Contacts of the helix formed by residues 3012 - 3024 (chain C) in PDB entry 1D1Z
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 SER3012 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3011C ILE* 1.3 77.5 - - - +
3013C ARG* 1.3 64.6 + - - +
3014C GLU* 3.4 10.2 + - - +
3015C THR* 3.0 28.8 + - - -
3016C GLY* 2.9 20.6 + - - -
3032C ARG* 4.1 4.8 - - - -
3035C GLU* 3.9 20.0 - - - -
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Residues in contact with ARG3013 (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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3012C SER* 1.3 70.7 - - - +
3014C GLU* 1.3 72.0 + - - +
3016C GLY* 3.3 2.1 + - - -
3017C GLU* 2.9 59.7 + - + +
3032C ARG* 3.3 39.7 + - - +
3035C GLU* 2.9 21.2 + - - +
5003C SO4 4.1 16.6 + - - +
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Residues in contact with GLU3014 (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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3012C SER* 3.1 10.2 + - - +
3013C ARG* 1.3 93.9 + - - +
3015C THR* 1.3 57.2 + - - +
3017C GLU* 3.3 5.6 + - - +
3018C LYS* 2.9 54.8 + - - +
3035C GLU* 4.7 0.4 + - - -
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Residues in contact with THR3015 (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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3011C ILE* 4.0 24.7 - - + -
3012C SER* 3.0 26.5 + - - -
3014C GLU* 1.3 75.7 - - - +
3016C GLY* 1.4 64.5 + - - +
3018C LYS* 3.3 9.7 + - - +
3019C LEU* 3.0 28.2 + - + +
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Residues in contact with GLY3016 (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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3011C ILE* 3.9 17.2 - - - +
3012C SER 2.9 14.2 + - - -
3013C ARG 3.7 2.7 - - - -
3015C THR* 1.4 78.3 - - - +
3017C GLU* 1.3 62.2 + - - +
3019C LEU* 3.4 3.7 + - - +
3020C LEU* 3.0 28.9 + - - +
3030C LEU* 3.8 16.6 - - - +
3032C ARG* 4.6 4.3 - - - -
3044C CYS* 6.2 0.9 - - - -
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Residues in contact with GLU3017 (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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3013C ARG* 2.9 49.4 + - + +
3014C GLU* 4.0 4.6 - - - +
3016C GLY* 1.3 76.3 - - - +
3018C LYS* 1.3 57.6 + - + +
3020C LEU* 3.2 2.4 + - + +
3021C LEU* 2.9 43.8 + - + +
3032C ARG* 4.8 3.7 + - - +
3044C CYS* 5.9 2.4 - - - -
3051C ILE* 4.1 42.4 - - + +
3053C THR* 4.3 8.1 + - - -
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Residues in contact with LYS3018 (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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3014C GLU* 2.9 41.5 + - - +
3015C THR* 3.3 8.9 + - - +
3017C GLU* 1.3 75.5 - - - +
3019C LEU* 1.3 64.0 + - - +
3021C LEU* 3.9 9.8 - - + +
3022C ALA* 3.0 24.3 + - - +
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Residues in contact with LEU3019 (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 HIS* 5.4 6.7 - - + +
3011C ILE* 5.4 5.8 - - + -
3015C THR* 3.0 20.6 + - + +
3016C GLY* 3.6 5.4 - - - +
3018C LYS* 1.3 75.2 - - - +
3020C LEU* 1.3 65.9 + - - +
3022C ALA* 3.2 13.3 + - - +
3023C THR* 3.4 11.2 + - + +
3030C LEU* 4.1 12.1 - - + -
3102C VAL* 3.6 32.5 - - + -
3104C LYS 4.9 9.6 - - - +
4010D LYS* 3.8 39.3 - - + -
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Residues in contact with LEU3020 (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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3016C GLY 3.0 22.1 + - - +
3017C GLU* 3.2 0.6 + - - +
3019C LEU* 1.3 74.9 - - - +
3021C LEU* 1.3 64.6 + - - +
3023C THR* 2.7 27.7 + - - -
3028C SER* 3.7 33.2 - - - +
3029C TYR* 3.7 11.0 - - - +
3030C LEU* 3.8 9.4 - - + -
3044C CYS* 3.5 40.6 - - + +
3045C VAL 4.2 0.9 - - - +
3046C LEU* 3.4 12.5 - - + +
3051C ILE* 3.6 27.8 - - + -
3102C VAL* 3.8 16.6 - - + -
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Residues in contact with LEU3021 (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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3017C GLU* 2.9 30.6 + - + +
3018C LYS* 3.9 8.7 - - + +
3020C LEU* 1.3 77.5 - - - +
3022C ALA* 1.3 63.6 + - - +
3024C GLY* 3.1 13.9 + - - -
3046C LEU* 3.8 17.9 - - + +
3049C GLY* 3.5 26.7 - - - +
3051C ILE* 4.0 15.9 - - + -
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Residues in contact with ALA3022 (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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3018C LYS 3.0 18.9 + - - +
3019C LEU* 3.5 7.4 - - - +
3020C LEU 3.1 0.6 - - - -
3021C LEU* 1.3 77.2 - - - +
3023C THR* 1.3 63.8 - - - +
3024C GLY* 3.3 0.9 + - - -
4007D TYR* 4.9 1.7 - - - +
4008D HIS* 4.2 1.6 - - - -
4009D GLY* 3.4 20.2 + - - +
4010D LYS* 3.7 22.2 - - + -
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Residues in contact with THR3023 (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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3019C LEU* 3.6 14.6 - - + +
3020C LEU* 2.7 19.2 + - - +
3022C ALA* 1.3 81.3 - - - +
3024C GLY* 1.3 59.5 + - - +
3025C LEU* 3.1 6.9 + - - +
3028C SER* 2.9 28.3 + - - +
3046C LEU* 3.8 0.2 - - - +
3102C VAL* 4.3 18.2 - - + -
4008D HIS* 2.8 30.9 - - - +
4009D GLY 3.2 15.7 - - - +
4010D LYS* 4.1 11.4 - - + +
4011D ILE* 3.8 17.3 - - + -
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Residues in contact with GLY3024 (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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3020C LEU 3.5 1.6 + - - -
3021C LEU 3.1 15.2 + - - -
3022C ALA 4.3 0.7 - - - -
3023C THR* 1.3 80.3 + - - +
3025C LEU* 1.3 56.9 + - - +
3046C LEU* 3.8 9.2 - - - -
4007D TYR 5.7 0.4 - - - -
4008D HIS* 3.3 20.7 + - - -
4103D GLU 3.4 3.9 - - - +
4104D LYS* 3.3 15.3 - - - +
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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