Contacts of the helix formed by residues 438 - 451 (chain G) in PDB entry 1GLE
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 VAL 438 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248G ALA 3.6 1.6 - - - +
249G ALA* 3.6 33.7 - - + +
252G GLY* 4.2 11.2 - - - +
253G GLN* 4.1 17.5 - - + +
409G ASP* 4.2 17.0 - - + -
433G PRO* 5.2 3.1 - - + -
435G VAL* 3.5 29.8 - - + +
436G ARG 3.0 9.5 + - - +
437G GLU* 1.3 71.1 - - - +
439G THR* 1.3 70.6 + - - +
440G ALA 2.9 2.8 + - - -
441G LEU* 3.2 11.9 + - + +
442G GLY* 3.1 18.2 + - - -
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Residues in contact with THR 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ASP* 3.1 24.9 - - - +
17G ARG* 5.2 2.2 - - - -
80G THR* 3.6 7.0 + - + -
245G ASP* 3.4 41.0 - - + +
246G GLN* 5.4 2.1 + - - +
248G ALA* 3.4 17.5 - - - +
249G ALA* 3.4 20.1 - - - +
264G THR* 4.8 6.4 + - - +
409G ASP* 4.3 7.2 + - - -
437G GLU 3.5 1.0 - - - -
438G VAL* 1.3 80.1 - - - +
440G ALA* 1.3 63.5 + - - +
442G GLY 3.6 0.9 + - - -
502G ZN 4.4 3.8 - - - -
504G ADP 5.8 0.3 + - - -
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Residues in contact with ALA 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA* 3.8 13.0 - - + +
10G ASP* 4.2 12.4 + - + +
17G ARG* 5.8 0.4 - - - -
19G VAL* 3.7 36.3 - - + -
21G MET* 4.7 0.4 - - - -
80G THR* 4.6 4.7 - - - -
437G GLU* 3.3 18.7 + - + +
439G THR* 1.3 75.3 - - - +
441G LEU* 1.3 69.0 + - - +
442G GLY 3.0 1.3 - - - -
443G ALA* 2.8 20.6 + - - +
444G ALA 3.2 7.3 + - - -
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Residues in contact with LEU 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G MET* 3.1 37.5 - - + -
25G ALA* 4.8 8.3 - - + +
27G ILE* 4.0 14.1 - - + -
252G GLY* 4.8 8.1 - - - +
435G VAL* 4.2 29.4 - - + -
437G GLU 3.6 8.9 + - - +
438G VAL* 3.4 17.0 - - + +
440G ALA* 1.3 77.2 - - - +
442G GLY* 1.3 64.1 + - - +
444G ALA* 3.0 13.7 + - - +
445G TYR* 3.1 47.2 + - + +
463G LYS* 5.7 5.8 - - + -
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Residues in contact with GLY 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ALA* 3.2 25.6 - - - -
251G PHE* 3.7 7.3 - - - -
252G GLY* 3.9 14.3 - - - -
438G VAL 3.1 5.9 + - - -
439G THR 4.0 0.2 - - - -
440G ALA 2.9 2.6 + - - -
441G LEU* 1.3 81.5 - - - +
443G ALA* 1.3 63.2 + - - -
445G TYR* 3.2 4.5 + - - +
446G LEU* 3.1 23.2 + - - +
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Residues in contact with ALA 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA* 4.1 5.6 - - + -
78G GLY* 3.8 8.8 - - - -
79G ILE 3.8 25.8 - - - +
80G THR* 3.3 25.8 - - + +
241G GLY* 4.7 1.2 - - - -
242G ILE 5.9 0.7 - - - +
243G ALA 6.0 0.9 - - - +
248G ALA* 4.1 5.4 - - - +
439G THR 3.7 4.4 + - - -
440G ALA 2.8 12.0 + - - +
442G GLY* 1.3 69.7 - - - -
444G ALA* 1.3 56.0 + - - +
446G LEU* 3.2 13.4 + - - +
447G ALA* 2.7 28.9 + - - +
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Residues in contact with ALA 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.2 11.1 - - + +
7G VAL 5.7 0.2 - - - -
8G ALA* 4.3 7.3 - - + +
21G MET* 3.4 37.0 - - + -
78G GLY* 5.0 1.1 - - - +
440G ALA 3.2 2.1 + - - +
441G LEU 3.0 10.8 + - - +
443G ALA* 1.3 78.6 - - - +
445G TYR* 1.3 52.2 + - - +
447G ALA* 2.7 9.8 + - - +
448G GLY 2.4 35.3 + - - -
454G TRP* 3.0 13.7 - - + -
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Residues in contact with TYR 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ALA* 4.6 9.6 - - + +
251G PHE* 3.5 24.9 - + + -
252G GLY* 4.3 14.7 + - - -
254G LEU* 4.0 21.6 - - + +
441G LEU* 3.3 46.7 - - + +
442G GLY 3.4 5.4 - - - +
444G ALA* 1.3 72.7 - - + +
446G LEU* 1.3 61.1 + - - +
447G ALA 2.8 0.7 + - - -
449G LEU* 2.6 41.9 + - + +
454G TRP* 3.0 28.7 - + + -
457G LEU* 4.3 7.4 - - + -
460G LEU* 3.6 37.2 + - + +
463G LYS* 4.9 6.8 - - - +
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Residues in contact with LEU 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G SER* 3.7 26.9 - - - +
221G SER* 3.2 9.9 - - - -
240G SER 3.7 1.4 - - - +
241G GLY* 4.4 6.3 - - - -
242G ILE 4.6 1.6 - - - +
243G ALA* 3.7 27.1 - - + -
248G ALA* 5.4 1.1 - - - -
251G PHE* 3.1 42.4 - - + -
292G CYS* 4.5 7.2 - - - -
295G THR 5.3 0.4 - - - -
296G GLY* 4.1 19.5 - - - +
442G GLY 3.1 16.0 + - - +
443G ALA* 3.5 9.6 - - - +
445G TYR* 1.3 80.1 - - - +
447G ALA* 1.3 56.0 + - - +
449G LEU* 4.6 3.6 - - + -
450G ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.9 15.5 - - + -
77G ILE 4.1 0.7 - - - +
78G GLY* 3.7 24.0 - - - +
240G SER* 2.8 29.2 + - - +
241G GLY 4.1 2.0 - - - +
443G ALA 2.7 11.9 + - - +
444G ALA* 2.7 11.6 + - - +
446G LEU* 1.3 75.0 - - - +
448G GLY* 1.3 69.4 + - - +
450G ALA* 3.0 9.7 + - - +
451G VAL* 3.1 8.5 + - - +
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Residues in contact with GLY 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.0 5.5 - - - +
444G ALA 2.4 14.3 + - - -
447G ALA* 1.3 69.1 - - - +
449G LEU* 1.3 51.0 + - - -
451G VAL* 2.5 29.7 + - - -
453G PHE* 3.0 40.6 + - - -
454G TRP* 3.3 16.2 - - - -
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Residues in contact with LEU 449 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G SER* 5.0 3.4 - - - +
251G PHE* 4.6 12.6 - - + -
294G PRO 3.6 23.8 - - - +
295G THR* 4.4 18.2 - - + -
445G TYR* 2.6 28.3 + - + +
446G LEU* 4.3 5.2 - - + +
448G GLY* 1.3 69.0 - - - -
450G ALA* 1.3 65.4 + - + +
451G VAL 2.9 1.0 + - - -
452G GLY* 3.1 12.3 + - - +
454G TRP* 3.5 30.3 - - + +
455G GLN* 4.1 24.7 + - - +
456G ASN* 4.4 7.9 - - - +
457G LEU* 4.6 10.5 - - + +
460G LEU* 5.7 1.8 - - + -
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Residues in contact with ALA 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G SER* 2.9 30.1 - - - +
222G GLU* 3.9 8.5 - - - +
223G VAL* 4.6 9.4 - - - +
240G SER* 3.7 15.3 - - - +
446G LEU 3.1 15.0 + - - +
447G ALA 3.0 6.0 + - - +
448G GLY 2.9 0.2 + - - -
449G LEU* 1.3 81.4 - - - +
451G VAL* 1.3 59.7 + - - +
452G GLY 3.5 0.2 - - - -
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Residues in contact with VAL 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ALA* 4.1 22.2 - - + +
76G ALA* 4.1 18.8 - - + -
223G VAL* 4.8 8.3 - - + -
238G PRO* 4.6 9.4 - - + -
240G SER* 4.2 9.4 - - - -
447G ALA 3.1 7.4 + - - +
448G GLY* 2.5 21.9 + - - +
450G ALA* 1.3 75.5 - - - +
452G GLY* 1.3 59.8 + - - +
453G PHE* 2.8 22.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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