Contacts of the helix formed by residues 1988 - 2000 (chain F) in PDB entry 6X34
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 THR1988 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1986F THR* 4.4 1.6 - - - -
1987F MET* 1.3 81.0 + - + +
1989F ALA* 1.3 70.6 + - - +
1990F ALA* 3.7 12.2 + - + +
1991F GLU* 3.5 29.9 - - + +
1992F THR* 3.3 22.0 + - - -
1994F ARG* 5.1 2.0 - - - +
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Residues in contact with ALA1989 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1988F THR* 1.3 75.9 + - - +
1990F ALA* 1.3 59.7 + - - +
1992F THR* 3.4 6.3 + - - -
1993F ALA* 2.9 31.1 + - - +
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Residues in contact with ALA1990 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1988F THR* 3.3 12.5 + - + +
1989F ALA* 1.3 80.2 - - - +
1991F GLU* 1.3 58.0 + - - +
1993F ALA* 3.3 5.5 + - - +
1994F ARG* 2.9 54.3 + - - +
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Residues in contact with GLU1991 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1985F PHE 5.9 1.6 - - - +
1986F THR* 6.2 0.9 - - - -
1987F MET* 5.7 3.4 - - + +
1988F THR* 3.5 22.2 - - + +
1989F ALA 3.4 0.2 - - - -
1990F ALA* 1.3 78.1 - - - +
1992F THR* 1.3 57.6 + - - +
1994F ARG* 3.3 23.2 + - - +
1995F ARG* 2.9 30.0 + - - +
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Residues in contact with THR1992 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1986F THR* 3.4 27.2 - - - -
1988F THR 3.3 13.8 + - - -
1989F ALA* 3.4 10.0 + - - -
1990F ALA 3.3 0.8 - - - -
1991F GLU* 1.3 78.1 - - - +
1993F ALA* 1.3 52.1 + - - +
1995F ARG* 3.3 7.2 + - + +
1996F THR* 2.6 44.4 + - - +
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Residues in contact with ALA1993 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1989F ALA 2.9 18.5 + - - +
1990F ALA* 3.7 6.7 - - - +
1991F GLU 3.3 0.2 - - - -
1992F THR* 1.3 77.0 - - - +
1994F ARG* 1.3 59.2 + - + +
1996F THR* 3.3 6.4 + - - -
1997F ARG* 2.9 40.7 + - + +
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Residues in contact with ARG1994 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1988F THR* 5.1 2.6 - - - +
1990F ALA* 2.9 43.2 + - - +
1991F GLU* 3.5 28.2 - - - +
1993F ALA* 1.3 77.3 - - + +
1995F ARG* 1.3 57.1 + - - +
1997F ARG* 3.3 18.5 + - - +
1998F GLU* 2.9 35.6 + - - +
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Residues in contact with ARG1995 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1981F LEU* 4.7 16.8 - - + -
1991F GLU 2.9 18.1 + - - +
1992F THR* 3.7 7.4 - - + +
1994F ARG* 1.3 76.1 - - - +
1996F THR* 1.3 57.3 + - - +
1998F GLU* 3.2 19.2 - - - +
1999F PHE* 2.9 33.8 + - - +
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Residues in contact with THR1996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1992F THR* 2.6 31.8 + - - +
1993F ALA* 3.7 6.5 - - - -
1995F ARG* 1.3 78.1 - - - +
1997F ARG* 1.3 57.9 + - - +
1999F PHE* 4.7 2.2 - - - -
2000F ARG* 2.9 44.1 + - + +
2001F SER 4.2 0.2 + - - -
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Residues in contact with ARG1997 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1993F ALA* 2.9 27.7 + - - +
1994F ARG* 3.8 17.1 + - - +
1996F THR* 1.3 77.5 - - + +
1998F GLU* 1.3 57.5 + - - +
2001F SER* 3.2 26.0 - - - +
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Residues in contact with GLU1998 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974F GLN* 4.1 22.9 + - - +
1978F TYR* 5.6 2.8 - - + -
1981F LEU* 3.3 30.9 - - - +
1994F ARG* 2.9 18.2 + - - +
1995F ARG* 3.2 21.8 - - - +
1997F ARG* 1.3 77.0 - - - +
1999F PHE* 1.3 61.9 + - + +
2001F SER* 4.6 3.1 + - - -
2006F GLN* 3.7 29.8 + - - +
2023F PRO* 4.9 14.3 - - + +
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Residues in contact with PHE1999 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1978F TYR* 3.8 30.5 - + + -
1995F ARG 2.9 17.7 + - - +
1996F THR* 4.2 1.8 - - - +
1998F GLU* 1.3 80.2 - - + +
2000F ARG* 1.3 66.2 + - + +
2001F SER 3.1 15.8 + - - +
3636F PRO* 4.0 40.4 - - + +
3638F TYR* 3.2 31.2 - + - -
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Residues in contact with ARG2000 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1996F THR* 2.9 32.8 + - + +
1999F PHE* 1.3 78.5 - - + +
2001F SER* 1.3 62.2 + - - +
2002F PRO* 3.8 2.8 - - - +
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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