Contacts of the helix formed by residues 414 - 419 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLU* 3.7 19.7 - - - +
392A TRP* 3.1 29.9 + - + +
394A ALA* 3.9 14.6 - - + +
412A ALA 4.3 0.4 - - - +
413A SER* 1.3 69.6 + - - +
415A GLN* 1.3 58.5 + - + +
417A ILE* 3.8 8.0 - - + +
418A LYS* 3.1 18.9 + - - +
480A THR* 3.3 33.3 - - - +
481A TYR* 3.9 33.7 - - + +
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Residues in contact with GLN 415 (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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388A GLY 3.8 23.7 + - - +
389A PHE* 3.8 9.2 - - + -
390A GLY 4.9 9.6 - - - +
392A TRP 5.0 0.2 + - - -
413A SER* 3.0 4.2 + - - +
414A VAL* 1.3 79.1 - - - +
416A ALA* 1.3 68.5 + - - +
417A ILE 3.2 0.2 - - - -
418A LYS* 3.6 9.6 + - - +
419A HIS* 3.1 57.1 + - + -
480A THR* 4.4 10.2 - - - +
415B GLN* 5.6 4.8 - - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 5.8 0.2 - - + -
389A PHE* 3.5 29.4 - - + -
413A SER* 2.9 17.1 + - - +
415A GLN* 1.3 78.6 - - - +
417A ILE* 1.3 51.7 + - + +
419A HIS* 3.0 3.7 + - - -
420A GLY 2.7 30.5 + - - -
421A HIS* 2.9 33.9 + - - +
422A VAL* 5.6 0.7 - - - -
424A PHE* 4.7 10.8 - - + +
428A ALA* 5.6 3.1 - - + -
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Residues in contact with ILE 417 (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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394A ALA* 4.9 2.2 - - + -
412A ALA* 4.1 19.7 - - + +
413A SER 3.1 12.2 + - - +
414A VAL* 3.8 14.1 - - - +
416A ALA* 1.3 75.3 - - - +
418A LYS* 1.3 56.9 + - - +
420A GLY 2.7 21.2 + - - +
422A VAL* 5.2 2.9 - - + +
428A ALA* 4.5 18.4 - - + +
431A VAL* 3.6 32.1 - - + -
432A PHE* 3.2 39.1 - - + +
435A VAL* 4.9 4.0 - - + -
436A ASN* 5.4 0.2 - - - +
481A TYR* 4.1 32.0 - - + +
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Residues in contact with LYS 418 (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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414A VAL 3.1 8.5 + - - +
415A GLN* 4.0 15.2 + - - +
417A ILE* 1.3 78.8 - - - +
419A HIS* 1.3 65.8 + - + +
432A PHE* 5.3 0.6 - - - -
479A ASP* 2.6 27.0 + - - +
480A THR* 3.2 28.8 - - - +
481A TYR 2.9 21.6 - - - +
482A LYS* 4.0 9.5 - - - +
483A PHE* 3.2 55.9 + - + +
493A ALA* 3.7 6.2 - - - +
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Residues in contact with HIS 419 (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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389A PHE* 4.8 7.2 - + - -
415A GLN* 3.1 44.6 + - + +
416A ALA 3.0 1.3 + - - +
417A ILE 2.9 0.8 - - - -
418A LYS* 1.3 88.6 - - + +
420A GLY* 1.3 62.1 + - - +
421A HIS* 3.2 22.4 - + + -
483A PHE* 3.7 24.0 - + - -
493A ALA* 3.8 8.5 - - - -
496A THR* 3.2 3.5 + - - -
387B VAL* 2.7 48.9 - - + +
388B GLY* 3.5 18.3 + - - -
415B GLN* 5.3 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