Contacts of the helix formed by residues 3133 - 3147 (chain D) in PDB entry 1Y1S
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 ASP3133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3131D VAL 3.8 1.8 + - - -
3132D ALA* 1.3 71.4 - - - +
3134D PHE* 1.3 61.3 + - - +
3135D ALA* 2.9 13.7 + - - +
3136D CYS* 2.8 34.7 + - - +
3137D THR* 2.7 32.6 + - - -
3211D LEU 5.3 0.4 - - - +
3212D ARG* 3.2 34.0 - - - +
3213D ALA* 2.9 29.3 + - - +
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Residues in contact with PHE3134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2111C THR* 4.6 8.5 - - + +
2134C PHE* 4.0 11.7 - + - -
2137C THR* 3.7 28.7 - - + -
2138C THR* 3.7 36.8 - - + -
2141C VAL* 3.9 29.6 - - + -
2153C VAL* 4.1 23.8 - - + -
3132D ALA 3.5 3.3 + - - -
3133D ASP* 1.3 73.5 + - - +
3135D ALA* 1.3 69.7 + - - +
3137D THR* 3.2 6.7 + - - -
3138D THR* 2.8 45.2 + - + -
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Residues in contact with ALA3135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3133D ASP* 2.9 15.2 + - - +
3134D PHE* 1.3 79.4 - - - +
3136D CYS* 1.3 57.4 + - - +
3138D THR* 3.1 6.7 + - - -
3139D ALA* 2.8 29.5 + - - +
3212D ARG* 3.4 25.1 - - - +
3252D LEU* 3.8 8.8 - - + +
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Residues in contact with CYS3136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3088D THR* 4.0 11.4 - - - -
3090D LEU* 3.9 5.8 - - + -
3133D ASP* 2.8 24.9 + - - +
3135D ALA* 1.3 73.5 - - - +
3137D THR* 1.3 52.7 + - - +
3139D ALA* 3.0 4.2 + - - +
3140D LEU* 2.8 39.8 + - - +
3212D ARG* 3.9 13.2 - - - -
3213D ALA 3.9 23.3 - - - -
3214D GLY* 3.7 21.5 - - - -
3252D LEU* 3.8 26.4 - - - +
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Residues in contact with THR3137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134C PHE* 4.0 22.9 - - + -
3109D VAL* 3.8 19.7 - - + -
3110D THR 4.3 2.5 + - - +
3111D THR* 4.4 17.1 - - + -
3132D ALA* 3.5 21.1 + - - +
3133D ASP 2.7 22.5 + - - -
3134D PHE* 3.6 6.9 - - - -
3136D CYS* 1.3 76.3 - - - +
3138D THR* 1.3 64.0 + - - +
3140D LEU* 3.4 11.6 + - - +
3141D VAL* 2.9 31.7 + - + +
3153D VAL* 4.9 0.4 - - + -
3214D GLY* 5.1 0.7 - - - -
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Residues in contact with THR3138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134C PHE* 3.9 19.2 - - + -
2138C THR* 6.4 1.6 - - + -
3134D PHE* 2.8 41.9 + - + -
3135D ALA* 3.3 11.7 - - - +
3137D THR* 1.3 76.3 - - - +
3139D ALA* 1.3 64.2 + - - +
3141D VAL* 3.2 3.5 + - - +
3142D GLU* 2.9 47.3 + - + +
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Residues in contact with ALA3139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135D ALA 2.8 9.1 + - - +
3136D CYS 3.4 7.9 - - - +
3138D THR* 1.3 74.1 - - - +
3140D LEU* 1.3 56.5 + - - +
3142D GLU* 3.7 5.6 - - - +
3143D ALA* 2.8 31.9 + - - +
3248D ALA* 3.8 14.6 - - + +
3251D ARG* 3.8 18.6 - - + +
3252D LEU* 3.5 36.1 - - + -
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Residues in contact with LEU3140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3090D LEU* 4.4 6.5 - - + -
3091D ARG 5.6 0.2 - - - +
3109D VAL* 4.2 19.4 - - + +
3136D CYS 2.8 24.6 + - - +
3137D THR* 3.7 5.2 - - - +
3139D ALA* 1.3 69.7 - - - +
3141D VAL* 1.3 66.8 + - - +
3143D ALA* 3.5 0.4 + - - -
3144D ALA* 3.0 23.6 + - - +
3214D GLY* 3.8 12.1 - - - -
3215D MET 3.4 39.3 - - - +
3216D VAL* 3.8 20.2 - - + -
3244D ILE* 3.6 8.2 - - + +
3245D VAL* 3.9 22.0 - - + -
3248D ALA* 3.6 22.7 - - + -
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Residues in contact with VAL3141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134C PHE* 3.8 31.9 - - + -
3109D VAL* 4.0 22.9 - - + -
3137D THR* 2.9 25.0 + - + +
3138D THR 3.6 3.6 - - - +
3140D LEU* 1.3 75.0 - - - +
3142D GLU* 1.3 68.0 + - + +
3144D ALA* 3.1 7.0 + - - +
3145D LYS* 3.0 23.8 + - + +
3151D THR* 5.5 4.2 - - + +
3153D VAL* 4.1 18.6 - - + -
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Residues in contact with GLU3142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3138D THR* 2.9 39.6 + - + +
3139D ALA* 3.7 4.7 - - - +
3141D VAL* 1.3 79.5 - - + +
3143D ALA* 1.3 56.9 + - - +
3145D LYS* 2.9 13.6 + - + +
3146D SER* 2.8 27.0 + - - -
3251D ARG* 3.6 32.6 + - - +
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Residues in contact with ALA3143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3139D ALA 2.8 18.8 + - - +
3140D LEU 3.8 3.6 - - - +
3141D VAL 3.3 0.2 - - - -
3142D GLU* 1.3 74.9 - - - +
3144D ALA* 1.3 51.1 + - - +
3146D SER* 3.0 12.1 + - - -
3147D ILE* 2.8 30.7 + - - +
3244D ILE* 3.3 28.0 - - + +
3247D GLU* 3.8 11.3 - - + +
3248D ALA* 3.8 10.8 - - - +
3251D ARG* 3.8 14.7 - - - +
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Residues in contact with ALA3144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3107D VAL* 4.6 6.7 - - + -
3109D VAL* 5.2 0.9 - - + -
3140D LEU 3.0 18.5 + - - +
3141D VAL 3.1 5.8 + - - +
3143D ALA* 1.3 76.2 - - - +
3145D LYS* 1.3 57.8 + - - +
3147D ILE* 3.8 1.8 - - - +
3148D GLY 3.0 6.4 + - - -
3149D ALA* 2.9 29.8 + - + +
3151D THR* 3.3 31.4 - - + +
3244D ILE* 3.7 24.0 - - + +
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Residues in contact with LYS3145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3141D VAL* 3.0 15.1 + - + +
3142D GLU* 2.9 14.6 + - + +
3144D ALA* 1.3 75.6 - - - +
3146D SER* 1.3 64.6 + - - +
3148D GLY* 3.4 11.2 + - - +
3149D ALA 4.9 1.1 - - - +
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Residues in contact with SER3146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3142D GLU 2.8 11.6 + - - -
3143D ALA* 3.0 10.5 + - - -
3145D LYS* 1.3 76.2 - - - +
3147D ILE* 1.3 61.3 + - - +
3148D GLY* 2.9 5.1 + - - -
3247D GLU* 4.4 10.3 + - - +
3251D ARG* 3.7 21.0 + - - -
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Residues in contact with ILE3147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3143D ALA 2.8 20.2 - - - +
3144D ALA 3.8 3.8 - - - +
3146D SER* 1.3 74.6 + - - +
3148D GLY* 1.3 63.1 + - - +
3149D ALA* 4.7 0.2 - - + -
3240D HIS* 3.5 35.7 - - + +
3243D LYS* 5.3 13.9 - - + -
3244D ILE* 3.7 29.8 - - + +
3247D GLU* 5.7 4.0 - - + -
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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