Contacts of the helix formed by residues 316 - 320 (chain F) in PDB entry 1DE4
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 316 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740C TRP* 3.2 48.5 - + + -
184F ASP* 3.7 9.4 - - - -
185F GLN 3.6 17.7 - - - -
186F HIS* 3.1 31.4 - + - -
187F PHE* 6.4 0.2 - - - -
314F PRO* 2.9 24.4 + - + +
315F SER* 1.3 80.1 - - - +
317F ASN* 1.3 61.5 + - - +
318F HIS* 4.1 11.2 - + + +
319F THR* 2.8 32.1 + - - +
321F PHE* 3.9 5.0 - - - -
469F GLY* 4.2 7.2 - - - -
470F TYR* 3.6 26.9 - + - -
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Residues in contact with ASN 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C TRP* 3.5 30.2 - - + -
187F PHE* 3.3 17.3 - - - -
316F PHE* 1.3 71.7 - - - +
318F HIS* 1.3 65.3 + - + +
319F THR 2.9 0.4 - - - -
320F GLN* 2.8 22.2 + - - +
321F PHE* 3.8 13.5 - - - -
901F NAG 1.5 69.1 + - + +
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Residues in contact with HIS 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 3.8 26.8 - - + +
641C TRP* 3.7 40.6 + + + +
644C SER* 4.6 2.6 + - - -
648C ASP* 5.7 0.4 - - - -
736C ALA* 5.0 1.3 - - - -
739C THR* 3.6 23.5 - - + +
740C TRP* 3.7 32.1 - + + -
743C GLN* 3.8 34.1 + - - +
316F PHE* 2.9 12.1 + + + +
317F ASN* 1.3 79.9 - - + +
319F THR* 1.3 59.6 + - - +
320F GLN* 3.5 10.4 + - - +
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Residues in contact with THR 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732C ARG 4.9 0.7 - - - +
736C ALA* 3.1 42.4 + - - +
737C LEU* 5.8 0.2 - - - +
740C TRP* 5.1 5.7 - - - +
313F PHE* 3.5 30.2 - - + -
314F PRO* 3.6 13.0 + - - +
316F PHE* 2.8 16.7 + - - +
318F HIS* 1.3 80.3 - - - +
320F GLN* 1.3 67.1 + - - +
321F PHE* 2.9 34.5 + - + +
322F PRO* 3.3 7.8 - - + +
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Residues in contact with GLN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C LEU* 3.5 24.7 - - + +
638C SER* 2.8 48.8 + - - -
641C TRP* 3.8 21.7 + - + +
732C ARG* 5.8 2.4 + - - -
735C LEU* 3.5 25.0 - - + +
736C ALA* 6.3 0.4 - - - +
739C THR* 5.4 2.0 + - - -
316F PHE 3.9 0.2 + - - -
317F ASN 2.8 21.0 + - - +
318F HIS 3.9 5.5 + - - +
319F THR* 1.3 81.4 + - - +
321F PHE* 1.3 74.3 + - - +
322F PRO* 3.2 3.3 - - - +
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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