Contacts of the helix formed by residues 2156 - 2168 (chain B) in PDB entry 4D0N
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 LYS2156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.1 26.8 - - + +
39A PHE 2.6 32.7 + - - +
40A GLU* 4.7 7.2 - - - +
59A ASP* 4.3 16.8 + - - +
61A ALA 4.6 13.5 + - - +
2152B GLN* 3.4 42.0 + - - +
2153B ARG* 2.9 37.4 + - - +
2155B THR* 1.3 80.1 - - - +
2157B TYR* 1.3 63.4 + - - +
2158B PRO 3.5 0.2 - - - -
2159B VAL* 3.3 8.6 + - + +
2160B LEU* 3.3 26.1 + - + +
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Residues in contact with TYR2157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006B LEU* 4.1 7.6 - - + -
2010B GLU* 2.6 30.1 + - - -
2053B HIS* 3.1 27.4 - + - -
2056B PHE* 3.8 17.9 - + - -
2089B PHE* 3.9 20.2 - + - -
2097B LEU* 5.9 2.5 - - + -
2101B TYR* 5.7 0.9 - + - -
2153B ARG* 3.3 29.0 + - + -
2154B ILE* 3.4 37.0 + - + -
2156B LYS* 1.3 78.5 - - - +
2158B PRO* 1.3 69.9 - - + +
2160B LEU* 3.2 3.9 + - + +
2161B PHE* 2.9 54.2 + + + -
2185B VAL* 3.7 12.8 - - + -
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Residues in contact with PRO2158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY* 5.9 0.7 - - - +
66A TYR* 5.2 3.6 - - + +
2154B ILE 3.6 8.3 - - - +
2155B THR 3.6 14.4 - - - +
2157B TYR* 1.3 95.0 - - + +
2159B VAL* 1.3 63.0 + - + +
2162B GLN* 3.0 27.7 + - - +
2182B LEU* 3.4 21.7 - - + +
2185B VAL* 3.9 11.9 - - + -
2186B LYS* 4.2 17.3 - - + -
2189B ILE* 3.3 24.0 - - + -
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Residues in contact with VAL2159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.7 26.5 - - + +
38A VAL* 4.3 8.3 - - + -
61A ALA* 5.1 5.8 - - + +
62A GLY* 4.3 17.5 - - - +
1182A GDP 5.9 2.7 - - - +
2155B THR 3.9 14.1 - - - +
2156B LYS* 3.7 12.1 - - + +
2157B TYR 3.2 0.4 - - - -
2158B PRO* 1.3 77.3 - - + +
2160B LEU* 1.3 58.0 + - - +
2162B GLN* 3.7 4.7 - - - +
2163B ARG* 3.0 29.1 + - - +
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Residues in contact with LEU2160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.9 26.5 - - - +
38A VAL* 4.0 16.2 - - + -
2002B VAL* 3.8 11.0 - - + +
2005B GLU* 3.9 24.0 - - + +
2006B LEU* 4.0 33.0 - - + +
2009B THR* 4.2 14.6 - - - +
2153B ARG* 4.5 3.1 - - - +
2156B LYS* 3.3 24.1 + - + +
2157B TYR* 3.2 7.5 + - - +
2159B VAL* 1.3 80.6 - - - +
2161B PHE* 1.3 63.6 + - + +
2163B ARG* 3.4 1.1 + - - -
2164B ILE* 3.0 34.1 + - + +
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Residues in contact with PHE2161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006B LEU* 3.9 27.8 - - + -
2056B PHE* 4.8 0.2 - + - -
2085B LEU* 3.8 30.1 - - + -
2089B PHE* 3.5 38.1 - + - -
2157B TYR* 2.9 35.0 + + + +
2158B PRO 4.1 2.2 - - - +
2160B LEU* 1.3 77.6 - - + +
2162B GLN* 1.3 60.8 + - - +
2164B ILE* 3.3 8.9 + - + +
2165B LEU* 3.0 28.2 + - - +
2178B LEU* 4.7 6.8 - - + +
2181B SER* 3.6 26.5 - - - +
2182B LEU* 4.5 12.1 - - + -
2185B VAL* 3.9 24.7 - - + -
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Residues in contact with GLN2162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2158B PRO 3.0 20.9 + - - +
2159B VAL* 3.7 5.5 - - - +
2161B PHE* 1.3 78.6 - - - +
2163B ARG* 1.3 67.3 + - - +
2165B LEU* 3.4 7.7 + - + +
2166B GLN* 3.1 31.5 + - - +
2182B LEU* 3.6 29.2 - - + -
2186B LYS* 5.6 2.2 - - - +
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Residues in contact with ARG2163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.4 21.7 + - - -
35A VAL* 2.8 34.1 + - - +
36A PRO 3.7 0.4 - - - -
37A THR* 2.9 42.0 + - + +
1998B LYS* 4.0 9.5 - - - +
2002B VAL* 3.9 16.9 - - + +
2159B VAL 3.0 17.8 + - - +
2160B LEU 3.8 4.0 - - - +
2162B GLN* 1.3 82.0 + - - +
2164B ILE* 1.3 64.4 + - - +
2166B GLN* 3.4 10.5 - - - +
2167B CYS* 3.0 24.6 + - - -
3342B SO4 3.1 42.5 + - - +
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Residues in contact with ILE2164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1999B ARG* 4.4 8.7 - - + +
2002B VAL* 3.5 24.2 - - + +
2003B ILE* 4.1 30.5 - - + -
2006B LEU* 4.4 24.2 - - + -
2081B ILE* 4.4 11.7 - - + -
2085B LEU* 4.8 2.5 - - + -
2160B LEU 3.0 25.7 + - - +
2161B PHE* 3.7 11.9 - - + +
2162B GLN 3.3 0.4 - - - -
2163B ARG* 1.3 75.7 - - - +
2165B LEU* 1.3 58.3 - - - +
2167B CYS* 3.1 7.6 + - - +
2168B THR* 2.7 35.8 + - - +
2178B LEU* 3.8 21.5 - - + -
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Residues in contact with LEU2165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2161B PHE 3.0 13.0 + - - +
2162B GLN* 3.5 10.8 - - + +
2163B ARG 3.3 0.2 - - - -
2164B ILE* 1.3 75.7 - - - +
2166B GLN* 1.3 60.0 + - + +
2168B THR* 2.9 29.3 + - - +
2175B GLN* 3.4 43.3 - - + +
2178B LEU* 3.7 16.3 - - + +
2179B ALA* 4.0 25.6 - - + -
2182B LEU* 4.6 15.0 - - + -
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Residues in contact with GLN2166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998B LYS* 5.8 1.1 - - - -
2162B GLN* 3.1 23.4 + - - +
2163B ARG* 3.4 22.8 - - + +
2165B LEU* 1.3 80.3 - - + +
2167B CYS* 1.3 61.7 + - - +
2168B THR 3.3 2.8 + - - +
2169B LYS* 4.9 5.4 - - - +
3342B SO4 3.2 37.9 + - - -
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Residues in contact with CYS2167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1995B ASP* 4.3 7.9 - - - +
1998B LYS* 3.8 42.0 - - - -
1999B ARG* 3.6 32.2 - - + +
2002B VAL* 4.2 12.1 - - + -
2163B ARG* 3.0 25.6 + - - +
2164B ILE* 3.1 7.5 + - - +
2166B GLN* 1.3 80.5 - - - +
2168B THR* 1.3 59.4 + - - +
2169B LYS* 3.7 11.6 + - - +
3342B SO4 4.8 0.2 - - - -
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Residues in contact with THR2168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1999B ARG* 2.8 26.1 + - - +
2164B ILE 2.7 17.8 + - - -
2165B LEU 2.9 17.0 + - - +
2166B GLN 4.7 1.7 - - - +
2167B CYS* 1.3 75.3 - - - +
2169B LYS* 1.3 60.0 - - - +
2170B ASP 5.1 0.2 - - - +
2171B ASN* 4.3 13.0 - - + -
2174B GLU* 3.7 27.4 - - + -
2175B GLN* 2.8 31.0 + - + +
2178B LEU* 3.5 13.9 - - - +
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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