Contacts of the helix formed by residues 1988 - 2000 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1986D THR* 4.4 1.5 - - - -
1987D MET* 1.3 81.4 + - + +
1989D ALA* 1.3 68.7 + - - +
1990D ALA* 3.7 11.4 + - + +
1991D GLU* 3.5 30.2 - - + +
1992D THR* 3.3 22.0 + - - -
1994D ARG* 5.1 2.9 - - - +
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Residues in contact with ALA1989 (chain D).
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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1988D THR* 1.3 75.7 + - - +
1990D ALA* 1.3 60.0 + - - +
1992D THR* 3.4 7.2 + - - -
1993D ALA* 2.9 30.0 + - - +
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Residues in contact with ALA1990 (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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1988D THR* 3.3 11.8 + - + +
1989D ALA* 1.3 79.5 - - - +
1991D GLU* 1.3 58.0 + - - +
1993D ALA* 3.3 6.4 + - - +
1994D ARG* 2.9 52.9 + - - +
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Residues in contact with GLU1991 (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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1985D PHE 5.9 1.6 - - - +
1986D THR* 6.2 1.1 - - - -
1987D MET* 5.7 3.1 - - + +
1988D THR* 3.5 22.6 - - + +
1989D ALA 3.4 0.2 - - - -
1990D ALA* 1.3 77.8 - - - +
1992D THR* 1.3 58.6 + - - +
1994D ARG* 3.3 24.1 + - - +
1995D ARG* 2.9 30.1 + - - +
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Residues in contact with THR1992 (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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1986D THR* 3.4 26.5 - - - -
1988D THR 3.3 12.8 + - - -
1989D ALA* 3.4 10.0 + - - -
1990D ALA 3.3 0.6 - - - -
1991D GLU* 1.3 78.3 - - - +
1993D ALA* 1.3 55.5 + - - +
1995D ARG* 3.3 5.5 + - - +
1996D THR* 2.6 44.8 + - - +
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Residues in contact with ALA1993 (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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1989D ALA 2.9 17.4 + - - +
1990D ALA* 3.7 7.2 - - - +
1991D GLU 3.3 0.2 - - - -
1992D THR* 1.3 78.5 - - - +
1994D ARG* 1.3 56.5 + - + +
1996D THR* 3.3 5.9 + - - -
1997D ARG* 2.9 42.0 + - + +
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Residues in contact with ARG1994 (chain D).
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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1988D THR* 5.1 2.6 - - - +
1990D ALA* 2.9 43.4 + - - +
1991D GLU* 3.5 28.2 - - - +
1993D ALA* 1.3 77.1 - - + +
1995D ARG* 1.3 56.5 + - - +
1997D ARG* 3.3 18.0 + - - +
1998D GLU* 2.9 34.4 + - - +
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Residues in contact with ARG1995 (chain D).
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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1981D LEU* 4.7 15.9 - - + -
1991D GLU 2.9 19.1 + - - +
1992D THR* 3.7 6.5 - - + +
1994D ARG* 1.3 75.4 - - - +
1996D THR* 1.3 58.1 + - - +
1998D GLU* 3.2 18.5 - - - +
1999D PHE* 2.9 34.3 + - - +
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Residues in contact with THR1996 (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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1992D THR* 2.6 31.6 + - - +
1993D ALA* 3.7 6.6 - - - -
1995D ARG* 1.3 77.0 - - - +
1997D ARG* 1.3 57.9 + - + +
1999D PHE* 4.7 1.6 - - - -
2000D ARG* 2.9 44.2 + - + +
2001D SER 4.2 0.2 + - - -
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Residues in contact with ARG1997 (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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1993D ALA* 2.9 27.7 + - + +
1994D ARG* 3.3 16.9 + - - +
1996D THR* 1.3 77.5 - - - +
1998D GLU* 1.3 57.4 + - - +
2001D SER* 3.2 26.4 - - - +
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Residues in contact with GLU1998 (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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1974D GLN* 4.1 21.1 + - - +
1978D TYR* 5.6 2.6 - - + -
1981D LEU* 3.3 30.6 - - - +
1994D ARG* 2.9 17.2 + - - +
1995D ARG* 3.2 21.9 - - - +
1997D ARG* 1.3 76.3 - - - +
1999D PHE* 1.3 62.4 + - + +
2001D SER* 4.6 3.2 + - - -
2006D GLN* 3.7 29.9 + - + +
2023D PRO* 4.9 14.4 - - + +
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Residues in contact with PHE1999 (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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1978D TYR* 3.8 30.5 - + + -
1995D ARG 2.9 18.1 + - - +
1996D THR* 4.2 2.2 - - - +
1998D GLU* 1.3 81.0 - - + +
2000D ARG* 1.3 63.7 + - + +
2001D SER 3.1 16.0 + - - +
3636D PRO* 4.0 41.4 - - + +
3638D TYR* 3.2 31.4 - + - -
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Residues in contact with ARG2000 (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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1996D THR* 2.9 31.7 + - + +
1999D PHE* 1.3 79.6 - - + +
2001D SER* 1.3 64.4 + - - +
2002D PRO* 3.8 2.3 - - - +
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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