Contacts of the helix formed by residues 414 - 419 (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 VAL 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLU* 3.3 24.5 - - - +
392B TRP* 3.2 27.1 + - + +
394B ALA* 4.2 15.0 - - + +
412B ALA 3.3 0.6 + - - -
413B SER* 1.3 70.3 - - - +
415B GLN* 1.3 53.2 + - + +
417B ILE* 2.9 11.3 + - - +
418B LYS* 2.7 33.4 + - - +
480B THR* 3.6 34.1 - - - +
481B TYR* 3.6 28.5 - - + +
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Residues in contact with GLN 415 (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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415A GLN* 5.6 4.8 - - - +
419A HIS* 5.3 5.9 + - - -
388B GLY 3.5 20.5 + - - +
389B PHE* 4.1 13.1 - - + -
390B GLY 4.9 8.5 - - - +
392B TRP 4.7 0.8 + - - -
413B SER* 3.2 8.9 + - - +
414B VAL* 1.3 79.9 - - + +
416B ALA* 1.3 59.9 + - - +
418B LYS* 3.8 12.3 - - - +
419B HIS* 2.8 58.8 + - - -
480B THR 5.2 0.7 - - - -
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Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.9 21.8 - - + -
413B SER* 2.9 24.9 + - - +
415B GLN* 1.3 76.5 - - - +
417B ILE* 1.3 66.1 + - - +
418B LYS 3.2 0.2 - - - -
419B HIS 3.5 0.4 + - - +
420B GLY* 3.0 4.2 + - - -
421B HIS* 2.8 52.1 + - + +
422B VAL* 5.5 0.2 - - - -
424B PHE* 5.0 6.7 - - + +
428B ALA* 5.5 4.0 - - + -
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Residues in contact with ILE 417 (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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394B ALA* 5.3 0.4 - - + -
412B ALA* 4.0 5.4 - - + +
413B SER 2.9 19.8 + - - +
414B VAL* 2.9 14.5 + - + +
416B ALA* 1.3 75.7 - - - +
418B LYS* 1.3 64.9 + - - +
420B GLY 3.0 12.5 + - - -
422B VAL* 5.2 0.7 - - - -
428B ALA* 3.4 42.4 - - + +
431B VAL* 3.6 22.4 - - + +
432B PHE* 3.1 42.4 - - + +
435B VAL* 4.8 4.0 - - + -
436B ASN* 5.4 0.2 - - - +
481B TYR* 4.2 30.9 - - + +
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Residues in contact with LYS 418 (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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414B VAL 2.7 11.1 + - - +
415B GLN* 3.9 15.0 - - - +
416B ALA 3.2 0.2 - - - -
417B ILE* 1.3 78.2 - - - +
419B HIS* 1.3 66.4 + - + +
432B PHE* 5.1 0.5 - - - -
479B ASP* 2.6 26.9 + - - +
480B THR* 2.8 30.9 - - - +
481B TYR 3.4 17.6 + - - +
482B LYS* 3.9 7.9 + - - +
483B PHE* 3.1 50.8 - - + +
493B ALA* 3.6 6.6 - - - +
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Residues in contact with HIS 419 (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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387A VAL* 3.8 29.4 + - + +
388A GLY* 4.1 22.4 - - - -
389B PHE* 4.7 4.5 - + - -
415B GLN* 2.8 53.0 + - - +
416B ALA 3.5 0.2 + - - -
417B ILE 3.2 0.4 - - - -
418B LYS* 1.3 83.9 - - + +
420B GLY* 1.3 61.8 + - - +
421B HIS* 3.3 27.5 + - + -
483B PHE* 3.3 32.8 - + - -
493B ALA* 3.9 12.0 - - - -
496B THR* 3.9 5.0 - - - +
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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