Contacts of the helix formed by residues 368 - 380 (chain B) in PDB entry 1GXD
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 LEU 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B THR* 4.7 1.6 - - + -
106B LEU* 3.9 25.8 - - + -
111B VAL* 4.2 23.6 - - + -
114B ALA* 4.5 11.0 - - + -
115B PHE* 4.2 11.7 - - + -
144B PHE* 3.9 31.0 - - + -
178B PHE* 4.1 24.5 - - + -
184B TRP* 3.9 24.5 - - + -
185B THR 2.9 14.4 + - - +
186B LEU* 5.2 1.3 - - + -
366B TYR 3.0 4.5 + - - -
367B SER* 1.3 71.0 - - - +
369B PHE* 1.3 57.2 + - - +
371B VAL 4.7 0.2 - - - +
372B ALA* 2.8 34.5 + - - +
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Residues in contact with PHE 369 (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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114B ALA* 3.9 20.5 - - + +
117B ARG* 3.3 72.7 - - + +
118B ALA* 4.0 2.5 - - - +
121B VAL* 3.7 21.5 - - + -
186B LEU* 4.9 5.4 - - + +
367B SER* 3.0 7.3 + - - +
368B LEU* 1.3 79.2 - - - +
370B LEU* 1.3 84.7 + - + +
372B ALA* 3.5 2.9 - - - +
373B ALA* 2.8 28.2 + - + +
402B PHE* 3.9 28.3 - + + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 3.1 19.2 + - - +
369B PHE* 1.3 87.6 - - + +
371B VAL* 1.3 67.4 + - - +
373B ALA* 3.2 5.4 + - - +
374B HIS* 3.1 21.8 + - - +
391B LEU* 4.1 10.0 - - + +
396B TYR* 4.7 9.9 - - + -
397B THR 4.3 10.5 - - - +
398B TYR* 3.6 34.3 - - + -
399B THR* 4.0 13.0 - - - +
402B PHE* 3.6 47.3 - - + -
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Residues in contact with VAL 371 (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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162B LEU* 4.0 14.1 - - + -
163B ALA* 3.9 27.1 - - + -
178B PHE* 3.9 10.1 - - + -
184B TRP* 3.6 25.8 - - + -
366B TYR* 4.3 0.9 - - + -
367B SER 2.9 19.7 + - - +
368B LEU 4.1 1.6 - - - +
370B LEU* 1.3 75.7 - - - +
372B ALA* 1.3 62.9 + - - +
374B HIS* 3.3 10.0 + - + +
375B ALA* 3.1 18.7 + - - +
396B TYR* 3.7 28.7 - - + -
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Residues in contact with ALA 372 (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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114B ALA 5.1 0.7 - - - +
115B PHE* 4.0 16.8 - - + -
118B ALA* 3.8 15.5 - - + -
178B PHE* 3.6 25.8 - - + -
368B LEU 2.8 20.4 + - - +
369B PHE* 3.5 4.7 - - - +
371B VAL* 1.3 76.2 - - - +
373B ALA* 1.3 64.2 + - - +
375B ALA* 3.0 2.9 + - - +
376B PHE* 2.9 29.0 + - + -
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Residues in contact with ALA 373 (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 ALA* 3.8 13.0 - - + +
121B VAL* 4.1 24.0 - - + -
122B TRP* 3.1 29.0 + - - +
369B PHE* 2.8 17.9 + - + +
370B LEU* 3.2 9.1 + - - +
372B ALA* 1.3 78.6 - - - +
374B HIS* 1.3 58.9 + - - +
376B PHE* 5.0 0.4 - - - -
377B GLY 3.4 3.8 + - - -
391B LEU* 3.6 20.6 - - + -
402B PHE* 4.9 2.9 - - + -
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Residues in contact with HIS 374 (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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73B CYS* 2.9 20.0 - - + -
370B LEU 3.1 11.9 + - - +
371B VAL* 3.6 13.5 - - + +
373B ALA* 1.3 74.1 - - - +
375B ALA* 1.3 69.9 + - + +
377B GLY 3.5 1.2 + - - -
378B HIS* 3.0 17.2 + + - -
384B HIS* 3.2 16.2 - + - -
391B LEU* 3.1 27.9 + - + +
392B MET* 3.4 19.3 - - + +
393B ALA 3.1 19.9 + - - -
394B PRO* 3.8 1.5 + - + -
1634B ZN 1.8 37.4 - - - -
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Residues in contact with ALA 375 (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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163B ALA* 5.2 4.9 - - + -
164B HIS 4.7 6.3 - - - +
165B ALA* 3.6 20.9 - - + +
176B SER* 4.3 12.8 - - - -
178B PHE* 4.4 10.5 - - + -
371B VAL 3.1 12.5 + - - +
372B ALA 3.0 7.7 + - - +
374B HIS* 1.3 80.0 - - + +
376B PHE* 1.3 60.3 + - + +
377B GLY 3.0 1.3 - - - -
378B HIS* 2.6 31.0 + - - +
379B ALA 2.8 8.3 + - - -
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Residues in contact with PHE 376 (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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115B PHE* 4.0 17.0 - + - -
118B ALA* 3.7 30.3 - - + -
119B PHE* 3.1 44.9 - + + -
122B TRP* 4.1 11.4 - - + +
140B ILE* 4.7 1.3 - - + -
142B ILE* 3.3 30.5 - - + -
176B SER* 3.6 30.3 - - - -
178B PHE* 4.4 7.4 - + - -
372B ALA* 2.9 11.6 + - + +
373B ALA 4.5 0.4 - - - +
375B ALA* 1.3 74.2 - - + +
377B GLY* 1.3 51.7 + - - +
379B ALA* 2.8 10.5 + - + +
380B MET* 2.7 50.5 + - + +
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Residues in contact with GLY 377 (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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122B TRP* 3.4 30.7 - - - +
373B ALA 3.4 8.3 + - - -
374B HIS 3.5 4.5 + - - -
375B ALA 2.9 1.4 + - - -
376B PHE* 1.3 76.9 - - - +
378B HIS* 1.3 62.0 + - - +
380B MET* 3.1 9.3 + - - +
381B GLY 3.4 0.3 + - - -
382B LEU* 3.0 32.4 + - - +
392B MET* 4.1 4.3 - - - -
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Residues in contact with HIS 378 (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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73B CYS* 3.3 1.7 - - - -
75B ASN* 3.1 33.5 + - + +
76B PRO 5.5 0.4 - - - -
164B HIS 5.6 0.2 - - - -
165B ALA* 3.7 17.7 - - + +
166B PHE 4.7 0.7 - - - -
167B ALA* 3.7 14.0 - - - +
374B HIS* 3.0 23.5 + + - -
375B ALA* 2.6 18.8 + - - +
377B GLY* 1.3 71.5 - - - +
379B ALA* 1.3 55.7 + - - +
381B GLY* 2.8 22.7 + - - -
382B LEU 3.5 16.7 + - - +
383B GLU* 4.6 2.8 + - - -
384B HIS* 2.8 25.5 + + - -
392B MET* 3.8 7.3 - - + +
1634B ZN 1.9 37.7 - - - -
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Residues in contact with ALA 379 (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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90B TRP* 2.9 23.2 + - - -
140B ILE* 3.8 17.0 - - + -
165B ALA* 4.4 1.9 - - + +
166B PHE 4.0 11.4 - - - -
168B PRO* 3.0 11.4 - - - +
174B GLY 3.3 24.5 - - - +
176B SER* 4.1 4.9 - - - +
375B ALA 2.8 5.5 + - - +
376B PHE* 2.8 22.7 + - - +
378B HIS* 1.3 77.6 - - - +
380B MET* 1.3 55.9 + - - -
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Residues in contact with MET 380 (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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88B PRO 4.2 1.6 - - - +
90B TRP* 3.7 16.8 - - - +
119B PHE* 3.7 8.7 - - + -
122B TRP* 4.8 7.2 - - + -
128B LEU* 4.2 16.4 - - + -
130B PHE* 3.1 41.3 - - + -
140B ILE* 3.6 19.3 - - + -
168B PRO* 3.4 6.1 - - - +
376B PHE* 2.7 34.1 + - + +
377B GLY* 3.8 7.9 - - - +
378B HIS 3.1 0.6 - - - -
379B ALA* 1.3 77.8 - - - +
381B GLY* 1.3 58.5 + - - +
382B LEU 3.6 0.4 - - - -
412B ILE* 3.9 22.2 - - + -
415B LEU* 4.1 3.0 - - - +
416B TYR* 2.5 34.8 + - + -
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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