Contacts of the helix formed by residues 426 - 442 (chain A) in PDB entry 1GM5
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 426 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A VAL* 3.0 3.5 + - - +
425A PRO* 1.3 82.9 - - + +
427A SER* 1.3 58.1 + - - +
428A ILE* 3.1 10.2 + - - +
429A LEU* 2.7 61.3 + - + +
430A ALA* 2.8 12.6 + - - +
478A THR* 3.6 6.5 - - - -
501A ARG* 5.1 2.5 - - - +
626A GLU* 4.1 12.9 + - - -
627A GLU* 3.3 14.9 + - - -
629A ASP* 2.6 32.1 + - + +
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A THR* 1.3 72.3 + - - +
428A ILE* 1.3 65.2 + - - +
429A LEU 3.1 0.2 + - - -
430A ALA* 3.3 5.5 + - - +
431A ILE* 3.0 32.9 + - - +
452A ILE* 3.8 34.8 + - - +
454A ALA* 5.6 1.8 - - - +
478A THR* 3.5 14.4 + - - +
627A GLU* 4.3 10.3 + - - -
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A THR* 3.1 6.0 - - - +
427A SER* 1.3 77.6 - - - +
429A LEU* 1.3 56.6 + - - +
431A ILE* 4.0 12.4 - - + +
432A GLN* 3.3 26.0 + - - +
627A GLU* 3.0 21.1 - - - +
629A ASP* 4.3 11.9 - - + -
630A ARG* 1.5 70.0 - - - +
633A LEU* 3.3 35.0 - - + -
653A ILE* 5.0 3.8 - - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A VAL* 3.5 12.8 - - + -
425A PRO* 3.8 20.9 - - + -
426A THR* 2.7 36.0 + - + +
428A ILE* 1.3 78.7 - - - +
430A ALA* 1.3 52.7 + - - +
432A GLN* 3.7 8.7 - - + +
433A HIS* 2.8 46.0 + - + +
497A ASP* 6.3 1.1 - - + -
629A ASP* 4.1 6.5 - - - +
652A GLY* 4.7 16.6 - - - +
653A ILE* 4.2 23.1 - - + +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A VAL* 4.1 6.1 - - + +
426A THR 2.8 10.6 + - - +
427A SER* 3.3 11.2 - - - +
429A LEU* 1.3 71.2 - - - +
431A ILE* 1.3 70.1 + - - +
433A HIS* 2.7 13.7 + - - +
434A TYR* 2.8 15.0 + - - +
450A LEU* 5.3 2.0 - - + -
452A ILE* 4.1 21.5 - - + -
476A ILE* 3.9 14.7 - - + +
477A GLY* 4.3 21.1 - - - +
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Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 3.0 19.7 + - - +
428A ILE* 4.0 12.8 - - + +
430A ALA* 1.3 79.9 - - - +
432A GLN* 1.3 65.6 + - + +
434A TYR* 3.1 15.1 + - - +
435A ARG* 3.3 8.1 + - - +
450A LEU* 4.3 17.4 - - + +
452A ILE* 3.8 24.7 - - + -
454A ALA* 5.8 2.0 - - + -
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE 3.3 17.8 + - - +
429A LEU* 3.7 12.3 - - + +
430A ALA 3.1 0.8 - - - -
431A ILE* 1.3 80.8 - - + +
433A HIS* 1.3 69.6 + - - +
435A ARG* 3.9 35.0 + - - +
436A ARG* 3.7 13.3 + - - +
633A LEU* 4.1 22.6 - - + +
636A ALA* 6.1 2.4 - - - +
653A ILE* 4.3 22.0 - - - +
654A ASP* 5.0 9.6 + - - +
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Residues in contact with HIS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A THR* 5.3 10.6 + - + +
422A PHE* 4.3 20.8 - + + -
424A VAL* 3.6 24.0 - - + +
429A LEU* 2.8 26.9 + - + +
430A ALA* 2.7 11.1 + - - +
432A GLN* 1.3 72.5 - - - +
434A TYR* 1.3 56.8 + - - +
436A ARG* 2.6 40.3 + - + +
437A THR* 3.2 14.4 + - + +
476A ILE* 4.6 7.4 - - + -
497A ASP* 3.3 28.2 + - - -
522A MET* 4.6 2.8 - - - +
1757A MG 4.3 10.9 - - - -
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA 2.8 10.9 + - - +
431A ILE 3.1 12.3 - - - +
433A HIS* 1.3 70.9 - - - +
435A ARG* 1.3 75.3 + - - +
436A ARG 2.7 2.1 + - - -
437A THR* 2.7 17.8 + - - -
438A VAL* 3.2 27.6 + - + +
448A VAL* 3.8 14.6 + - + -
449A ALA* 3.2 13.4 - - - -
450A LEU* 2.5 56.0 - - + +
476A ILE* 3.6 20.5 - - + +
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Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ILE 3.3 7.2 + - - +
432A GLN* 3.9 41.8 + - - +
434A TYR* 1.3 90.5 - - - +
436A ARG* 1.3 66.7 + - - +
438A VAL* 3.2 1.5 + - - +
439A GLU* 2.8 48.6 + - + +
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Residues in contact with ARG 436 (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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403A THR* 3.5 29.1 + - + +
404A VAL* 5.1 1.4 - - - +
407A GLN* 4.8 3.2 + - - +
432A GLN 3.7 6.2 + - - +
433A HIS* 2.6 25.4 + - + +
435A ARG* 1.3 87.1 - - + +
437A THR* 1.3 50.6 + - + +
439A GLU* 4.8 4.3 - - + +
440A SER* 2.1 57.6 + - - +
1756A ADP 2.7 48.5 + - - -
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Residues in contact with THR 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A THR* 6.3 0.9 - - + -
407A GLN* 4.1 13.5 - - - +
410A ILE* 5.1 8.3 - - + -
422A PHE* 4.1 20.9 - - + -
433A HIS* 3.2 10.7 + - + +
434A TYR 2.7 16.4 + - - -
436A ARG* 1.3 74.7 - - + +
438A VAL* 1.3 54.4 + - - +
440A SER* 3.8 4.0 - - - -
441A PHE* 2.6 54.6 + - - +
448A VAL* 4.2 4.1 - - - +
474A VAL* 5.7 0.4 - - - -
476A ILE* 3.1 31.3 - - + +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TYR* 3.2 44.9 - - + +
435A ARG* 3.5 3.1 - - - +
436A ARG 2.8 1.2 + - - -
437A THR* 1.3 81.6 - - - +
439A GLU* 1.3 55.9 + - - +
440A SER 2.7 0.7 - - - -
441A PHE* 2.8 9.5 - - + -
442A SER* 2.2 38.2 + - - -
443A LYS* 3.5 16.5 + - + +
446A ILE 5.9 2.7 - - - +
448A VAL* 4.2 14.6 - - + +
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Residues in contact with GLU 439 (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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435A ARG* 2.8 33.8 + - + +
436A ARG* 5.4 3.5 - - + +
438A VAL* 1.3 78.8 - - - +
440A SER* 1.3 57.1 + - - +
442A SER* 2.5 32.2 + - - +
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Residues in contact with SER 440 (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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361A PHE* 4.6 13.5 - - - -
407A GLN* 3.3 31.8 + - - -
436A ARG* 2.1 55.2 + - - +
437A THR 3.7 0.4 - - - -
439A GLU* 1.3 72.7 - - - +
441A PHE* 1.3 55.7 + - - -
442A SER* 2.3 20.7 + - - -
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 4.3 10.5 - + - -
407A GLN* 4.0 22.4 - - + -
410A ILE* 2.6 43.5 - - + -
411A LEU* 3.8 23.1 - - + -
437A THR* 2.6 34.5 + - + +
438A VAL* 2.8 9.1 + - + +
440A SER* 1.3 72.2 - - - +
442A SER* 1.3 47.3 - - - +
443A LYS* 1.7 52.6 + - - +
444A PHE* 4.3 14.1 - + + -
446A ILE* 4.5 22.0 - - + +
448A VAL* 4.5 8.7 - - + -
474A VAL* 4.3 15.0 - - + -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A VAL* 2.2 18.0 + - - -
439A GLU* 2.6 21.1 - - - +
440A SER 2.3 17.0 + - - -
441A PHE 1.3 60.2 + - - -
443A LYS* 1.3 71.4 + - - +
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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