Contacts of the helix formed by residues 404 - 410 (chain C) in PDB entry 5YL4
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 404 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C VAL* 3.5 31.4 - - + -
182C VAL* 3.5 26.5 - - + -
185C TYR* 4.2 5.2 - + + -
398C MET* 4.0 10.5 - - - -
403C ALA* 1.3 81.7 - - + +
405C VAL* 1.3 62.0 + - - +
406C HIS* 3.3 6.3 - - - -
407C TRP* 3.3 25.6 + + + +
408C TYR* 3.5 7.0 - - + -
255D VAL 3.1 27.1 - - - -
256D ASN* 3.8 16.8 - - - -
258D VAL 3.7 4.9 - - - -
259D PRO* 2.9 50.1 + - + -
312D THR* 4.0 9.9 - - + -
345D ILE* 3.8 13.0 - - + -
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Residues in contact with VAL 405 (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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185C TYR* 3.7 26.5 - - + +
399C TYR* 3.9 17.7 - - + -
402C ARG* 3.1 33.1 + - + +
403C ALA 3.8 0.2 - - - +
404C PHE* 1.3 76.4 - - - +
406C HIS* 1.3 57.8 + - - +
408C TYR* 2.9 25.6 + - - +
409C VAL* 3.0 27.8 + - + +
415C GLU* 4.6 17.3 - - + +
418C PHE* 4.4 16.4 - - + -
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Residues in contact with HIS 406 (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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402C ARG 4.6 1.4 + - - -
404C PHE* 4.1 1.0 - - - -
405C VAL* 1.3 77.8 + - - +
407C TRP* 1.3 97.7 + + - +
409C VAL* 3.9 8.6 - - - +
410C GLY* 2.8 32.6 + - - -
258D VAL* 3.3 25.3 + - - +
259D PRO 3.4 24.4 + - - -
260D PHE* 3.8 0.6 - - - -
261D PRO* 3.6 45.7 - - + +
115E HIS* 5.5 0.5 + - - -
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Residues in contact with TRP 407 (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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102C ASN* 2.9 26.0 + - - +
404C PHE* 3.3 17.5 + - + +
405C VAL 3.2 0.6 - - - -
406C HIS* 1.3 107.4 + + - +
408C TYR* 1.3 63.9 + - + +
410C GLY* 4.5 1.2 - - - -
411C GLU* 3.5 15.4 + - + +
163D ILE* 4.7 10.8 - - + -
197D ASP* 4.7 14.8 - - + -
251D ARG* 4.6 15.9 - - + -
254D ALA* 3.5 45.0 + - + -
255D VAL* 3.7 35.7 - - + +
258D VAL* 3.0 29.2 + - + -
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Residues in contact with TYR 408 (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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101C ASN 3.8 0.4 + - - -
102C ASN* 3.3 29.6 - - - +
103C TYR 3.8 2.5 - - - -
104C ALA* 3.9 2.3 - - - +
182C VAL* 3.4 27.5 - - + +
185C TYR* 3.6 22.3 - + + +
186C ASN* 2.7 35.0 + - - -
189C LEU* 3.8 22.0 - - + -
404C PHE 3.5 17.0 - - - -
405C VAL* 2.9 9.4 + - - +
407C TRP* 1.3 81.1 - - + +
409C VAL* 1.3 64.6 + - + +
410C GLY 3.4 0.2 - - - -
411C GLU* 3.2 13.0 + - - +
412C GLY 3.4 0.9 + - - -
413C MET* 3.2 33.0 + - + +
418C PHE* 3.7 29.4 - + + -
255D VAL* 5.9 1.3 - - + -
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Residues in contact with VAL 409 (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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405C VAL* 3.0 33.0 + - + +
406C HIS* 3.9 7.4 - - - +
408C TYR* 1.3 77.1 - - + +
410C GLY* 1.3 57.3 + - - +
412C GLY* 2.9 21.7 + - - -
413C MET 3.3 21.9 + - - +
414C GLU* 5.0 0.4 - - - -
415C GLU* 4.9 13.7 - - + +
418C PHE* 5.9 1.1 - - + -
111E ASN* 5.1 2.1 - - - +
115E HIS* 4.9 14.0 - - + +
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Residues in contact with GLY 410 (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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406C HIS 2.8 20.9 + - - -
407C TRP* 4.5 2.0 - - - -
409C VAL* 1.3 72.4 - - - +
411C GLU* 1.3 60.9 + - - +
412C GLY 3.3 0.8 + - - -
112E ARG* 4.1 16.1 + - - +
115E HIS* 3.7 40.5 + - - +
116E LEU* 5.8 1.0 - - - +
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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