Contacts of the helix formed by residues 342 - 353 (chain D) in PDB entry 2G4C
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 342 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D ARG* 4.4 15.2 - - + -
110D LEU* 3.6 41.8 - - + +
111D ALA* 3.6 35.0 - - + +
114D TRP* 4.9 11.7 - - + -
211D ILE* 3.8 26.9 - - + -
235D THR* 3.2 22.2 + - + +
237D ALA* 4.2 14.8 - - + -
262D TRP* 5.1 2.9 - - + -
263D TRP* 5.4 4.0 - - + -
340D GLY 3.6 2.6 + - - -
341D ASP* 1.3 72.5 - - - +
343D ASP* 1.3 58.0 + - - +
345D GLY* 3.3 1.1 + - - -
346D MET* 3.0 26.6 + - - +
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Residues in contact with ASP 343 (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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91D LEU 6.0 0.4 - - - +
96D HIS* 5.3 8.3 - - + -
99D PHE* 3.1 21.9 - - + -
107D ARG* 3.0 28.3 + - - -
233D GLU 4.6 1.5 - - - +
234D LYS* 3.6 15.0 - - - +
235D THR* 2.7 38.3 + - - -
341D ASP* 3.2 7.5 + - - +
342D LEU* 1.3 72.7 - - - +
344D ARG* 1.3 66.7 + - - +
345D GLY 3.0 1.8 - - - -
346D MET* 3.1 16.6 + - - +
347D LEU* 3.2 20.1 + - + +
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Residues in contact with ARG 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 2.8 60.4 + - + +
93D SER* 4.7 1.2 - - - +
234D LYS* 3.6 21.3 - - - +
293D PHE* 3.9 7.6 - - + -
298D GLU* 3.6 29.2 + - - +
299D LEU* 3.0 35.5 + - - +
300D ILE* 4.2 12.6 - - + +
341D ASP* 3.2 20.0 + - + +
343D ASP* 1.3 78.7 - - - +
345D GLY* 1.3 51.9 + - - +
347D LEU* 3.2 10.5 + - + +
348D ALA* 2.7 34.4 + - - +
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Residues in contact with GLY 345 (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* 3.7 6.1 - - - -
263D TRP* 3.6 29.1 - - - -
300D ILE* 5.3 1.1 - - - +
341D ASP 3.0 10.6 + - - -
342D LEU 3.6 5.4 - - - -
343D ASP 3.0 0.4 - - - -
344D ARG* 1.3 76.8 - - - +
346D MET* 1.3 57.9 + - - +
348D ALA* 3.5 5.3 - - - +
349D TYR* 2.9 36.7 + - - -
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Residues in contact with MET 346 (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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79D LEU* 4.5 3.6 - - + -
99D PHE* 3.4 47.8 - - + -
103D GLY* 3.9 18.6 - - - +
106D LEU* 3.3 31.4 - - + +
107D ARG* 3.6 31.6 - - + +
110D LEU* 4.1 6.3 - - + -
342D LEU 3.0 12.6 + - - +
343D ASP* 3.3 13.0 - - - +
345D GLY* 1.3 77.5 - - - +
347D LEU* 1.3 64.5 + - + +
349D TYR* 3.9 2.3 + - - +
350D LEU* 3.0 40.6 + - + +
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 4.5 7.4 - - + -
91D LEU* 3.9 49.1 - - + +
92D LEU* 4.5 15.5 - - + -
96D HIS* 5.8 1.3 - - + -
99D PHE* 4.4 23.1 - - + -
293D PHE* 4.0 9.9 - - + -
295D TRP* 6.5 0.7 - - + -
343D ASP* 3.2 17.7 + - + +
344D ARG* 3.6 8.7 - - - +
346D MET* 1.3 81.2 - - + +
348D ALA* 1.3 69.4 + - - +
349D TYR 3.1 1.8 - - - -
350D LEU* 3.3 9.3 + - + +
351D TYR* 3.2 35.3 + - + -
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Residues in contact with ALA 348 (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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273D PHE* 4.2 13.0 - - + -
291D TYR* 3.5 36.2 - - + -
293D PHE* 3.7 14.5 - - + -
300D ILE* 5.1 2.5 - - + -
344D ARG 2.7 18.3 + - - +
345D GLY* 3.5 14.1 - - - +
347D LEU* 1.3 78.9 - - - +
349D TYR* 1.3 58.4 + - - +
351D TYR 3.5 0.3 + - - -
352D ASP* 3.0 24.4 + - - +
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Residues in contact with TYR 349 (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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106D LEU* 5.4 2.9 - - + -
110D LEU* 3.5 28.4 - - + +
262D TRP* 4.8 1.3 - + - -
263D TRP* 2.8 52.4 + + - -
266D PHE* 3.2 43.6 - - + +
267D ALA* 4.1 3.1 - - - -
273D PHE* 4.1 10.3 - + - -
345D GLY 2.9 24.4 + - - +
346D MET* 4.3 5.2 - - - +
347D LEU 3.1 0.2 - - - -
348D ALA* 1.3 79.5 - - - +
350D LEU* 1.3 66.1 + - - +
352D ASP* 3.2 16.5 + - + +
353D SER* 3.0 25.9 + - - -
374D LEU* 4.1 17.8 - - + +
378D LEU* 3.8 14.1 - - + -
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Residues in contact with LEU 350 (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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69D LEU* 3.7 14.8 - - + +
73D CYS* 3.4 27.6 - - - -
78D PHE* 3.9 29.2 - - + -
79D LEU* 4.2 19.1 - - + -
106D LEU* 4.0 8.1 - - + -
346D MET* 3.0 42.2 + - + +
347D LEU* 3.3 12.6 + - + +
349D TYR* 1.3 76.3 - - - +
351D TYR* 1.3 64.0 + - + +
353D SER* 2.9 20.3 + - - -
354D PHE 3.6 5.2 + - - -
372D LEU* 4.0 14.2 - - + +
374D LEU* 4.6 4.0 - - + +
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Residues in contact with TYR 351 (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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67D GLU* 3.7 25.3 + - - -
69D LEU* 3.3 31.2 - - + -
70D LEU* 5.2 12.5 - - + +
91D LEU* 6.1 4.5 - - + +
291D TYR* 4.2 11.7 - - + +
293D PHE* 4.0 15.5 - + - -
294D PRO* 3.4 37.5 - - + -
295D TRP* 3.6 22.9 - + - -
347D LEU* 3.2 27.6 + - + +
348D ALA 3.7 7.0 - - - +
349D TYR 3.1 0.6 - - - -
350D LEU* 1.3 76.5 - - + +
352D ASP* 1.3 54.7 + - - +
353D SER 2.5 17.9 + - - -
354D PHE* 2.8 16.1 + - - +
355D GLN* 4.1 6.5 + - - +
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Residues in contact with ASP 352 (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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266D PHE 3.9 4.7 - - - +
267D ALA* 3.3 15.3 - - - +
268D MET* 2.7 35.9 + - - +
269D SER* 2.8 36.7 + - - +
272D ASN* 5.5 0.9 - - - +
273D PHE* 5.1 0.2 - - + -
291D TYR* 3.4 24.9 + - + +
348D ALA 3.0 15.3 + - - +
349D TYR* 3.2 15.6 + - + +
351D TYR* 1.3 72.6 - - - +
353D SER* 1.3 58.4 + - - +
354D PHE 3.7 0.7 - - - -
355D GLN 5.4 2.8 - - - +
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Residues in contact with SER 353 (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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268D MET* 4.6 4.7 - - - -
349D TYR 3.0 10.8 + - - -
350D LEU* 2.9 15.9 + - - -
351D TYR 2.5 11.5 + - - -
352D ASP* 1.3 78.6 - - - +
354D PHE* 1.3 56.4 + - - +
355D GLN 5.0 1.6 - - - -
371D VAL 3.4 2.6 - - - +
372D LEU* 3.0 13.9 - - - +
373D LYS* 2.7 59.3 + - - +
374D LEU* 3.5 14.2 + - - +
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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