Contacts of the helix formed by residues 1216 - 1221 (chain A) in PDB entry 5C51
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 GLU1216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PRO* 4.3 26.5 - - + +
123A VAL* 6.0 2.1 - - - +
924A ARG* 5.9 1.0 + - - -
1215A GLY* 1.3 77.2 - - - +
1217A ALA* 1.3 63.3 - - - +
1218A LEU 3.3 2.5 - - - -
1219A ASP* 3.3 35.7 + - - +
1220A ILE* 4.8 3.3 - - - +
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Residues in contact with ALA1217 (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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1214A GLN* 3.3 12.0 + - - +
1216A GLU* 1.3 76.4 - - - +
1218A LEU* 1.3 55.8 + - - +
1219A ASP 3.1 5.6 - - - -
1220A ILE* 3.2 33.4 - - + +
1221A TYR* 3.4 8.9 - - + +
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Residues in contact with LEU1218 (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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1147A TYR* 4.6 14.3 - - + +
1150A ALA* 3.9 8.7 - - + -
1151A LEU* 3.7 41.7 - - + +
1154A GLN* 3.7 24.7 - - + +
1183A VAL* 5.7 0.2 - - + -
1214A GLN* 3.1 27.4 + - + +
1215A GLY 3.3 23.3 - - - +
1217A ALA* 1.3 74.3 - - - +
1219A ASP* 1.3 80.4 + - - +
1220A ILE 3.0 10.3 + - - -
1221A TYR* 3.5 30.7 + - + +
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Residues in contact with ASP1219 (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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123A VAL* 4.9 22.1 - - + +
125A LEU* 5.8 8.5 - - + +
1151A LEU* 4.8 10.8 - - - +
1154A GLN* 4.8 9.5 - - - +
1179A PHE* 5.3 7.8 - - - -
1215A GLY 3.5 2.4 - - - +
1216A GLU* 3.3 36.8 - - - +
1217A ALA 3.1 1.8 - - - -
1218A LEU* 1.3 104.0 - - - +
1220A ILE* 1.3 62.1 + - - +
1221A TYR 3.7 1.3 - - - -
1222A GLN* 4.8 5.3 + - - -
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Residues in contact with ILE1220 (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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1216A GLU 4.8 3.8 - - - +
1217A ALA* 3.2 27.1 - - + +
1218A LEU 3.0 1.2 - - - -
1219A ASP* 1.3 83.7 - - - +
1221A TYR* 1.3 94.4 + - + +
1222A GLN* 2.9 21.5 + - - +
1227A THR* 5.7 0.5 - - - -
1228A LYS 5.9 0.2 + - - -
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Residues in contact with TYR1221 (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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1147A TYR* 3.7 43.9 - + + -
1148A ARG* 4.7 7.2 - - + -
1151A LEU* 3.3 23.7 - - - +
1217A ALA* 3.4 18.5 + - + +
1218A LEU* 3.5 18.3 + - - +
1219A ASP 5.3 0.7 - - - -
1220A ILE* 1.3 104.0 - - + +
1222A GLN* 1.3 66.6 + - - +
1227A THR* 4.2 15.3 - - + -
1228A LYS* 3.7 42.7 - - + -
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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