Contacts of the helix formed by residues 436 - 441 (chain C) in PDB entry 4LEY
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 GLN 436 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A GLU* 3.8 20.2 + - - +
380C ILE* 3.4 32.7 - - - +
381C GLU* 5.5 1.7 - - - +
394C ARG* 3.7 0.2 - - - -
435C PRO* 1.3 79.2 - - + +
437C ASP* 1.3 61.0 + - - +
438C SER* 3.7 17.0 + - - +
439C GLN* 3.0 35.8 + - + +
440C TRP* 3.0 24.6 - - - -
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Residues in contact with ASP 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLY* 3.2 3.3 - - - -
380C ILE* 3.0 23.7 + - - +
381C GLU* 2.9 42.0 + - + +
384C CYS* 4.0 13.9 - - - -
390C ALA 6.2 0.2 - - - +
391C LYS 5.3 1.6 - - - +
392C CYS* 4.5 4.2 - - + +
394C ARG* 2.8 33.9 + - - +
436C GLN* 1.3 76.5 + - - +
438C SER* 1.3 56.8 + - - +
439C GLN 3.1 0.4 - - - -
440C TRP* 2.9 28.1 + - - +
441C ASP* 3.6 1.6 + - - -
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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
----------------------------------------------------------
436C GLN* 3.7 18.1 + - - +
437C ASP* 1.3 75.2 - - - +
439C GLN* 1.3 59.7 + - - +
440C TRP 3.0 7.3 + - - -
441C ASP* 3.9 21.7 + - - +
444C ASN* 5.1 3.8 + - - -
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Residues in contact with GLN 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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433C GLN 4.7 1.0 + - - -
434C ASP* 3.1 44.6 + - + +
435C PRO* 3.5 6.1 - - - +
436C GLN* 3.0 45.3 + - + +
438C SER* 1.3 78.1 + - - +
440C TRP* 1.3 68.9 + - + +
441C ASP 3.8 0.9 - - - -
444C ASN* 6.4 0.2 - - - -
448C CYS* 3.5 7.4 - - - -
451C LYS* 3.3 19.5 + - - +
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Residues in contact with TRP 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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392C CYS* 3.2 13.0 - - + +
393C CYS* 3.0 27.4 + - - +
394C ARG* 3.6 42.2 - - + +
397C CYS* 4.4 15.3 - - + -
427C ILE* 4.6 4.5 - - + -
430C MET* 4.0 24.0 - - + -
431C TRP* 3.3 30.5 - + - -
434C ASP* 2.7 40.0 + - + +
436C GLN 3.0 25.6 - - - -
437C ASP 2.9 11.0 + - - +
439C GLN* 1.3 84.3 - - + +
441C ASP* 1.3 60.0 + - - +
448C CYS* 3.9 34.3 - - + -
451C LYS* 4.3 12.6 - - - -
452C LEU* 5.3 3.4 - - + -
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Residues in contact with ASP 441 (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 LYS 5.1 0.8 - - - +
393C CYS* 3.5 3.7 - - - -
437C ASP 3.6 2.8 + - - -
438C SER* 3.9 17.3 + - - +
439C GLN 3.8 1.4 - - - -
440C TRP* 1.3 76.9 - - - +
442C PRO* 1.3 68.1 - - - +
443C ARG* 2.6 59.8 + - - +
444C ASN* 2.8 44.0 + - - +
445C LEU 3.5 6.8 + - - -
448C CYS* 4.4 2.2 - - - -
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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