Contacts of the helix formed by residues 414 - 423 (chain B) in PDB entry 3GUU
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 GLY 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B ASP* 3.0 21.0 + - - -
411B GLN 4.5 1.2 + - - -
412B VAL 3.6 1.6 - - - -
413B LEU* 1.3 77.7 - - - +
415B SER* 1.3 64.6 + - - -
416B ASP* 3.4 3.5 + - - -
417B LEU 3.7 0.2 + - - -
418B ALA* 3.0 23.2 + - - +
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Residues in contact with SER 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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410B ASP* 4.0 19.8 + - - +
414B GLY* 1.3 70.0 - - - -
416B ASP* 1.3 65.0 + - - +
418B ALA* 3.8 0.3 - - - +
419B ASN* 2.9 43.7 + - - +
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Residues in contact with ASP 416 (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 GLY 5.1 0.4 - - - -
415B SER* 1.3 84.4 + - - +
417B LEU* 1.3 67.9 + - + +
419B ASN* 3.1 8.3 + - - +
420B GLN* 3.0 42.0 + - - +
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Residues in contact with LEU 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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50B ASN* 5.4 2.9 - - - +
124B PRO 4.5 4.9 - - - +
125B ILE* 4.1 28.6 - - + +
128B GLY* 3.9 7.2 - - - +
129B TRP* 3.4 38.8 - - + +
132B GLN* 4.3 13.7 - - + -
413B LEU* 3.6 31.4 + - + +
414B GLY 3.7 1.8 + - - -
415B SER 3.5 0.2 - - - -
416B ASP* 1.3 83.3 - - + +
418B ALA* 1.4 56.2 + - - +
420B GLN* 3.2 28.0 + - - +
421B LEU* 3.0 26.9 + - - +
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Residues in contact with ALA 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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409B ALA* 3.8 20.0 - - + -
410B ASP* 3.0 29.2 - - - +
413B LEU* 3.8 11.9 - - - +
414B GLY 3.0 18.1 + - - +
415B SER 3.8 0.9 - - - +
417B LEU* 1.4 71.2 - - - +
419B ASN* 1.3 60.4 + - - +
421B LEU* 3.2 3.8 + - - +
422B ARG* 2.9 42.7 + - - +
438B ILE* 4.3 0.7 - - - +
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Residues in contact with ASN 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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415B SER* 2.9 28.7 + - - +
416B ASP* 3.3 7.4 - - - +
418B ALA* 1.3 74.4 - - - +
420B GLN* 1.3 65.2 + - + +
422B ARG* 2.8 35.7 + - - +
423B SER* 3.0 27.5 + - - -
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Residues in contact with GLN 420 (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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124B PRO* 5.6 3.5 - - - +
125B ILE* 3.7 18.9 + - + +
416B ASP* 3.0 47.1 + - - +
417B LEU* 3.2 28.1 + - - +
419B ASN* 1.3 76.2 - - + +
421B LEU* 1.3 61.2 + - - +
423B SER* 3.3 20.1 + - - -
424B LEU* 3.5 12.0 + - - +
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Residues in contact with LEU 421 (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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125B ILE* 3.5 11.6 - - + +
371B ILE* 3.9 29.6 - - + +
374B LEU* 4.0 29.6 - - + -
375B VAL* 3.6 30.5 - - + -
413B LEU* 3.8 12.1 - - + -
417B LEU 3.0 13.2 + - - +
418B ALA 3.2 8.2 + - - +
420B GLN* 1.3 74.8 - - - +
422B ARG* 1.3 57.8 + - - +
424B LEU* 3.0 31.6 + - + +
425B ASP* 4.1 1.6 + - - +
436B GLY 5.2 1.2 - - - +
438B ILE* 3.6 29.0 - - + +
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Residues in contact with ARG 422 (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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409B ALA* 4.2 6.7 - - - +
410B ASP* 2.8 44.6 + - - +
418B ALA* 2.9 28.3 + - - +
419B ASN* 2.8 38.9 + - - +
421B LEU* 1.3 70.3 - - - +
423B SER* 1.3 64.5 + - - +
424B LEU 3.0 2.8 + - - -
425B ASP* 3.3 22.7 + - - +
438B ILE* 3.6 20.5 - - + +
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Residues in contact with SER 423 (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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419B ASN 3.0 16.1 + - - -
420B GLN* 3.5 13.6 - - - -
421B LEU 3.3 0.2 - - - -
422B ARG* 1.3 76.0 - - - +
424B LEU* 1.3 62.7 + - - +
425B ASP 3.2 1.8 + - - +
427B LYS* 2.6 37.9 + - - +
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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