Contacts of the helix formed by residues 435 - 440 (chain C) in PDB entry 2O1S
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 PHE 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C SER* 4.5 1.0 + - - -
397C GLN* 3.6 22.8 - - - +
432C GLN* 4.9 4.0 - - + -
433C GLY 3.6 0.4 - - - -
434C ALA* 1.3 102.8 - - + +
436C ASP* 1.3 58.0 + - - +
437C LEU 3.1 3.1 - - - -
438C SER* 2.7 23.6 + - - -
439C TYR* 2.8 31.2 + - + -
559C ASN* 3.3 4.7 - - - +
560C ALA* 3.9 13.0 - - + -
591C PHE* 3.9 18.2 - + - -
592C ILE* 6.4 0.7 - - + -
400D TYR* 4.8 0.7 - - - +
404D LEU* 3.8 23.6 - - + -
442D CYS* 3.4 41.5 - - - -
443D ILE* 4.9 0.2 - - - -
444D PRO* 3.9 22.7 - - + -
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Residues in contact with ASP 436 (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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393C SER* 2.7 30.3 + - - +
418C ILE* 4.5 10.5 - - + +
421C ALA* 4.3 0.3 - - - +
433C GLY 3.6 1.7 - - - +
435C PHE* 1.3 76.4 - - - +
437C LEU* 1.3 63.9 + - - +
438C SER 3.0 0.2 - - - -
439C TYR* 3.4 31.6 - - + +
440C LEU* 3.1 47.6 + - + +
448C ILE* 4.9 0.5 - - - +
475C ARG* 2.6 55.2 + - - +
559C ASN* 3.5 0.4 + - - -
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ASP* 1.3 83.4 + - - +
438C SER* 1.3 58.6 + - - +
440C LEU* 5.4 0.2 - - - -
441C ARG* 3.3 27.4 - - - +
448C ILE* 4.1 16.2 - - + -
450C THR* 3.9 19.3 - - + -
475C ARG* 3.1 45.3 - - + +
511C PHE* 5.2 3.1 - - + +
535C VAL* 3.9 18.9 - - + +
557C GLU* 3.7 22.0 - - + +
558C GLU 5.1 0.4 - - - +
559C ASN* 3.0 37.5 + - + +
563C GLY 3.7 4.3 - - - +
564C GLY* 3.8 2.3 - - - -
565C ALA* 4.5 2.0 - - + +
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Residues in contact with SER 438 (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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435C PHE* 2.7 10.6 + - - -
437C LEU* 1.3 79.1 - - - +
439C TYR* 1.3 63.5 + - - -
440C LEU 3.3 1.9 + - - -
441C ARG* 3.5 12.2 + - - +
442C CYS* 3.9 9.2 + - - +
559C ASN* 3.0 17.3 + - - +
560C ALA* 3.8 0.9 + - - +
562C MSE 2.9 20.0 + - - -
563C GLY* 3.5 12.3 - - - +
564C GLY 3.0 6.2 + - - -
438D SER* 5.3 5.7 - - - +
442D CYS* 3.7 26.7 - - - +
563D GLY* 6.0 1.6 - - - -
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Residues in contact with TYR 439 (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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393C SER 2.9 23.8 + - - -
396C LEU* 3.2 26.0 - - + +
397C GLN* 3.8 24.6 + - + -
400C TYR* 2.6 55.0 + + + -
435C PHE* 2.8 36.2 + - + -
436C ASP* 3.4 26.3 - - - +
438C SER* 1.3 74.9 - - - +
440C LEU* 1.3 85.6 + - + +
442C CYS* 3.5 7.7 - - - -
443C ILE* 3.7 1.6 - - - +
400D TYR* 3.7 31.0 - + + +
439D TYR* 4.5 6.3 - - + +
442D CYS* 4.7 0.4 - - - -
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Residues in contact with LEU 440 (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 LEU* 4.3 7.0 - - + -
400C TYR* 5.0 1.1 - - + -
403C VAL* 4.2 16.4 - - + -
416C PHE* 6.3 1.1 - - + -
418C ILE* 3.6 30.5 - - + -
436C ASP* 3.1 28.9 + - + +
439C TYR* 1.3 97.2 - - + +
441C ARG* 1.3 64.4 + - - +
442C CYS 3.2 0.7 - - - -
443C ILE* 3.0 41.4 + - + +
446C MSE 4.0 12.8 - - + +
448C ILE* 3.7 21.8 - - + +
473C ALA* 4.4 13.2 - - + -
536C LYS* 4.8 0.2 + - - -
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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