Contacts of the helix formed by residues 2182 - 2188 (chain A) in PDB entry 5DZZ
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 SER2182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2126A GLU* 3.2 13.0 - - - -
2169A GLN* 4.4 8.3 - - - -
2170A LYS* 3.8 18.9 - - - +
2172A PHE* 4.5 2.0 - - - -
2181A VAL* 1.3 76.2 - - - +
2183A TYR* 1.3 64.0 + - - +
2184A VAL* 3.7 8.2 + - - +
2185A GLN* 3.1 39.1 + - - +
2186A LEU* 3.4 21.7 + - - +
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Residues in contact with TYR2183 (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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2017A SER* 3.4 15.5 - - - -
2018A ILE* 3.0 37.9 + - + +
2048A LEU* 4.1 19.2 + - + +
2051A ALA* 3.6 27.3 - - + +
2052A GLN* 5.5 0.2 - - - +
2126A GLU* 2.9 20.6 + - + +
2127A ALA* 4.2 14.1 - - + -
2130A ALA* 3.9 15.5 - - + -
2131A SER* 4.9 1.8 - - - -
2172A PHE* 3.5 38.7 - + + -
2182A SER* 1.3 70.8 - - - +
2184A VAL* 1.3 61.5 + - - +
2186A LEU* 3.3 7.1 + - + +
2187A LYS* 3.0 56.8 + - + +
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Residues in contact with VAL2184 (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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2126A GLU* 6.0 2.2 - - + +
2130A ALA* 4.0 23.8 - - + -
2182A SER* 3.3 7.6 + - - +
2183A TYR* 1.3 76.5 - - + +
2185A GLN* 1.3 60.4 + - + +
2187A LYS* 3.1 11.7 + - + +
2188A GLU* 3.0 47.9 + - + +
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Residues in contact with GLN2185 (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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2170A LYS* 4.0 19.0 - - - +
2180A LYS 4.9 0.2 - - - +
2181A VAL* 3.6 19.1 - - + +
2182A SER* 3.1 38.1 + - - +
2184A VAL* 1.3 78.3 - - + +
2186A LEU* 1.3 62.0 + - - +
2188A GLU* 3.5 24.8 + - - +
2189A ARG* 3.7 19.8 + - - +
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Residues in contact with LEU2186 (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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2018A ILE* 3.8 12.1 - - + -
2048A LEU* 4.0 28.0 - - + -
2172A PHE* 4.3 12.8 - - + -
2173A VAL 4.2 9.9 - - - +
2175A PRO* 4.1 21.1 - - + -
2181A VAL* 3.9 25.6 - - + -
2182A SER 3.4 9.3 + - - +
2183A TYR* 3.3 10.2 + - + +
2184A VAL 3.2 0.4 - - - -
2185A GLN* 1.3 74.9 - - - +
2187A LYS* 1.3 60.8 + - - +
2188A GLU 3.2 0.4 - - - -
2189A ARG* 3.0 45.5 + - - +
2190A CYS* 3.2 15.2 - - - -
2201A LEU* 3.5 8.8 - - + +
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Residues in contact with LYS2187 (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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2015A ALA* 5.2 4.8 - - - +
2016A GLY 3.9 13.1 + - - +
2018A ILE* 4.1 5.6 - - + -
2130A ALA* 2.7 33.4 + - + +
2131A SER* 4.8 1.0 + - - +
2183A TYR* 3.0 47.1 + - + +
2184A VAL* 3.1 11.9 + - + +
2186A LEU* 1.3 71.8 - - - +
2188A GLU* 1.3 58.6 + - + +
2189A ARG 3.0 8.3 + - - -
2190A CYS* 3.3 24.7 + - - +
2199A LEU* 3.8 30.4 - - + +
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Residues in contact with GLU2188 (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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2184A VAL* 3.0 38.0 + - + +
2185A GLN* 3.7 19.3 - - - +
2186A LEU 3.2 0.4 - - - -
2187A LYS* 1.3 76.0 - - + +
2189A ARG* 1.3 55.9 + - - +
2190A CYS 3.4 3.4 + - - +
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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