Contacts of the helix formed by residues 399 - 408 (chain C) in PDB entry 4OIO
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 ASN 399 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C GLU 3.9 5.5 - - - +
398C THR* 1.3 73.6 - - - +
400C PRO* 1.3 70.6 - - + +
401C LEU* 3.0 34.0 + - - +
402C SER* 2.8 39.5 + - - -
403C SER* 3.5 5.9 + - - -
565C GLN 3.2 13.4 + - - +
566C THR 3.1 22.8 + - - -
568C ALA* 2.6 27.9 + - - +
570C PRO* 4.7 7.9 - - + -
637C LEU* 5.7 0.9 - - - -
660C ALA* 5.0 1.3 - - + -
668C LEU* 3.7 18.2 - - + +
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Residues in contact with PRO 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ASN* 1.3 88.4 - - + +
401C LEU* 1.3 56.8 + - - +
403C SER* 3.3 9.7 + - - +
404C LEU* 2.9 27.9 + - - +
587C VAL* 5.4 2.0 - - + +
588C VAL* 5.7 2.0 - - + -
591C SER* 3.5 28.6 - - - +
593C ALA* 3.6 23.6 - - + -
637C LEU* 6.0 1.1 - - + -
659C PRO* 4.2 17.5 - - + -
660C ALA* 4.4 24.5 - - + +
666C LEU* 5.2 9.0 - - + -
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ASN* 3.0 12.3 + - - +
400C PRO* 1.3 76.3 - - - +
402C SER* 1.3 59.5 + - - +
404C LEU* 4.2 8.3 - - + -
405C ARG* 2.9 30.0 + - + +
542C VAL* 3.8 24.0 - - + -
543C ASN* 3.4 36.3 - - - +
546C LEU* 3.6 24.5 - - + -
565C GLN* 3.7 13.9 - - + +
566C THR 5.1 0.2 - - - +
587C VAL* 4.3 14.1 - - + +
666C LEU* 4.8 4.4 - - + +
668C LEU* 3.7 26.2 - - + -
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Residues in contact with SER 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASP* 3.4 35.6 - - - +
398C THR* 3.5 0.5 - - - -
399C ASN* 2.8 31.2 + - - -
401C LEU* 1.3 77.3 - - - +
403C SER* 1.3 56.4 + - - -
405C ARG* 3.5 2.6 + - - +
406C HIS* 2.9 29.5 + - - +
566C THR* 2.8 37.8 + - - +
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Residues in contact with SER 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASP* 5.2 0.2 - - - -
395C LYS* 3.4 29.8 + - - +
396C ASP 2.9 18.5 + - - -
397C GLU* 3.8 8.8 - - - +
399C ASN 3.9 4.7 + - - -
400C PRO* 3.3 9.2 + - - +
402C SER* 1.3 74.0 - - - +
404C LEU* 1.3 66.8 + - - +
406C HIS* 3.0 6.8 + - - +
407C LYS* 2.9 40.5 + - - +
591C SER* 6.1 1.6 - - - -
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Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.7 41.5 - - + -
19C THR* 3.7 28.9 - - + -
400C PRO 2.9 17.9 + - - +
401C LEU* 3.9 6.1 - - + +
403C SER* 1.3 79.4 - - - +
405C ARG* 1.3 59.0 + - - +
407C LYS* 3.7 5.8 + - - +
408C ARG* 3.2 32.8 + - + +
542C VAL* 4.6 10.1 - - + -
587C VAL* 3.8 36.1 - - + +
591C SER* 4.3 15.2 - - - +
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Residues in contact with ARG 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C ASP* 4.8 4.4 + - - +
401C LEU* 2.9 19.6 + - + +
402C SER 3.9 1.9 + - - +
404C LEU* 1.3 73.4 - - - +
406C HIS* 1.3 71.8 + - - +
407C LYS 3.2 0.4 - - - -
408C ARG* 3.0 17.1 + - - +
409C ARG* 3.0 49.4 + - - +
442C GLU* 3.2 23.5 + - - +
454C SER* 4.5 4.0 - - - +
542C VAL* 6.2 1.8 - - - -
543C ASN* 3.2 28.0 - - - +
563C ASN* 3.3 22.6 + - - +
566C THR* 3.4 38.2 + - - +
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Residues in contact with HIS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 5.0 0.2 + - - -
135C VAL* 3.7 22.9 - - + +
137C VAL* 4.0 7.5 - - + +
393C GLN* 2.7 39.3 + - + +
394C PHE 3.2 26.0 - - - -
395C LYS* 3.7 6.9 - - - -
396C ASP* 3.0 27.1 + - + +
402C SER 2.9 18.6 + - - +
403C SER* 3.0 8.7 + - - +
405C ARG* 1.3 81.6 - - - +
407C LYS* 1.3 62.2 + - - +
408C ARG 3.5 0.2 + - - -
409C ARG* 3.5 23.2 + - + +
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Residues in contact with LYS 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 4.2 14.0 - - + +
21C ILE* 4.2 4.9 - - - +
22C GLN* 2.7 48.7 + - + +
124C ASP* 2.6 57.4 + - - +
125C GLY 4.4 2.9 - - - +
126C SER* 4.0 18.2 - - - +
135C VAL* 4.1 15.7 - - + -
138C SER* 4.6 1.7 + - - -
395C LYS* 3.6 12.3 - - - +
403C SER* 2.9 33.7 + - - +
404C LEU* 4.0 6.0 - - - +
405C ARG 3.2 0.2 - - - -
406C HIS* 1.3 76.7 - - - +
408C ARG* 1.3 63.2 + - + +
409C ARG 3.3 5.2 + - - +
591C SER* 5.3 3.2 + - - +
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Residues in contact with ARG 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.1 50.4 + - - +
21C ILE* 4.8 9.9 - - + -
404C LEU* 3.2 21.5 - - - +
405C ARG* 3.0 8.9 + - - +
407C LYS* 1.3 78.9 - - + +
409C ARG* 1.3 65.7 + - - +
410C ILE* 4.0 0.5 - - - +
454C SER* 3.9 7.2 + - - +
455C LEU* 2.7 71.7 + - + +
456C ALA 2.8 24.0 + - - -
457C ALA 3.4 15.4 + - - +
459C ALA 4.4 2.4 + - - -
542C VAL* 3.9 24.0 - - - +
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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