Contacts of the helix formed by residues 393 - 401 (chain C) in PDB entry 5W5T
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 ASP 393 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C GLY 5.4 0.2 - - - -
392C GLU* 1.3 83.5 - - + +
394C PRO* 1.3 57.2 - - - +
395C GLU* 3.0 21.9 + - - +
396C LEU* 3.1 32.6 + - + +
397C ASP* 2.8 43.9 + - - +
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Residues in contact with PRO 394 (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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391C GLY 5.9 0.7 - - - -
392C GLU 3.7 7.9 - - - +
393C ASP* 1.3 87.8 - - - +
395C GLU* 1.3 57.5 + - + +
397C ASP* 3.4 1.8 + - + +
398C ALA* 2.7 37.5 + - - +
403C ARG* 3.7 39.4 - - - +
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Residues in contact with GLU 395 (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 ASP* 3.0 8.7 + - - +
394C PRO* 1.3 77.3 - - + +
396C LEU* 1.3 61.5 + - - +
398C ALA* 3.8 5.9 - - - +
399C LYS* 2.9 29.1 + - - +
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Residues in contact with LEU 396 (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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389C ILE 5.6 0.7 - - - +
393C ASP* 3.1 33.4 + - + +
395C GLU* 1.3 75.8 - - - +
397C ASP* 1.3 67.0 + - - +
399C LYS* 3.2 8.6 + - + +
400C ARG* 3.0 79.6 + - + +
421C LEU* 3.8 28.7 - - + -
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Residues in contact with ASP 397 (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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389C ILE 3.8 17.7 - - - +
390C VAL* 3.8 9.2 - - - +
391C GLY* 2.7 33.5 + - - -
392C GLU 3.5 3.8 + - - -
393C ASP* 2.8 27.7 + - - +
394C PRO* 3.7 4.9 - - - +
396C LEU* 1.3 79.1 - - - +
398C ALA* 1.3 56.2 - - - +
400C ARG* 4.6 6.8 + - - +
401C PHE* 2.8 42.4 + - + +
403C ARG* 4.3 8.0 + - - +
409C CYS* 3.7 19.2 - - - -
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Residues in contact with ALA 398 (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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394C PRO 2.7 22.1 + - - +
395C GLU* 3.8 6.7 - - - +
397C ASP* 1.3 70.7 - - - +
399C LYS* 1.3 65.6 + - - +
401C PHE 3.0 15.0 - - - +
403C ARG* 4.0 23.5 - - + +
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Residues in contact with LYS 399 (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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395C GLU 2.9 18.0 + - - +
396C LEU* 3.2 12.1 + - + +
398C ALA* 1.3 77.9 - - - +
400C ARG* 1.3 65.1 + - + +
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Residues in contact with ARG 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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388C LEU* 3.8 19.6 - - - +
389C ILE* 3.7 21.8 + - - +
396C LEU* 3.0 50.0 + - + +
397C ASP* 4.6 1.8 + - - +
399C LYS* 1.3 80.7 - - + +
401C PHE* 1.3 88.5 + - + +
415C MET* 3.8 16.8 - - - +
419C LEU* 3.6 28.1 - - + +
421C LEU* 3.1 53.0 - - - +
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Residues in contact with PHE 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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388C LEU* 4.1 18.6 - - + -
390C VAL* 3.7 29.6 - - + -
397C ASP* 2.8 26.2 + - - +
398C ALA 3.0 17.3 - - - +
400C ARG* 1.3 108.8 - - + +
402C ARG* 1.3 61.2 + - - +
403C ARG 3.3 5.8 + - - -
409C CYS* 4.4 10.8 - - + -
410C LEU 3.5 9.9 - - - +
411C ILE* 3.9 18.6 - - + -
415C MET* 3.7 24.7 - - + -
416C ILE* 3.9 20.0 - - + -
419C LEU* 4.0 18.4 - - + -
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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