Contacts of the helix formed by residues 249 - 258 (chain A) in PDB entry 1GGE
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 THR 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A PHE* 3.0 32.9 - - + +
208A ILE* 4.4 0.9 - - + -
217A PHE* 4.6 2.0 - - + -
242A TYR* 3.8 32.1 - - + -
243A VAL* 3.5 31.3 + - + +
246A GLN* 2.8 24.9 + - + +
248A GLU* 1.3 80.6 - - + +
250A LEU* 1.3 64.6 + - - +
251A HIS 3.2 1.3 + - - -
252A ASN* 3.3 5.0 + - - -
253A VAL* 3.1 22.4 + - - +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A VAL* 4.1 21.1 - - + +
247A PRO* 3.0 27.0 + - + +
248A GLU 3.3 0.2 - - - -
249A THR* 1.3 78.9 + - - +
251A HIS* 1.3 56.9 + - - +
253A VAL* 3.3 10.8 + - + +
254A MET* 2.9 33.1 + - + +
504A TYR 4.3 0.4 - - - +
505A TYR* 3.5 33.7 - - + -
508A PRO* 4.1 7.6 - - + -
527A PHE* 5.6 0.9 - - + -
543A VAL* 5.5 3.1 - - + -
546A GLN* 3.6 31.2 - - + +
547A LEU* 4.8 9.9 - - + -
550A ILE* 4.2 20.2 - - + -
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ILE* 3.5 26.8 - - + +
248A GLU 4.2 6.8 + - - +
249A THR 3.3 1.2 - - - -
250A LEU* 1.3 76.4 - - - +
252A ASN* 1.3 63.5 + - - +
254A MET* 3.1 13.3 + - - +
255A TRP* 3.1 40.0 + + - -
357A THR* 2.8 28.3 + - - +
359A LEU* 3.5 23.9 - - + +
504A TYR 4.8 1.5 + - - +
507A HIS* 3.4 39.6 + - + +
508A PRO* 3.6 21.9 - - + +
511A PHE* 4.4 4.1 - - + +
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 3.7 12.6 - - - +
203A THR* 2.7 30.8 + - - -
205A ILE* 3.2 30.6 + - + +
206A PHE* 3.7 20.2 + - - +
207A PHE* 3.4 44.2 + - + +
248A GLU 5.2 0.2 + - - -
249A THR 3.3 3.2 + - - -
251A HIS* 1.3 78.7 - - - +
253A VAL* 1.3 56.6 + - - +
255A TRP* 3.2 3.5 + - - +
256A ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 3.8 20.2 - - + -
239A PHE* 3.9 5.2 - - + -
240A TRP* 3.5 32.5 - - + -
243A VAL* 3.7 31.6 - - + -
249A THR* 3.1 15.7 + - - +
250A LEU* 3.6 12.1 - - + +
251A HIS 3.2 0.2 - - - -
252A ASN* 1.3 74.0 - - - +
254A MET* 1.3 66.9 + - - +
256A ALA* 3.2 3.7 + - - +
257A MET* 2.9 27.0 + - + +
527A PHE* 3.6 15.3 - - + -
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Residues in contact with MET 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU 2.9 19.5 + - - +
251A HIS* 3.1 8.9 + - - +
253A VAL* 1.3 76.3 - - - +
255A TRP* 1.3 61.8 + - - +
257A MET* 3.4 2.3 + - - +
258A SER* 3.1 22.9 + - - -
508A PRO* 3.8 26.0 - - + +
511A PHE* 3.7 23.1 - - + -
512A TRP* 3.8 37.2 - - + -
523A ILE* 4.2 12.5 - - + +
527A PHE* 3.7 26.7 - - - -
547A LEU* 4.8 0.2 - - - -
550A ILE* 4.5 11.0 - - + -
554A LEU* 3.8 21.3 - - + -
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Residues in contact with TRP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 3.6 28.3 - - + -
204A PRO* 3.3 37.7 - - + -
205A ILE* 3.5 13.7 - - + +
251A HIS* 3.1 44.6 + + - -
252A ASN* 3.2 9.5 + - - +
254A MET* 1.3 79.3 - - - +
256A ALA* 1.3 62.3 + - - +
258A SER* 2.6 25.5 + - - +
260A ARG* 3.4 64.4 - - + +
261A GLY 3.7 0.2 + - - -
270A GLU* 5.1 0.2 - - - -
272A PHE* 4.9 4.9 - + - -
359A LEU* 3.8 10.8 - - + -
511A PHE* 3.4 34.1 - + - -
588A LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 2.9 32.2 + - + +
181A ASP* 5.3 4.9 - - - -
182A ILE* 4.2 19.4 - - + +
207A PHE* 4.6 8.7 - - + -
234A SER* 5.9 0.4 - - - +
239A PHE* 6.0 1.8 - - + -
252A ASN 2.9 16.7 + - - +
253A VAL* 3.2 8.5 + - + +
255A TRP* 1.3 76.3 - - - +
257A MET* 1.3 71.5 + - + +
258A SER 3.3 2.8 - - - +
261A GLY* 3.5 11.0 - - - -
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Residues in contact with MET 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 3.2 32.9 + - + +
234A SER* 4.0 7.2 - - - +
239A PHE* 5.0 2.7 - - + -
240A TRP* 3.7 24.0 - - + -
253A VAL* 2.9 19.8 + - + +
254A MET 3.9 3.1 - - - +
256A ALA* 1.3 85.5 - - + +
258A SER* 1.3 64.2 + - - +
522A HIS 3.5 18.4 - - - +
523A ILE* 3.6 7.5 - - + +
526A GLY* 3.8 12.9 - - - -
527A PHE* 3.9 40.2 - - + +
530A GLU* 3.7 30.3 - - - +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 3.1 7.8 + - - -
254A MET 3.1 10.3 + - - -
255A TRP* 2.6 22.7 + - - -
256A ALA 3.3 0.3 - - - +
257A MET* 1.3 81.4 - - - +
259A ASP* 1.3 61.0 + - - +
260A ARG* 3.0 26.3 + - - +
261A GLY 3.0 12.5 + - - -
511A PHE* 3.8 13.6 - - - -
515A GLN* 5.1 4.3 - - - -
519A GLU* 5.3 1.6 - - - -
523A ILE* 3.4 28.9 - - - +
590A LEU* 6.2 0.2 - - - -
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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