Contacts of the helix formed by residues 3252 - 3266 (chain C) in PDB entry 5Y3R
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 PHE3252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2958C LEU* 6.3 2.9 - - + -
2960C GLU* 5.6 1.9 + - - +
2964C ASP* 4.9 12.8 - - - +
3250C ASN 4.2 4.7 - - - -
3251C ASN* 1.3 72.0 - - - +
3253C SER* 1.3 74.7 + - - +
3255C ALA* 3.0 17.9 - - - +
3256C MET* 3.2 7.3 + - - +
3282C ARG* 4.4 16.3 + - + +
3285C HIS* 3.1 55.4 - - + -
3286C CYS* 3.5 21.5 - - - -
3289C ARG* 3.6 36.8 - - - -
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Residues in contact with SER3253 (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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2960C GLU* 2.9 30.0 + - - -
2962C ARG* 3.5 29.7 - - - +
2963C SER* 4.7 2.8 - - - -
2964C ASP* 4.5 6.1 + - - -
3251C ASN* 3.8 0.6 - - - +
3252C PHE* 1.3 79.6 - - - +
3254C LEU* 1.3 67.4 + - - +
3255C ALA 2.8 1.9 + - - -
3256C MET* 3.0 3.8 + - - +
3257C LYS* 3.0 19.1 + - - +
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Residues in contact with LEU3254 (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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2961C ALA* 4.6 8.1 - - + +
2962C ARG* 3.1 56.8 - - + +
3006C ALA* 3.5 23.6 - - + +
3176C MET* 4.9 17.5 - - + -
3179C TRP* 5.3 4.9 - - + -
3180C ASP* 3.7 24.9 - - - +
3251C ASN* 4.9 2.3 + - + +
3252C PHE 3.7 0.4 - - - -
3253C SER* 1.3 81.1 - - - +
3255C ALA* 1.3 65.0 + - - +
3257C LYS* 3.4 16.6 - - + +
3258C LEU* 2.9 30.5 + - + +
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Residues in contact with ALA3255 (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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3179C TRP* 5.6 1.0 - - - -
3246C ALA* 4.4 20.6 - - + -
3251C ASN* 3.1 17.2 + - - +
3252C PHE* 3.0 14.4 + - - +
3253C SER 2.8 1.0 + - - -
3254C LEU* 1.3 75.8 - - - +
3256C MET* 1.3 54.5 - - - +
3258C LEU* 2.2 37.7 + - - +
3259C LEU* 2.8 21.8 + - + +
3278C GLN* 5.5 1.3 - - + -
3282C ARG* 4.6 13.0 - - + -
3285C HIS* 6.5 0.2 - - + -
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Residues in contact with MET3256 (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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3252C PHE 3.2 2.6 + - - +
3253C SER* 3.0 7.0 + - - +
3255C ALA* 1.3 77.6 - - - +
3257C LYS* 1.3 63.8 + - - +
3259C LEU* 3.4 21.7 - - + +
3260C LYS* 2.8 74.8 + - + +
3263C HIS* 4.6 11.7 - - + +
3279C SER* 4.8 1.3 - - - +
3282C ARG* 2.6 51.5 - - - +
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Residues in contact with LYS3257 (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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2962C ARG* 3.4 34.1 - - - +
3006C ALA 3.9 5.0 + - - -
3007C GLU* 5.1 3.6 - - - +
3008C TRP* 3.9 41.3 - - + +
3053C LEU* 6.2 1.8 - - - +
3180C ASP* 5.8 3.0 + - - -
3253C SER 3.0 7.6 + - - +
3254C LEU* 3.0 31.4 - - + +
3256C MET* 1.3 74.8 - - - +
3258C LEU* 1.3 74.7 + - + +
3260C LYS* 3.8 10.8 - - - +
3261C GLU* 3.0 30.1 + - - +
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Residues in contact with LEU3258 (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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3179C TRP* 3.9 30.1 - - + +
3180C ASP* 4.9 5.6 - - - +
3183C ILE* 5.0 10.1 - - + -
3239C LYS* 2.8 32.7 + - - +
3242C MET* 4.3 19.1 - - + -
3243C ILE* 5.6 5.3 - - + +
3246C ALA* 6.0 0.2 - - + -
3254C LEU* 2.9 24.3 + - + +
3255C ALA* 2.2 26.8 + - - +
3257C LYS* 1.3 94.6 - - + +
3259C LEU* 1.3 60.2 + - + -
3261C GLU* 3.0 23.7 - - - +
3262C LEU* 2.8 14.6 + - - +
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Residues in contact with LEU3259 (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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3243C ILE* 5.8 7.0 - - + -
3246C ALA* 6.3 0.2 - - + -
3255C ALA* 2.8 30.1 + - + +
3256C MET* 3.0 17.9 + - + +
3258C LEU* 1.3 77.2 - - + +
3260C LYS* 1.3 59.8 + - - +
3262C LEU* 2.7 26.7 + - + +
3263C HIS* 2.9 23.1 + - - +
3275C SER* 3.3 22.4 + - - +
3278C GLN* 3.7 23.3 - - + -
3279C SER* 3.1 30.1 - - - +
3282C ARG* 3.2 22.7 - - - +
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Residues in contact with LYS3260 (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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3008C TRP* 6.1 5.4 - - + -
3256C MET* 2.8 67.3 + - + +
3257C LYS* 3.8 7.4 - - - +
3259C LEU* 1.3 70.8 - - - +
3261C GLU* 1.3 65.3 + - - +
3262C LEU 3.0 0.3 + - - -
3263C HIS* 3.0 15.3 + - + +
3264C LYS* 2.9 23.5 + - - +
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Residues in contact with GLU3261 (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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3053C LEU* 6.1 2.9 - - - +
3183C ILE* 3.7 20.3 - - - +
3187C CYS* 5.2 4.3 - - - -
3238C MET* 5.0 2.4 - - - +
3239C LYS* 2.9 20.4 + - - +
3257C LYS* 3.0 19.1 + - - +
3258C LEU* 3.0 36.7 - - - +
3260C LYS* 1.3 75.5 - - - +
3262C LEU* 1.3 55.3 + - - +
3264C LYS* 3.2 30.0 + - - +
3265C GLU* 2.8 29.4 + - - +
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Residues in contact with LEU3262 (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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3239C LYS* 3.5 28.5 - - + +
3240C MET* 3.9 6.7 - - + -
3243C ILE* 3.8 19.7 - - + -
3258C LEU 2.8 11.4 + - - +
3259C LEU* 2.7 21.0 + - + +
3261C GLU* 1.3 68.9 - - - +
3263C HIS* 1.3 53.5 + - - -
3264C LYS 3.0 1.6 - - - -
3265C GLU* 2.5 22.5 + - - +
3266C SER* 2.8 34.5 + - - +
3271C ASP* 2.6 39.3 - - - +
3274C VAL* 4.0 5.2 - - + -
3275C SER* 3.1 31.4 - - - +
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Residues in contact with HIS3263 (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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3256C MET* 4.6 11.4 - - + +
3259C LEU* 2.9 42.0 + - - +
3260C LYS* 3.5 11.7 - - - +
3262C LEU* 1.3 71.1 - - - +
3264C LYS* 1.3 63.3 + - - +
3267C LYS* 3.7 14.9 + - - +
3271C ASP* 3.3 14.6 + - - +
3272C TRP* 3.3 30.7 + + - +
3275C SER* 3.1 33.3 + - - -
3276C TRP* 6.1 1.1 - + - -
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Residues in contact with LYS3264 (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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3053C LEU* 6.2 1.8 - - - +
3260C LYS 2.9 11.0 + - - +
3261C GLU* 3.2 41.7 - - - +
3263C HIS* 1.3 80.1 - - - +
3265C GLU* 1.3 70.7 + - - +
3267C LYS* 4.0 10.2 - - - +
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Residues in contact with GLU3265 (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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3232C ARG* 2.5 25.4 + - - +
3235C LYS* 2.7 49.2 - - + +
3238C MET* 3.5 17.4 - - - +
3239C LYS* 3.0 37.9 - - - +
3261C GLU* 2.8 18.4 + - - +
3262C LEU* 2.5 11.3 + - - +
3264C LYS* 1.3 83.3 - - - +
3266C SER* 1.3 60.4 + - - +
3267C LYS* 4.7 0.7 - - - +
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Residues in contact with SER3266 (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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3232C ARG* 2.1 37.8 + - - +
3236C PHE* 4.6 14.8 + - - +
3240C MET* 4.3 9.4 - - - +
3262C LEU* 2.8 26.7 + - - +
3265C GLU* 1.3 76.5 - - - +
3267C LYS* 1.3 64.6 + - - +
3268C THR* 2.8 17.7 + - - +
3271C ASP* 3.3 23.6 - - - -
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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