Contacts of the helix formed by residues 1996 - 2002 (chain A) in PDB entry 4M6W
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 SER1996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1976A TYR* 4.5 1.8 - - - -
1994A PHE* 4.1 7.0 - - - +
1995A SER* 1.3 84.9 + - - +
1997A VAL* 1.3 60.7 + - - +
1998A LYS* 4.0 5.0 - - - +
1999A ARG* 3.2 19.8 + - - +
2000A MET* 2.9 27.4 + - - +
211B PHE 3.5 15.0 - - - -
212B THR* 4.6 0.5 - - - -
213B GLN* 3.2 27.0 + - - -
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Residues in contact with VAL1997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972A ALA* 5.5 6.7 - - + -
1975A PHE* 3.6 34.8 - - + -
1976A TYR* 3.4 24.3 + - + +
1996A SER* 1.3 71.6 - - - +
1998A LYS* 1.3 58.4 + - - +
2000A MET* 3.5 7.0 - - + +
2001A ALA* 3.0 27.7 + - - +
210B PHE* 3.4 40.4 - - + +
211B PHE* 3.7 23.1 - - + +
213B GLN 4.5 2.5 + - - +
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Residues in contact with LYS1998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1996A SER* 4.0 4.9 - - - -
1997A VAL* 1.3 79.2 - - - +
1999A ARG* 1.3 61.5 + - + +
2001A ALA* 3.3 8.8 + - - +
2002A ASN* 3.0 32.6 + - - +
188B SER* 4.0 14.4 + - - +
189B ASN* 3.6 31.9 - - - +
208B HIS* 6.0 2.2 + - - -
211B PHE* 3.2 36.1 + - + +
212B THR* 4.8 14.1 - - + +
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Residues in contact with ARG1999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1994A PHE* 4.8 4.5 - - + -
1995A SER* 3.6 24.9 + - - +
1996A SER* 3.2 13.8 + - - +
1998A LYS* 1.3 79.0 - - + +
2000A MET* 1.3 58.6 + - - +
2002A ASN* 3.2 8.0 + - + +
2003A SER* 2.5 37.5 + - - +
2007A GLU* 4.7 9.4 + - - +
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Residues in contact with MET2000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975A PHE* 4.4 5.6 - - + -
1976A TYR* 3.8 35.0 - - + +
1979A ILE* 5.5 0.2 - - + -
1990A MET* 3.8 19.5 - - + -
1994A PHE* 3.8 33.3 - - + -
1996A SER 2.9 14.3 + - - +
1997A VAL* 3.5 19.7 - - + +
1999A ARG* 1.3 77.4 - - - +
2001A ALA* 1.3 76.3 + - + +
2002A ASN 3.4 0.5 + - - -
2003A SER* 3.5 19.9 + - - +
2008A ILE* 4.9 4.6 - - - +
2022A ILE* 4.4 15.3 - - - +
2026A ILE* 4.0 22.0 - - + +
184B ILE* 5.7 0.4 - - + -
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Residues in contact with ALA2001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1997A VAL 3.0 13.5 + - - +
1998A LYS 3.5 10.1 - - - +
1999A ARG 3.2 0.6 - - - -
2000A MET* 1.3 81.4 - - + +
2002A ASN* 1.3 61.3 + - - +
2003A SER 3.5 0.7 - - - -
2026A ILE* 3.7 24.6 - - + +
2027A HIS* 3.2 27.1 + - - -
184B ILE* 4.4 5.6 - - + +
185B GLN* 4.1 6.1 - - - +
188B SER* 3.6 23.3 - - - +
211B PHE* 5.3 0.7 - - + -
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Residues in contact with ASN2002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A LYS* 3.0 32.3 + - - +
1999A ARG* 3.2 10.1 + - + +
2000A MET 3.2 0.8 - - - -
2001A ALA* 1.3 77.6 - - - +
2003A SER* 1.3 61.5 + - - +
2004A SER 3.9 1.0 + - - -
2027A HIS* 5.0 4.0 - - - -
185B GLN* 3.5 23.3 + - - +
188B SER* 3.4 11.0 + - - -
189B ASN* 2.9 33.7 + - - +
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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