Contacts of the helix formed by residues 3135 - 3148 (chain B) in PDB entry 1DJO
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 ASP3135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3125B SER* 3.4 8.3 - - - -
3126B MET* 2.9 25.4 + - - +
3127B ARG* 2.9 30.3 + - - +
3133B SER 3.5 3.4 + - - +
3134B ALA* 1.3 72.3 - - - +
3136B GLY* 1.3 61.3 + - - +
3137B MET 3.5 1.3 + - - -
3138B LEU* 3.8 6.9 + - - +
3139B ASN* 3.1 38.0 + - - +
3161B MET* 4.7 2.1 - - - +
3179B THR* 3.8 32.1 - - + +
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Residues in contact with GLY3136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3021B ILE* 4.1 13.8 - - - +
3125B SER* 3.6 26.0 - - - -
3127B ARG 4.8 0.6 + - - -
3129B GLY* 6.3 1.6 - - - -
3134B ALA* 3.4 4.2 - - - +
3135B ASP* 1.3 76.2 - - - +
3137B MET* 1.3 69.6 + - - +
3139B ASN* 3.4 4.2 + - - +
3140B LEU* 3.0 25.7 + - - +
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Residues in contact with MET3137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3047B GLY 4.7 8.7 - - - +
3048B VAL* 4.0 26.6 - - + +
3129B GLY* 5.1 12.1 - - - +
3131B ALA 5.5 0.7 - - - +
3134B ALA* 3.2 48.0 - - + +
3135B ASP 3.5 0.2 - - - -
3136B GLY* 1.3 77.6 - - - +
3138B LEU* 1.3 59.4 + - - +
3140B LEU* 3.4 2.9 + - - +
3141B TYR* 3.0 26.6 + - - +
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Residues in contact with LEU3138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3134B ALA 5.6 0.2 + - - -
3135B ASP* 3.8 7.1 + - - +
3136B GLY 3.4 0.2 - - - -
3137B MET* 1.3 75.8 - - - +
3139B ASN* 1.3 63.6 + - - +
3141B TYR* 3.5 18.5 - - + +
3142B ASN* 2.8 52.3 + - - +
3163B ASP* 3.9 18.4 - - - +
3194B GLU 6.3 1.1 - - - +
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Residues in contact with ASN3139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3021B ILE* 5.3 0.4 - - + -
3123B VAL* 3.6 18.4 - - + +
3124B GLY 3.0 22.6 + - - +
3125B SER* 4.0 0.4 - - - +
3135B ASP* 3.1 42.6 + - - +
3136B GLY* 3.6 4.5 - - - +
3138B LEU* 1.3 80.5 - - - +
3140B LEU* 1.3 57.7 + - - +
3142B ASN* 3.4 7.3 + - - +
3143B ALA* 2.9 28.2 + - - +
3160B THR* 3.8 5.1 + - - +
3161B MET* 3.7 20.1 - - - +
3162B ASN* 3.6 18.1 + - - +
3163B ASP 5.0 1.0 + - - -
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Residues in contact with LEU3140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3014B ILE* 4.0 24.9 - - + -
3021B ILE* 4.6 13.9 - - + -
3044B LEU* 3.8 36.3 - - + +
3045B ILE* 4.9 0.4 - - + +
3048B VAL* 4.3 10.8 - - + -
3051B LEU* 4.5 13.0 - - + -
3095B VAL* 4.3 17.3 - - + -
3097B THR* 4.4 13.7 - - + -
3123B VAL* 4.3 5.1 - - + +
3136B GLY 3.0 17.2 + - - +
3137B MET 3.7 4.3 - - - +
3139B ASN* 1.3 72.3 - - - +
3141B TYR* 1.3 68.3 + - - +
3143B ALA* 3.0 6.0 + - + +
3144B VAL* 2.9 26.1 + - + +
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Residues in contact with TYR3141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3048B VAL* 4.2 11.9 - - + -
3050B GLU* 3.8 28.6 + - + +
3051B LEU* 3.9 20.8 - - + +
3053B ASP* 5.3 4.0 - - - +
3054B LEU* 3.3 47.9 - - + +
3137B MET 3.0 16.6 + - - +
3138B LEU* 3.5 20.0 - - + +
3140B LEU* 1.3 78.5 - - - +
3142B ASN* 1.3 67.8 + - - +
3144B VAL* 3.3 0.5 + - - +
3145B ALA* 3.0 24.4 + - + +
3194B GLU* 4.9 4.8 - - - -
3195B GLY* 4.3 24.0 + - - -
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Residues in contact with ASN3142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3138B LEU* 2.8 38.4 + - - +
3139B ASN* 3.7 7.9 + - - +
3141B TYR* 1.3 87.9 - - - +
3143B ALA* 1.3 66.6 + - - +
3145B ALA* 3.6 5.7 - - - +
3146B VAL* 3.0 29.3 + - - +
3160B THR* 4.0 11.4 - - - +
3163B ASP* 3.9 23.0 + - - +
3192B VAL* 3.5 33.6 + - + +
3193B VAL* 5.8 0.2 - - - +
3194B GLU* 5.1 2.6 + - - -
3195B GLY 4.7 4.2 + - - -
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Residues in contact with ALA3143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3095B VAL* 3.6 28.8 - - + +
3121B VAL* 4.0 9.7 - - + +
3123B VAL* 3.8 13.5 - - + -
3139B ASN 2.9 14.7 + - - +
3140B LEU* 3.0 9.2 + - - +
3142B ASN* 1.3 78.7 - - - +
3144B VAL* 1.3 56.9 + - - +
3146B VAL* 3.4 2.4 + - - +
3147B ALA* 3.0 27.9 + - - +
3160B THR* 3.2 18.1 + - - +
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Residues in contact with VAL3144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3012B VAL* 4.7 4.5 - - + -
3014B ILE* 4.3 21.1 - - + -
3051B LEU* 4.2 21.5 - - + -
3054B LEU* 3.9 24.5 - - + -
3055B ALA* 4.3 1.1 - - + -
3057B VAL* 3.9 24.5 - - + -
3095B VAL* 4.2 12.1 - - + -
3140B LEU* 2.9 19.5 + - + +
3141B TYR 3.7 6.5 - - - +
3143B ALA* 1.3 73.0 - - - +
3145B ALA* 1.3 66.0 + - - +
3147B ALA* 3.1 1.9 + - - +
3148B SER* 2.9 30.7 + - - +
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Residues in contact with ALA3145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3054B LEU* 3.7 23.2 - - + +
3141B TYR* 3.0 17.7 + - + +
3142B ASN* 3.6 10.8 - - - +
3143B ALA 3.3 0.2 - - - -
3144B VAL* 1.3 77.5 - - - +
3146B VAL* 1.3 60.6 + - - +
3148B SER* 3.6 5.6 + - - -
3149B ASN* 3.4 21.0 + - - +
3192B VAL* 4.5 5.6 - - + -
3195B GLY* 3.9 30.5 - - - +
3197B SER* 4.7 1.8 + - - -
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Residues in contact with VAL3146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121B VAL* 3.9 10.8 - - + -
3142B ASN 3.0 19.0 + - - +
3143B ALA 3.8 3.6 - - - +
3145B ALA* 1.3 74.8 - - - +
3147B ALA* 1.3 64.7 + - - +
3148B SER 3.1 1.6 - - - -
3149B ASN* 3.1 6.3 + - - -
3152B SER* 2.6 38.5 + - - +
3158B LEU* 3.8 24.9 - - + -
3160B THR* 3.8 17.5 - - + -
3165B ILE* 4.2 6.7 - - + -
3192B VAL* 3.2 34.8 - - + -
3197B SER* 3.7 10.5 - - - +
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Residues in contact with ALA3147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3010B ALA* 5.4 0.2 - - - +
3012B VAL* 3.9 15.4 - - + +
3092B ASP* 4.5 1.9 - - - +
3093B GLY* 3.8 15.8 + - - -
3094B ILE 4.3 10.5 - - - +
3095B VAL* 3.6 21.5 - - + -
3119B PRO* 3.8 22.2 - - + +
3121B VAL* 4.2 8.1 - - + -
3143B ALA 3.0 17.9 + - - +
3144B VAL 3.1 3.6 + - - +
3146B VAL* 1.3 78.4 - - - +
3148B SER* 1.3 59.5 + - - +
3149B ASN 3.6 0.9 + - - +
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Residues in contact with SER3148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3010B ALA* 4.0 20.5 - - - +
3012B VAL* 3.3 6.3 - - - +
3054B LEU* 3.6 13.6 + - - -
3055B ALA* 2.9 31.3 - - - +
3144B VAL* 2.9 18.4 + - - +
3145B ALA* 3.8 7.4 - - - -
3147B ALA* 1.3 78.6 - - - +
3149B ASN* 1.3 59.9 + - - +
3150B LYS 3.7 1.7 + - - -
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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