Contacts of the helix formed by residues 428 - 436 (chain B) in PDB entry 1GGT
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 ALA 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ALA* 3.7 17.9 - - + -
413B SER 5.5 0.4 - - - +
416B ALA* 5.5 3.8 - - + -
417B ILE* 3.4 18.5 - - + +
421B HIS 4.5 3.4 - - - +
422B VAL* 3.8 19.3 - - + -
424B PHE 3.7 20.7 + - - +
426B PHE 2.9 6.5 + - - -
427B ASP* 1.3 71.0 - - - +
429B PRO* 1.3 58.1 - - + +
431B VAL 3.0 3.1 + - - -
432B PHE* 2.7 34.7 + - - +
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Residues in contact with PRO 429 (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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346B ALA* 4.6 14.4 - - + -
422B VAL* 3.4 37.0 - - + +
427B ASP* 3.2 3.8 - - - -
428B ALA* 1.3 87.4 - - + +
430B PHE* 1.3 82.1 + - + +
432B PHE* 3.5 9.5 - - + +
433B ALA* 2.9 31.9 + - - +
500B TYR 5.1 4.0 - - - +
501B GLY 5.4 1.1 - - - -
502B ALA* 5.0 12.4 - - + +
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ASN* 3.2 28.5 + - - -
345B ASP* 3.7 14.6 - - - -
346B ALA* 3.6 33.9 - - + -
400B GLN* 3.9 10.9 + - - +
401B GLU 3.3 25.6 - - - -
402B ASN* 3.8 31.0 - - + -
403B SER* 4.1 12.3 - - - -
409B CYS* 4.1 16.6 - - - -
427B ASP* 3.1 14.3 + - + +
429B PRO* 1.3 96.4 - - + +
431B VAL* 1.3 59.0 - - - +
434B GLU* 3.3 8.5 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TRP* 5.0 9.9 - - + -
394B ALA* 4.2 20.2 - - + +
396B ASP* 6.0 4.9 - - + -
400B GLN* 5.6 0.7 - - - +
409B CYS* 4.2 20.2 - - + +
412B ALA* 3.8 16.2 - - + -
417B ILE* 3.6 25.8 - - + +
426B PHE 4.8 0.4 - - - +
427B ASP 3.2 18.6 - - - +
428B ALA 3.0 3.8 + - - +
430B PHE* 1.3 76.2 - - - +
432B PHE* 1.3 62.9 + - - +
433B ALA 3.5 0.2 - - - -
434B GLU* 3.5 20.9 - - + +
435B VAL* 4.2 8.5 + - - +
481B TYR* 5.0 6.7 - - + -
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.9 27.1 - - + -
417B ILE* 3.1 42.8 - - + -
418B LYS 5.1 1.8 - - - -
420B GLY* 3.6 15.0 - - - -
422B VAL* 3.8 20.0 - - + -
428B ALA 2.7 15.3 + - - +
429B PRO* 3.1 5.8 + - + +
431B VAL* 1.3 74.6 - - - +
433B ALA* 1.3 62.5 + - - +
434B GLU 3.1 5.6 + - - -
435B VAL* 3.2 13.5 + - - +
436B ASN* 3.3 39.1 + - + +
493B ALA* 4.3 3.4 - - + -
494B LEU* 4.3 16.8 - - + -
497B ALA* 3.3 27.6 - - + -
502B ALA* 4.9 3.6 - - + -
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA* 3.3 4.7 - - - +
344B ASN* 3.3 29.4 - - - +
346B ALA* 4.3 7.0 - - - -
347B ASN 3.9 11.9 - - - +
348B LEU* 3.8 25.8 - - + -
429B PRO 2.9 11.7 + - - +
432B PHE* 1.3 76.7 - - - +
434B GLU* 1.3 60.5 + - - +
435B VAL 3.1 2.0 + - - -
436B ASN 4.0 1.3 - - - +
437B SER* 2.6 26.6 + - - -
502B ALA* 6.2 0.2 - - + -
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Residues in contact with GLU 434 (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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337B ASN* 3.1 13.3 - - - +
340B SER* 3.1 23.2 + - - -
341B ALA* 3.2 22.9 + - - -
342B HIS* 2.5 50.2 + - - -
344B ASN* 3.6 3.8 - - - +
373B HIS* 3.7 11.4 - - - -
375B TRP* 4.1 16.9 - - + -
396B ASP* 4.1 2.7 - - - +
400B GLN* 3.1 10.7 + - - +
430B PHE 3.3 17.9 - - - +
431B VAL* 3.5 15.9 - - + +
432B PHE 3.1 1.2 - - - -
433B ALA* 1.3 77.9 - - - +
435B VAL* 1.3 57.6 + - - +
436B ASN 3.7 0.2 - - - -
460B ILE 3.8 3.9 - - - +
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Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ASN* 3.2 34.1 - - - +
375B TRP* 4.6 5.6 - - + -
417B ILE* 4.8 4.0 - - + -
431B VAL 4.3 7.6 - - - +
432B PHE 3.8 5.8 - - - +
433B ALA 3.1 0.2 - - - -
434B GLU* 1.3 83.7 - - + +
436B ASN* 1.3 68.6 + - - +
437B SER 4.0 0.7 - - - -
460B ILE* 3.9 10.4 - - - +
461B GLY* 4.0 5.4 - - - -
464B ILE* 3.4 22.0 - - + -
481B TYR* 4.3 24.0 - - + -
482B LYS* 2.6 37.1 + - + +
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Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.2 9.0 - - + +
432B PHE* 3.3 45.4 + - + +
433B ALA 4.4 0.9 - - - -
435B VAL* 1.3 100.2 + - - +
437B SER* 1.3 64.5 + - - +
438B ASP* 4.1 3.5 + - - +
460B ILE* 3.8 4.9 - - - -
481B TYR 4.3 10.7 + - - -
482B LYS* 4.3 16.0 - - - +
490B GLU* 6.0 1.7 - - - +
494B LEU* 4.0 27.9 - - + +
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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