Contacts of the helix formed by residues 401 - 411 (chain B) in PDB entry 3OUY
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 401 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B GLN* 3.7 7.2 - - - -
299B ARG* 3.8 16.8 - - - +
397B TRP 4.5 0.5 - - - +
398B HIS 4.5 6.8 + - - +
399B THR 3.4 5.7 + - - -
400B LEU* 1.3 75.9 + - - +
402B LYS* 1.3 67.4 + - - +
403B ASN 3.4 2.5 - - - -
404B VAL* 3.7 7.4 - - - -
405B GLY* 2.9 20.3 + - - -
406B GLU 4.3 0.2 + - - -
2D G 3.5 10.3 - - - -
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Residues in contact with LYS 402 (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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296B GLN* 3.6 1.4 + - - -
398B HIS 5.8 0.2 - - - -
401B GLY* 1.3 73.4 - - - +
403B ASN* 1.3 67.6 + - - +
406B GLU* 3.1 47.7 + - - +
1D G 3.7 40.8 + - - +
2D G 2.7 23.5 + - - +
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Residues in contact with ASN 403 (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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286B PRO* 3.6 14.9 - - + +
288B ILE* 3.7 38.2 - - + +
292B ASN* 5.2 1.6 - - - +
296B GLN* 2.8 36.0 + - - +
402B LYS* 1.3 79.1 - - - +
404B VAL* 1.3 62.1 + - - +
406B GLU* 3.7 17.2 + - - +
407B SER* 3.3 21.7 + - - -
1D G 3.7 18.4 - - - -
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 3.6 27.1 - - + -
286B PRO* 4.1 7.6 - - + -
293B LEU* 3.9 18.4 - - + -
296B GLN* 3.0 34.9 + - + +
297B LEU* 3.7 22.2 - - + -
300B ALA* 4.5 3.8 - - + -
400B LEU 2.8 27.6 - - - +
401B GLY* 3.7 2.0 - - - -
403B ASN* 1.3 70.3 - - - +
405B GLY* 1.3 63.8 + - - +
407B SER* 3.3 2.5 + - - -
408B ILE* 3.1 31.0 + - + +
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TRP* 3.2 36.6 - - - +
400B LEU* 3.5 6.9 + - - -
401B GLY 2.9 17.5 + - - -
404B VAL* 1.3 75.3 - - - +
406B GLU* 1.3 63.7 + - - +
407B SER 3.1 0.2 + - - -
408B ILE* 3.1 6.5 + - - +
409B ARG* 2.9 21.3 + - - +
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TRP* 4.1 15.9 - - + -
402B LYS* 3.1 46.5 + - - +
403B ASN* 3.7 20.4 - - - +
404B VAL 3.4 0.4 - - - -
405B GLY* 1.3 74.2 - - - +
407B SER* 1.3 60.6 + - - +
409B ARG* 3.2 21.0 + - - +
410B GLU* 3.3 18.1 + - - +
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 3.7 9.4 - - - -
284B ARG* 2.6 40.2 + - - +
286B PRO* 4.4 7.0 - - - -
403B ASN 3.3 12.3 + - - -
404B VAL 3.6 8.5 - - - -
405B GLY 3.1 1.0 - - - -
406B GLU* 1.3 75.1 - - - +
408B ILE* 1.3 65.1 + - - +
409B ARG 3.1 1.3 - - - -
410B GLU* 3.2 13.8 + - - +
411B TYR 2.9 24.7 + - - +
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Residues in contact with ILE 408 (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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281B VAL* 4.8 7.9 - - + -
283B PHE* 3.6 37.7 - - + -
300B ALA* 5.2 0.7 - - + -
304B ILE* 5.9 0.2 - - + -
329B LEU* 4.8 6.3 - - + -
393B ALA* 4.1 24.2 - - + +
397B TRP* 4.6 3.8 - - + -
400B LEU* 4.0 26.0 - - + -
404B VAL* 3.1 21.9 + - + +
405B GLY* 3.5 5.2 - - - +
407B SER* 1.3 73.8 - - - +
409B ARG* 1.3 66.5 + - - +
411B TYR* 3.5 12.1 + - - -
412B PHE* 3.4 38.9 - - + -
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Residues in contact with ARG 409 (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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397B TRP* 3.4 64.2 - - + +
405B GLY 2.9 12.5 + - - +
406B GLU* 3.3 12.3 - - - +
407B SER 3.1 0.4 - - - -
408B ILE* 1.3 79.8 - - - +
410B GLU* 1.3 66.1 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 5.5 8.5 - - - +
406B GLU* 3.3 15.4 + - - +
407B SER* 3.2 13.1 + - - +
409B ARG* 1.3 83.3 - - + +
411B TYR* 1.3 63.2 + - + +
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Residues in contact with TYR 411 (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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282B LYS* 4.3 13.8 - - + +
283B PHE* 3.6 13.0 - - - +
284B ARG* 3.7 39.2 + - + +
326B PHE* 4.9 9.1 - + - -
407B SER 2.9 14.7 + - - +
408B ILE* 3.5 7.1 - - - -
409B ARG 3.4 0.4 - - - -
410B GLU* 1.3 86.1 - - + +
412B PHE* 1.3 82.6 + - - +
413B GLU* 2.8 45.6 + - + +
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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