Contacts of the helix formed by residues 220 - 227 (chain A) in PDB entry 5TQB
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 LYS 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A TYR* 5.6 5.8 - - + +
215A PRO* 5.7 7.9 - - + +
219A GLY* 1.3 76.9 - - - +
221A GLU* 1.3 66.9 + - - +
222A LEU 3.3 3.1 - - - -
223A VAL* 3.3 27.5 + - + +
224A LYS* 3.8 17.5 - - - +
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Residues in contact with GLU 221 (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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160A GLY* 3.3 31.9 - - - +
161A ASP* 4.4 7.2 - - + +
164A ALA* 3.6 28.8 - - + +
218A ASP 5.1 1.3 + - - +
219A GLY* 3.7 1.2 - - - -
220A LYS* 1.3 81.4 - - - +
222A LEU* 1.3 62.6 + - - +
224A LYS* 3.0 31.3 + - - +
225A GLY 3.6 2.9 + - - -
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Residues in contact with LEU 222 (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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158A VAL* 3.8 23.8 - - + +
160A GLY 4.4 2.1 + - - +
163A VAL* 3.5 33.0 - - + +
211A ILE* 5.1 6.3 - - + -
213A TYR* 3.8 35.4 - - + -
218A ASP* 3.6 37.6 + - + +
219A GLY 4.5 2.9 - - - +
221A GLU* 1.3 79.2 - - - +
223A VAL* 1.3 86.0 + - + +
225A GLY* 3.1 3.3 + - - -
226A PHE* 3.1 38.9 + - + -
234A THR* 5.2 1.3 - - - +
258A THR* 5.2 0.9 - - + -
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Residues in contact with VAL 223 (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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213A TYR* 3.4 35.9 - - + +
220A LYS* 3.5 17.0 - - + +
221A GLU 3.2 0.6 - - - -
222A LEU* 1.3 83.6 - - + +
224A LYS* 1.3 67.5 + - + +
226A PHE* 4.5 4.5 - - - +
227A ARG* 2.9 34.8 + - + +
234A THR* 3.5 34.8 - - + +
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Residues in contact with LYS 224 (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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164A ALA* 3.9 7.6 - - + +
220A LYS* 3.8 19.7 - - - +
221A GLU* 3.0 25.3 + - - +
223A VAL* 1.3 85.5 - - + +
225A GLY* 1.3 55.9 + - - +
227A ARG* 4.4 4.1 - - + +
228A ASN* 2.8 23.9 + - - +
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Residues in contact with GLY 225 (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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163A VAL 3.6 12.3 - - - -
164A ALA 3.2 20.8 + - - -
165A LYS 4.1 5.6 - - - -
166A THR* 3.7 18.3 + - - -
169A ALA* 4.0 8.9 - - - +
221A GLU 3.6 1.8 + - - -
222A LEU 3.1 3.2 + - - -
223A VAL 3.1 0.6 - - - -
224A LYS* 1.3 79.4 - - - +
226A PHE* 1.3 61.0 + - - +
227A ARG 3.4 0.4 - - - -
228A ASN* 3.7 11.9 - - - +
229A ILE* 4.2 2.3 - - - +
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Residues in contact with PHE 226 (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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158A VAL* 5.1 3.6 - - + -
163A VAL* 4.3 14.8 - - + -
169A ALA* 4.0 24.7 - - + -
172A LEU* 4.5 14.6 - - + -
173A LEU* 3.6 35.0 - - + -
211A ILE* 4.1 39.0 - - + -
222A LEU* 3.1 34.4 + - + +
223A VAL* 4.1 4.9 - - - +
225A GLY* 1.3 73.2 - - - +
227A ARG* 1.3 66.5 + - - +
228A ASN 3.0 2.7 - - - -
229A ILE* 2.9 26.8 + - + +
232A VAL* 3.3 29.0 - - + +
234A THR* 5.3 8.7 - - - -
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Residues in contact with ARG 227 (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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203A HIS* 5.7 7.6 - - - +
223A VAL* 2.9 24.0 + - + +
224A LYS* 4.6 3.4 - - - +
225A GLY 3.4 0.2 - - - -
226A PHE* 1.3 78.9 - - - +
228A ASN* 1.3 67.4 + - - +
229A ILE 3.5 6.0 + - - +
232A VAL 5.9 1.1 - - - -
234A THR* 5.4 12.1 - - + +
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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