Contacts of the helix formed by residues 1032 - 1040 (chain N) in PDB entry 2FDB
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 PHE1032 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033N THR* 1.3 60.0 + - - +
1034N GLN 3.4 2.0 - - - -
1035N HIS* 3.7 9.6 - + + +
1036N VAL* 2.7 38.4 + - + +
3291R ILE* 4.0 21.8 - - + -
3293R HIS* 3.8 15.9 - + - -
3309R LEU* 3.8 35.9 - - + -
3341R THR* 3.6 26.0 - - + -
3343R LEU* 4.1 22.4 - - + -
3350R ILE* 4.4 6.7 - - + -
3352R PHE* 3.5 56.2 - + + -
3354R SER* 5.1 0.7 - - - -
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Residues in contact with THR1033 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE* 1.3 79.4 + - - +
1034N GLN* 1.3 61.1 + - - +
1036N VAL* 3.7 2.7 - - - +
1037N ARG* 2.9 30.3 + - + +
3350R ILE* 4.4 17.7 - - + +
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Residues in contact with GLN1034 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE 3.4 0.4 - - - +
1033N THR* 1.3 79.3 - - - +
1035N HIS* 1.3 66.5 + - - +
1037N ARG* 3.3 7.5 + - - +
1038N GLU* 3.0 25.1 + - - +
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Residues in contact with HIS1035 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE* 3.2 16.8 + + - +
1034N GLN* 1.3 80.2 - - - +
1036N VAL* 1.3 58.3 + - - +
1038N GLU* 3.6 5.1 - - - +
1039N GLN* 2.9 32.4 + - + +
1093N PHE* 4.7 1.1 - + - -
3289R GLN* 2.7 27.9 + - - -
3291R ILE* 3.4 13.2 - - + +
3309R LEU* 3.9 27.2 - - + +
3311R VAL* 4.1 18.4 - - + -
3343R LEU* 3.6 26.0 - - + -
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Residues in contact with VAL1036 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE 2.7 23.0 + - - +
1033N THR* 3.7 5.6 - - - +
1035N HIS* 1.3 70.4 - - - +
1037N ARG* 1.3 64.2 + - - +
1040N SER* 2.5 44.7 + - - +
1093N PHE* 4.0 25.8 - - + -
3343R LEU* 3.7 29.8 - - + -
3350R ILE* 4.1 31.4 - - + -
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Residues in contact with ARG1037 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033N THR* 2.9 19.6 + - + +
1034N GLN* 3.3 8.5 + - - +
1036N VAL* 1.3 78.2 - - - +
1038N GLU* 1.3 63.0 + - - +
1040N SER* 3.4 12.7 + - - -
1041N LEU* 3.7 15.8 - - - +
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Residues in contact with GLU1038 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034N GLN 3.0 17.0 + - - +
1035N HIS* 3.6 5.8 - - - +
1037N ARG* 1.3 77.3 - - - +
1039N GLN* 1.3 63.7 + - - +
1040N SER 3.1 0.9 + - - -
1041N LEU* 3.2 30.2 + - + +
1042N VAL* 4.5 2.4 + - - +
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Residues in contact with GLN1039 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035N HIS* 2.9 28.1 + - + +
1036N VAL 4.0 2.5 - - - +
1038N GLU* 1.3 72.7 - - - +
1040N SER* 1.3 57.0 + - - +
1041N LEU 3.1 1.2 + - - -
1042N VAL* 3.0 20.3 + - - +
1044N ASP* 5.7 2.2 - - + +
1092N THR* 2.8 18.2 + - - +
1093N PHE* 4.0 22.4 - - + -
3289R GLN* 4.5 12.3 - - - +
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Residues in contact with SER1040 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036N VAL* 2.5 34.8 + - - +
1037N ARG* 3.7 8.2 - - - -
1038N GLU 3.1 0.6 - - - -
1039N GLN* 1.3 71.5 - - - +
1041N LEU* 1.3 63.1 + - - +
1042N VAL 3.4 0.4 + - - -
1092N THR* 3.8 11.2 - - - +
1093N PHE* 3.3 24.7 - - - +
1094N GLY* 4.7 1.4 + - - -
1096N ARG* 3.2 36.9 + - - -
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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