Contacts of the helix formed by residues 388 - 393 (chain C) in PDB entry 3WF4
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 ALA 388 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C LYS* 4.3 7.0 - - + -
384C THR 3.4 13.0 + - - +
385C VAL* 2.9 9.3 + - - +
387C ALA* 1.3 78.6 - - - +
389C LEU* 1.3 58.9 + - - +
390C ASP 3.2 3.4 - - - -
391C ILE* 3.1 10.3 - - + +
392C LEU* 2.9 38.3 + - + +
524C LEU* 3.6 31.4 - - + -
551C PHE* 4.8 0.7 - - + -
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Residues in contact with LEU 389 (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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385C VAL* 4.0 9.2 - - + +
386C GLY 3.6 19.5 - - - +
387C ALA 3.4 2.6 - - - -
388C ALA* 1.3 78.8 - - - +
390C ASP* 1.3 61.2 + - - +
391C ILE 3.4 0.2 - - - -
392C LEU* 4.3 3.6 - - + -
393C CYS* 3.0 32.3 + - + +
417C LEU* 3.9 27.8 - - + -
419C ARG* 3.9 26.7 - - - +
512C PHE* 3.9 30.2 - - + -
514C LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 390 (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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387C ALA 5.1 1.9 + - - +
388C ALA 3.2 1.4 - - - -
389C LEU* 1.3 82.1 - - - +
391C ILE* 1.3 58.8 + - - +
393C CYS 4.7 1.6 - - - -
394C PRO* 3.5 25.1 - - - +
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Residues in contact with ILE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C LYS* 5.9 0.9 - - + +
388C ALA* 3.1 27.3 - - + +
390C ASP* 1.3 79.1 - - - +
392C LEU* 1.3 62.7 + - + +
393C CYS 3.4 0.4 + - - -
394C PRO* 3.7 12.8 - - + +
515C ASP* 5.0 3.3 - - - +
518C ASP* 6.0 1.2 - - - +
519C ALA* 4.0 23.9 - - + +
522C SER* 3.9 16.8 - - - +
524C LEU* 3.9 24.2 - - + +
525C GLY* 3.9 22.4 - - - +
528C GLY 5.2 8.1 - - - -
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C VAL* 4.1 25.8 - - + +
388C ALA* 2.9 39.0 + - + +
389C LEU* 4.3 2.9 - - - +
391C ILE* 1.3 76.5 - - + +
393C CYS* 1.3 58.3 + - - +
394C PRO* 3.6 0.4 - - - -
513C PRO 3.7 1.9 - - - +
514C LEU* 3.9 21.3 - - + -
515C ASP* 2.8 37.7 + - - +
516C THR* 3.7 42.6 - - + +
519C ALA* 3.8 15.5 - - + -
551C PHE* 4.2 15.0 - - + -
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Residues in contact with CYS 393 (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 LEU* 3.0 21.2 + - - +
390C ASP* 3.8 3.2 - - - +
392C LEU* 1.3 80.7 - - + +
394C PRO* 1.3 66.3 - - - +
395C SER* 3.3 4.9 - - - -
396C GLY* 3.2 41.9 + - - -
397C PRO* 4.1 0.7 - - - -
512C PHE* 4.1 30.5 - - + -
513C PRO* 3.4 26.0 - - - +
514C LEU* 5.1 0.9 - - + -
515C ASP* 5.2 0.4 - - - -
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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