Contacts of the helix formed by residues 2187 - 2198 (chain A) in PDB entry 3ZBF
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 PRO2187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2053A LEU* 3.6 36.3 - - + -
2155A LEU* 5.3 1.6 - - + -
2185A ASN 3.5 7.4 - - - +
2186A CYS* 1.3 90.8 - - - +
2188A ASP* 1.3 66.1 + - - +
2189A ASP 3.3 0.2 - - - -
2190A LEU* 2.9 29.0 + - + +
2191A TRP* 3.1 9.5 + - - +
2218A PHE* 3.7 30.3 - - + -
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Residues in contact with ASP2188 (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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2186A CYS 3.5 4.4 + - - -
2187A PRO* 1.3 71.9 - - - +
2189A ASP* 1.3 62.2 + - - +
2191A TRP* 3.2 11.6 + - - +
2192A ASN* 2.9 61.4 + - - +
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Residues in contact with ASP2189 (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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2187A PRO* 3.3 0.8 - - - +
2188A ASP* 1.3 83.2 - - - +
2190A LEU* 1.3 62.5 + - - +
2192A ASN* 3.6 9.7 + - - +
2193A LEU* 3.2 20.6 + - - +
2214A GLN* 4.9 8.5 + - - +
2218A PHE* 3.6 37.1 - - + +
2221A PHE* 4.2 15.4 - - - +
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Residues in contact with LEU2190 (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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2053A LEU* 4.5 0.9 - - + -
2057A VAL* 4.1 15.7 - - + -
2060A CYS* 6.2 1.1 - - - -
2151A ILE* 5.5 0.8 - - + +
2155A LEU* 4.2 22.2 - - + -
2186A CYS* 4.0 7.9 - - - -
2187A PRO* 2.9 27.3 + - + +
2189A ASP* 1.3 76.5 - - - +
2191A TRP* 1.3 66.6 + - - +
2193A LEU* 3.2 10.4 + - + +
2194A MET* 3.1 30.8 + - + +
2214A GLN 6.2 0.2 - - - -
2215A LEU* 4.2 24.2 - - + -
2218A PHE* 3.9 43.7 - - + -
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Residues in contact with TRP2191 (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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2152A TRP* 4.3 0.7 - + - -
2179A ARG* 6.0 1.3 - - + -
2180A LEU 3.4 23.8 - - - -
2181A GLU 3.7 2.5 - - - -
2182A PRO* 3.4 53.5 - - + +
2183A PRO* 3.8 8.1 - - + -
2186A CYS* 3.9 8.9 - - + +
2187A PRO 3.1 11.6 + - - +
2188A ASP* 3.2 14.6 + - - +
2190A LEU* 1.3 74.5 - - - +
2192A ASN* 1.3 75.0 + - - +
2194A MET* 3.3 26.0 + - + +
2195A THR* 3.0 46.2 + - - -
2198A TRP* 3.8 25.6 - + - -
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Residues in contact with ASN2192 (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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2188A ASP* 2.9 46.6 + - - +
2189A ASP* 3.7 11.6 - - - +
2191A TRP* 1.3 85.6 - - - +
2193A LEU* 1.3 62.2 + - - +
2195A THR* 3.8 5.6 - - - +
2196A GLN* 3.0 26.3 + - - +
2214A GLN* 6.0 2.2 - - - +
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Residues in contact with LEU2193 (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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2151A ILE* 4.4 14.6 - - + -
2189A ASP 3.2 11.9 + - - +
2190A LEU* 3.5 13.0 - - + +
2191A TRP 3.2 0.6 - - - -
2192A ASN* 1.3 79.8 - - - +
2194A MET* 1.3 63.0 + - - +
2196A GLN* 3.2 8.3 + - + +
2197A CYS* 3.0 26.7 + - - -
2206A PRO* 4.7 9.6 - - + -
2211A ILE* 4.3 26.9 - - + +
2214A GLN* 3.9 39.0 - - + +
2215A LEU* 3.7 35.7 - - + -
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Residues in contact with MET2194 (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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2148A GLY 3.8 4.9 - - - +
2151A ILE* 3.5 27.1 - - + -
2152A TRP* 3.8 38.8 - - - -
2155A LEU* 5.3 4.5 - - + -
2183A PRO* 4.0 6.5 - - + -
2186A CYS* 3.7 20.4 - - - -
2190A LEU* 3.1 19.8 + - + +
2191A TRP* 3.3 27.8 + - + +
2193A LEU* 1.3 75.5 - - - +
2195A THR* 1.3 60.2 + - - +
2197A CYS* 2.7 32.2 + - - +
2198A TRP* 3.1 34.7 + - + -
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Residues in contact with THR2195 (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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2191A TRP* 3.0 47.6 + - - -
2192A ASN* 3.8 7.9 - - - -
2194A MET* 1.3 76.0 - - - +
2196A GLN* 1.3 65.1 + - - +
2198A TRP* 3.3 24.1 + - - +
2199A ALA* 3.5 9.2 + - - -
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Residues in contact with GLN2196 (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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2192A ASN 3.0 19.3 + - - +
2193A LEU* 3.4 7.9 - - + +
2194A MET 3.0 0.2 - - - -
2195A THR* 1.3 77.6 - - - +
2197A CYS* 1.3 65.7 + - - +
2199A ALA* 3.3 16.0 + - - +
2204A GLN* 3.2 26.2 + - - +
2205A ARG* 3.6 6.8 - - - -
2206A PRO* 3.2 34.7 - - + +
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Residues in contact with CYS2197 (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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2144A VAL* 3.5 26.7 - - - +
2145A TRP* 3.6 15.4 + - - -
2147A PHE* 4.8 3.4 - - - -
2148A GLY* 3.9 19.7 - - - -
2151A ILE* 5.2 1.1 - - - -
2193A LEU* 3.0 23.4 + - - -
2194A MET* 2.7 17.7 + - - +
2196A GLN* 1.3 72.1 - - - +
2198A TRP* 1.3 56.8 + - + +
2199A ALA 3.4 0.2 - - - -
2205A ARG* 3.0 19.6 - - - +
2206A PRO* 4.0 5.8 - - - -
2211A ILE* 3.6 31.4 - - - -
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Residues in contact with TRP2198 (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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2145A TRP* 3.2 46.8 + + + -
2148A GLY* 3.1 25.4 - - - -
2149A ILE* 3.1 29.2 - - + +
2152A TRP* 4.0 7.4 - + + -
2162A TYR* 5.9 0.7 - - - -
2179A ARG* 2.3 59.4 + - + +
2180A LEU* 3.9 32.5 - - + -
2191A TRP* 3.8 24.5 - + - -
2194A MET* 3.1 40.5 + - + -
2195A THR* 3.3 16.0 + - - +
2196A GLN 3.2 0.4 - - - -
2197A CYS* 1.3 82.8 - - + +
2199A ALA* 1.3 58.5 + - - +
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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