Contacts of the strand formed by residues 1998 - 2009 (chain C) in PDB entry 6TM1
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 LYS1998 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1982C PRO* 3.6 24.2 - - + -
1984C THR* 5.2 1.1 - - - +
1997C CYS* 1.3 75.9 - - - +
1999C ARG* 1.3 56.4 + - - +
2025C GLU* 3.2 2.9 - - - +
2026C LEU* 2.2 50.2 + - + +
2031C VAL* 4.6 17.2 - - + +
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Residues in contact with ARG1999 (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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1980C GLU* 3.7 2.8 - - - +
1981C THR* 2.8 40.7 + - - +
1982C PRO* 3.6 4.0 - - - +
1983C PHE* 4.3 6.3 - - + +
1998C LYS* 1.3 75.8 - - - +
2000C ARG* 1.3 66.1 + - - +
2023C SER* 6.0 1.8 - - - +
2024C THR 3.3 7.0 - - - +
2025C GLU* 3.6 18.8 - - + +
2026C LEU* 5.9 0.7 - - - -
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Residues in contact with ARG2000 (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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1978C VAL* 6.1 2.9 - - + -
1979C PHE 3.6 5.6 - - - +
1980C GLU* 3.9 17.5 - - + -
1981C THR* 3.8 3.3 - - - +
1999C ARG* 1.3 79.1 - - - +
2001C THR* 1.3 59.0 + - - +
2002C ILE* 4.0 1.3 + - + +
2022C SER 4.0 0.7 - - - +
2023C SER* 3.1 3.3 - - - -
2024C THR* 2.8 41.3 + - - +
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Residues in contact with THR2001 (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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1879C ARG* 5.5 6.1 - - - +
1977C PHE 4.5 0.3 - - - +
1978C VAL* 3.4 1.2 - - - -
1979C PHE* 2.8 75.9 + - + +
1981C THR* 4.9 5.1 - - - -
2000C ARG* 1.3 71.4 - - - +
2002C ILE* 1.3 57.3 + - - +
2003C LEU* 3.7 21.2 + - + +
2021C GLN* 4.5 6.4 - - - +
2022C SER 3.3 11.1 + - - -
2023C SER* 3.6 15.7 - - - -
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Residues in contact with ILE2002 (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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1976C ARG* 5.4 6.2 - - + +
1977C PHE 4.0 0.7 - - - -
1978C VAL* 3.5 24.5 - - + -
2000C ARG* 4.0 2.4 + - + +
2001C THR* 1.3 65.2 - - - +
2003C LEU* 1.3 63.9 + - - +
2004C THR* 3.7 8.8 + - - +
2022C SER* 2.3 45.5 + - - +
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Residues in contact with LEU2003 (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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1879C ARG* 3.3 39.5 - - + +
1895C GLU* 4.1 6.7 - - - +
1897C ILE* 3.5 37.2 - - + -
1952C VAL* 5.2 5.6 - - + -
1976C ARG* 3.7 1.4 - - - +
1977C PHE* 2.8 40.3 + - + +
1979C PHE* 5.9 1.3 - - + -
2001C THR* 3.7 15.7 - - + +
2002C ILE* 1.3 76.2 - - - +
2004C THR* 1.3 60.2 + - - +
2018C VAL* 3.9 13.5 - - + -
2020C SER 3.1 13.7 - - - +
2021C GLN* 3.7 15.7 - - + +
2022C SER 4.1 0.6 - - - +
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Residues in contact with THR2004 (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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1975C ASN* 3.4 13.9 - - - -
1976C ARG* 3.7 18.8 - - + -
2002C ILE 4.0 8.7 - - - +
2003C LEU* 1.3 77.7 - - - +
2005C THR* 1.3 61.5 + - - +
2018C VAL* 3.5 6.3 - - - +
2019C ILE* 3.1 37.9 + - - +
2020C SER* 2.8 20.3 + - - +
2022C SER* 5.8 2.5 - - - -
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Residues in contact with THR2005 (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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1897C ILE* 3.7 25.5 - - + +
1974C ILE 4.3 4.5 - - - +
1975C ASN* 2.7 40.3 + - - +
1976C ARG* 4.2 2.1 - - - +
1977C PHE* 5.2 3.6 - - + -
2003C LEU 4.2 0.4 + - - -
2004C THR* 1.3 78.2 + - - +
2006C SER* 1.3 71.3 + - - +
2007C HIS 3.3 17.4 - - - +
2009C PHE* 4.9 3.8 - - + -
2016C ILE* 3.0 27.5 - - + +
2017C GLN 2.8 13.0 + - - -
2018C VAL* 3.7 6.1 - - - +
2019C ILE* 4.3 6.2 - - - +
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Residues in contact with SER2006 (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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1975C ASN* 5.6 1.4 - - - +
2005C THR* 1.3 81.8 + - - +
2007C HIS* 1.3 78.0 + - - -
2008C LEU* 5.5 1.4 - - - +
2016C ILE* 6.1 0.2 - - - -
2017C GLN* 2.8 20.9 + - - -
2018C VAL* 4.2 0.6 - - - +
2019C ILE* 3.5 32.2 - - - +
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Residues in contact with HIS2007 (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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1786C ASN* 3.7 21.1 - - + +
1789C GLU* 5.6 8.2 - - + +
1974C ILE 3.9 2.1 - - - +
1975C ASN* 4.0 2.3 - - - +
2005C THR* 3.3 24.3 - - - +
2006C SER* 1.3 96.6 + - - +
2008C LEU* 1.3 66.6 + - - +
2011C TYR* 3.1 42.3 + + + -
2016C ILE* 3.4 23.0 - - + +
2017C GLN 4.6 0.2 + - - -
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Residues in contact with LEU2008 (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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1784C THR* 4.5 4.2 + - - +
1785C PRO* 3.8 35.2 - - + -
1786C ASN* 2.5 39.1 + - + +
1973C ASN* 3.5 36.1 - - + +
1974C ILE 3.7 0.9 - - - -
1975C ASN* 3.5 29.4 - - + +
2006C SER 5.5 0.9 - - - +
2007C HIS* 1.3 78.4 - - - +
2009C PHE* 1.3 59.2 + - - +
2010C PRO 2.6 16.8 - - - +
2011C TYR* 4.5 0.3 - - - -
2016C ILE* 4.7 1.6 - - - -
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Residues in contact with PHE2009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1784C THR* 5.3 0.2 + - - -
1877C TYR* 3.3 42.6 - + - +
1897C ILE* 4.1 18.6 - - + -
1899C LYS* 3.4 30.7 - - + -
1971C HIS 5.0 2.0 - - - +
1972C HIS* 4.0 2.9 - - - -
1973C ASN* 3.1 26.7 + - - +
1974C ILE* 3.4 25.7 + - + -
1977C PHE* 3.9 24.5 - + - -
2005C THR* 4.9 1.8 - - + -
2008C LEU* 1.3 72.7 - - - +
2010C PRO* 1.3 68.3 - - + +
2011C TYR* 5.6 2.0 - - + -
2013C LYS 5.9 0.9 - - - -
2014C LYS 4.5 4.5 - - - -
2015C ARG* 5.0 1.6 - - - -
2016C ILE* 3.4 38.4 - - + -
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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