +
38D ASP* 2.9 27.9 + - - -
196D TYR* 3.4 21.5 + - - -
200D ARG* 4.1 1.9 + - - -
246D MET* 3.2 22.6 + - - +
247D LYS 3.2 2.2 + - - -
249D LYS* 1.3 106.1 - - + +
251D TRP* 1.3 81.9 - - + +
252D ARG 4.7 1.2 - - - +
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Residues in contact with TRP 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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15D PRO* 3.6 28.5 - - + -
16D TYR* 3.4 43.7 - + - -
35D TYR* 4.0 16.4 - + + -
106D MET* 4.0 5.2 - - + -
192D THR* 3.1 26.6 + - - -
195D GLU* 3.8 30.0 + - + +
196D TYR* 3.7 20.8 - + + +
199D GLN* 5.6 2.3 - - - +
200D ARG* 3.0 18.2 + - - +
247D LYS* 2.9 61.8 + - + +
248D GLU* 4.5 2.0 - - - +
250D TRP* 1.3 88.7 - - + +
252D ARG* 1.3 66.5 + - - +
253D GLY 3.4 1.0 + - - -
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Residues in contact with ARG 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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200D ARG* 3.2 11.4 + - - -
248D GLU* 2.9 49.5 + - - +
249D LYS* 4.2 9.3 - - - +
250D TRP 3.5 2.7 - - - +
251D TRP* 1.3 76.5 - - - +
253D GLY* 1.3 64.6 + - - +
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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