Contacts of the helix formed by residues 385 - 392 (chain C) in PDB entry 5MLE
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 SER 385 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PRO* 3.6 12.2 + - - +
68C GLY 3.6 24.0 - - - -
69C GLY* 4.3 2.0 - - - -
70C ILE* 3.8 15.5 - - - +
381C VAL* 2.8 14.6 + - - +
383C VAL 3.6 1.0 - - - -
384C THR* 1.3 82.5 - - - +
386C THR* 1.3 75.2 + - - +
387C ASN 3.3 3.4 + - - -
388C ALA* 3.3 7.7 + - - +
389C ALA* 3.0 21.5 + - - +
399C GLY* 3.4 18.0 - - - -
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Residues in contact with THR 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 3.7 31.7 + - - +
381C VAL* 3.2 23.0 + - - +
382C ALA* 4.1 4.0 - - - -
385C SER* 1.3 76.9 + - - +
387C ASN* 1.3 62.6 + - - +
389C ALA* 3.4 1.9 + - - +
390C LYS* 3.1 29.3 + - - +
395C TYR* 3.5 28.7 - - + -
399C GLY* 2.7 29.7 + - - +
400C ARG* 5.8 0.2 - - - +
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Residues in contact with ASN 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 5.4 2.1 - - - +
327C GLN* 2.7 43.4 + - + +
328C VAL* 3.8 7.4 - - + -
379C GLN* 4.9 5.1 + - - +
382C ALA* 2.7 39.4 + - - +
383C VAL* 4.2 4.6 - - - +
386C THR* 1.3 70.4 - - - +
388C ALA* 1.3 66.8 + - - +
390C LYS* 3.1 15.2 + - - +
391C VAL* 3.0 27.7 + - + +
477C PHE* 5.5 9.2 - - + -
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Residues in contact with ALA 388 (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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70C ILE* 4.1 19.5 - - + +
72C VAL* 3.4 31.4 - - + -
105C ILE* 5.8 0.2 - - + -
328C VAL* 3.5 16.4 - - + +
329C THR 5.8 0.7 - - - +
382C ALA 4.4 0.4 + - - -
383C VAL 6.0 1.5 + - - +
384C THR 5.4 0.7 - - - +
385C SER* 3.3 11.5 + - - +
387C ASN* 1.3 81.0 - - - +
389C ALA* 1.3 62.6 + - - +
390C LYS 3.1 0.7 + - - -
391C VAL* 3.3 1.0 + - - -
392C PHE* 3.3 29.0 + - - +
394C LEU* 4.9 2.5 - - - +
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Residues in contact with ALA 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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70C ILE* 4.2 5.3 - - + +
385C SER 3.0 13.6 + - - +
386C THR* 3.6 11.7 - - - +
387C ASN 3.2 0.2 - - - -
388C ALA* 1.3 76.6 - - - +
390C LYS* 1.3 57.0 + - - +
393C ASN 3.2 5.5 + - - -
394C LEU* 2.6 49.1 + - + +
395C TYR* 3.3 12.6 + - + -
398C LYS 3.8 27.8 - - - +
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Residues in contact with LYS 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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27C ASP* 3.4 32.1 + - - -
386C THR* 3.1 22.5 + - + +
387C ASN* 3.1 13.9 + - - +
389C ALA* 1.3 76.9 - - - +
391C VAL* 1.3 64.9 + - - +
393C ASN* 3.7 7.3 + - - +
395C TYR* 3.9 45.6 + - + -
475C PRO* 3.8 8.5 - - - +
477C PHE* 3.7 54.8 + - + +
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Residues in contact with VAL 391 (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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194C ILE* 3.8 16.8 - - + +
251C TYR* 4.5 5.2 - - + -
275C TYR* 4.1 46.2 - - + -
327C GLN* 5.9 0.7 - - + -
328C VAL* 4.9 9.6 - - + -
387C ASN* 3.0 22.5 + - + +
388C ALA* 3.3 4.0 + - - +
390C LYS* 1.3 77.7 - - - +
392C PHE* 1.3 84.8 + - + +
393C ASN 3.3 0.7 - - - -
475C PRO* 3.2 23.7 - - - +
477C PHE* 4.7 7.6 - - + -
478C VAL* 3.8 7.1 - - + +
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Residues in contact with PHE 392 (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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72C VAL* 3.9 25.4 - - + -
105C ILE* 4.4 7.6 - - + -
138C HIS* 3.9 21.8 - + - -
162C ASN* 3.2 17.7 + - - +
163C SER* 4.0 25.4 - - - -
194C ILE* 4.2 15.9 - - + -
196C GLN* 4.0 4.9 - - - -
251C TYR* 3.3 41.1 - + - -
328C VAL* 5.9 0.2 - - + -
388C ALA* 3.3 19.2 + - - +
389C ALA 3.9 0.9 - - - -
391C VAL* 1.3 90.1 - - + +
393C ASN* 1.3 69.1 + - - +
394C LEU* 3.5 10.5 + - + +
471C ARG* 3.5 26.4 - - - +
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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