Contacts of the helix formed by residues 2002 - 2011 (chain H) 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 PRO2002 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2000H ARG 3.8 2.9 - - - +
2001H SER* 1.3 91.8 - - - +
2003H PRO* 1.3 70.5 - - + +
2004H GLN* 3.4 20.4 + - + +
2005H GLU* 3.4 20.1 + - + +
2006H GLN* 2.9 26.7 + - - +
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Residues in contact with PRO2003 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001H SER 3.8 1.1 - - - +
2002H PRO* 1.3 88.4 - - + +
2004H GLN* 1.3 67.7 + - - +
2006H GLN* 3.2 12.6 + - + +
2007H ILE* 2.9 38.9 + - + +
3636H PRO* 5.3 13.9 - - + +
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Residues in contact with GLN2004 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002H PRO* 3.9 20.8 - - + +
2003H PRO* 1.3 85.7 - - - +
2005H GLU* 1.3 65.4 + - + +
2007H ILE* 3.3 6.1 + - - +
2008H ASN* 2.9 40.4 + - - +
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Residues in contact with GLU2005 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001H SER* 4.8 5.4 - - - -
2002H PRO* 3.4 27.5 + - + -
2003H PRO 3.4 0.4 - - - -
2004H GLN* 1.3 82.7 - - + +
2006H GLN* 1.3 57.3 + - - +
2008H ASN* 3.7 9.7 - - - +
2009H MET* 2.9 31.6 + - - +
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Residues in contact with GLN2006 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974H GLN* 4.4 15.2 - - - +
1998H GLU* 3.7 23.6 + - + +
1999H PHE 5.1 0.2 - - - +
2001H SER* 4.5 13.2 - - - +
2002H PRO 2.9 16.9 + - - +
2003H PRO* 3.5 11.0 - - - +
2005H GLU* 1.3 77.6 - - - +
2007H ILE* 1.3 59.6 + - + +
2009H MET* 3.2 5.2 + - - +
2010H LEU* 2.9 42.9 + - + +
3636H PRO* 3.3 25.9 - - - +
3637H LEU* 3.2 35.2 + - - +
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Residues in contact with ILE2007 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967H VAL* 5.9 7.2 - - + -
2003H PRO* 2.9 21.7 + - + +
2004H GLN* 3.9 5.4 - - - +
2006H GLN* 1.3 79.8 - - + +
2008H ASN* 1.3 63.0 + - - +
2010H LEU* 3.7 27.1 - - + +
2011H LEU* 3.1 29.5 + - + +
3637H LEU* 3.7 26.9 - - + -
3645H ALA* 5.5 5.8 - - + +
3648H MET* 4.6 33.0 - - + +
3649H PHE* 4.9 9.9 - - + +
3652H SER* 4.9 4.4 - - - -
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Residues in contact with ASN2008 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004H GLN* 2.9 31.5 + - - +
2005H GLU* 3.7 9.0 - - - +
2006H GLN 3.2 0.2 - - - -
2007H ILE* 1.3 77.6 - - - +
2009H MET* 1.3 60.9 + - - +
2011H LEU* 4.3 1.1 - - - +
2012H HIS* 3.4 21.5 + - - +
3652H SER* 3.3 28.9 + - - -
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Residues in contact with MET2009 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005H GLU 2.9 18.0 + - - +
2006H GLN* 3.7 5.4 - - - +
2008H ASN* 1.3 76.2 - - - +
2010H LEU* 1.3 64.8 + - - +
2012H HIS* 3.5 18.1 + - - +
2023H PRO* 4.6 15.2 - - + +
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Residues in contact with LEU2010 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967H VAL* 6.4 1.8 - - + -
1970H LEU* 3.6 32.1 - - + -
1974H GLN* 5.0 12.3 - - + +
2006H GLN* 2.9 34.7 + - + +
2007H ILE* 3.7 34.1 - - + +
2009H MET* 1.3 76.4 - - - +
2011H LEU* 1.3 75.5 + - + +
2012H HIS 3.4 5.2 + - - +
2023H PRO* 5.0 13.8 - - + +
2024H LEU* 3.2 29.2 - - + +
3637H LEU* 3.8 19.1 - - + -
3649H PHE* 6.3 0.4 - - + -
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Residues in contact with LEU2011 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966H TYR* 5.7 2.6 + - - -
1970H LEU* 4.8 5.4 - - + -
2007H ILE* 3.1 20.5 + - + +
2008H ASN 4.3 1.3 - - - +
2010H LEU* 1.3 84.0 - - + +
2012H HIS* 1.3 61.9 + - - +
2013H PHE* 3.5 6.3 + - - +
2024H LEU* 5.3 0.4 - - - -
2032H LEU* 4.9 9.7 - - - +
3649H PHE* 3.8 32.3 - - + -
3652H SER* 5.0 9.4 - - - -
3656H ALA* 5.3 6.2 - - - +
3657H TRP* 5.1 4.7 + - - -
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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