Contacts of the helix formed by residues 401 - 411 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A GLN* 3.9 15.0 - - - -
299A ARG* 3.8 10.0 - - - +
398A HIS 4.1 6.2 + - - +
399A THR 3.1 7.7 + - - -
400A LEU* 1.3 74.9 - - - +
402A LYS* 1.3 59.9 + - - -
403A ASN 3.4 2.7 - - - -
404A VAL* 4.3 0.7 - - - -
405A GLY* 2.6 32.7 + - - -
2C G 3.5 11.9 - - - -
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 3.7 2.0 + - - -
397A TRP* 5.9 0.2 - - - -
398A HIS* 5.4 7.4 - - + -
401A GLY* 1.3 74.2 - - - +
403A ASN* 1.3 69.0 + - - +
406A GLU* 3.2 48.3 + - + +
1C G 3.3 51.6 - - - +
2C G 3.1 18.9 + - - +
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Residues in contact with ASN 403 (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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286A PRO* 3.8 23.7 - - + +
288A ILE* 3.2 35.8 - - + +
292A ASN* 4.9 3.0 - - - +
296A GLN* 2.8 28.4 + - - +
402A LYS* 1.3 78.5 - - - +
404A VAL* 1.3 60.0 + - - +
405A GLY 3.2 1.1 - - - -
406A GLU* 3.3 19.5 + - - +
407A SER* 2.9 26.7 + - - -
1C G 4.5 9.7 - - - +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 3.8 14.6 - - + -
286A PRO* 3.8 11.2 - - + +
293A LEU* 4.2 13.9 - - + -
296A GLN* 3.2 26.7 + - + +
297A LEU* 4.1 20.4 - - + -
300A ALA* 4.2 15.3 - - + -
400A LEU 2.5 31.9 - - - +
401A GLY* 4.2 1.3 - - - +
403A ASN* 1.3 76.3 - - - +
405A GLY* 1.3 57.2 + - - +
407A SER* 3.5 2.9 - - - -
408A ILE* 2.8 41.1 + - + +
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TRP* 3.2 39.9 - - - +
398A HIS* 5.1 0.4 - - - -
400A LEU* 4.2 4.9 - - - -
401A GLY 2.6 27.9 + - - -
404A VAL* 1.3 78.5 - - - +
406A GLU* 1.3 54.7 + - - +
408A ILE* 3.5 1.0 + - - +
409A ARG 3.1 23.0 + - - -
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Residues in contact with GLU 406 (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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397A TRP* 4.2 12.2 - - + -
402A LYS* 3.2 43.9 + - - +
403A ASN* 3.6 19.9 - - - +
405A GLY* 1.3 73.5 - - - +
407A SER* 1.3 63.7 + - - +
409A ARG* 3.7 9.8 + - - +
410A GLU* 3.3 30.3 + - - +
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 3.8 8.4 - - - -
284A ARG* 2.7 40.2 + - - +
285A LYS 5.1 0.2 - - - -
286A PRO* 4.1 8.9 - - - +
403A ASN 2.9 14.0 + - - -
404A VAL* 3.1 9.4 + - - -
406A GLU* 1.3 74.9 - - - +
408A ILE* 1.3 66.5 + - - +
410A GLU* 3.0 25.0 + - - +
411A TYR* 3.1 13.2 + - - +
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Residues in contact with ILE 408 (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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281A VAL* 4.9 5.2 - - + -
283A PHE* 3.8 36.5 - - + -
329A LEU* 4.7 9.2 - - + -
393A ALA* 3.7 28.0 - - + +
397A TRP* 4.2 4.9 - - + -
400A LEU* 3.6 29.8 - - + -
404A VAL* 2.8 29.8 + - + +
405A GLY 3.8 3.6 - - - +
407A SER* 1.3 72.1 - - - +
409A ARG* 1.3 63.2 + - - +
411A TYR* 3.1 23.6 + - - +
412A PHE* 3.4 28.7 - - + -
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Residues in contact with ARG 409 (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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393A ALA 5.7 0.2 - - - -
394A SER* 6.6 0.4 - - - +
397A TRP* 3.4 63.6 - - + +
405A GLY 3.1 16.7 + - - +
406A GLU* 3.8 8.5 - - - +
407A SER 3.2 0.2 - - - -
408A ILE* 1.3 78.0 - - - +
410A GLU* 1.3 66.7 + - - +
411A TYR* 3.3 1.0 + - - -
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Residues in contact with GLU 410 (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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284A ARG* 6.0 1.4 - - - +
406A GLU* 3.3 18.5 - - - +
407A SER* 3.0 15.5 + - - +
409A ARG* 1.3 81.9 - - + +
411A TYR* 1.3 64.7 + - + +
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Residues in contact with TYR 411 (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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282A LYS* 4.0 9.5 + - - +
283A PHE* 3.6 24.9 - - - +
284A ARG* 3.9 24.5 - - + -
326A PHE* 4.4 13.5 - + - -
407A SER 3.1 14.7 + - - +
408A ILE* 3.1 8.2 - - - +
409A ARG 3.1 2.8 - - - -
410A GLU* 1.3 86.0 - - + +
412A PHE* 1.3 90.0 + - - +
413A GLU* 2.6 34.6 + - + +
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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