Contacts of the helix formed by residues 219 - 227 (chain A) in PDB entry 1RQD
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 SER 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.9 2.0 - - - +
117A ARG* 3.9 1.6 - - - -
138A ASP* 2.7 24.6 + - - -
139A LEU* 4.2 2.8 - - - +
142A CYS* 3.7 14.5 - - - -
214A ILE* 3.4 23.9 - - - +
216A ASN* 3.1 14.2 + - - -
218A GLU* 1.3 78.9 - - - +
220A VAL* 1.3 64.5 + - - +
221A TYR* 3.5 0.5 + - - -
222A TYR* 3.2 18.7 + - - +
223A TRP* 3.2 20.6 + - - -
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Residues in contact with VAL 220 (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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103A TYR* 4.1 11.2 - - - +
108A ILE* 4.6 5.8 - - + -
113A ARG* 3.6 31.2 - - + +
116A ILE* 4.2 7.6 - - + -
117A ARG* 3.6 20.6 - - + +
120A VAL* 3.7 23.7 - - + +
128A LEU* 4.1 3.6 - - + -
138A ASP* 3.0 23.5 + - - +
218A GLU 3.8 1.2 + - - -
219A SER* 1.3 72.2 - - - +
221A TYR* 1.3 79.1 + - + +
223A TRP* 3.3 7.6 + - - +
224A ALA* 2.9 22.5 + - - +
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Residues in contact with TYR 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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103A TYR* 2.9 29.6 + - - -
108A ILE* 4.4 0.7 - - + +
130A THR* 3.2 10.2 - - + +
134A GLY 2.7 29.6 + - - -
135A VAL* 3.6 18.6 - - + -
138A ASP* 2.8 39.4 + - + +
139A LEU* 4.7 5.2 - - + -
207A ILE* 3.8 20.5 - - + +
208A ALA* 5.4 0.3 - - - -
210A LEU* 6.2 0.2 - - + -
211A GLY* 3.6 15.7 - - - +
219A SER* 4.2 0.7 - - - +
220A VAL* 1.3 84.0 - - + +
222A TYR* 1.3 67.9 + - - +
224A ALA* 3.5 4.3 - - + +
225A GLN* 3.2 22.9 + - - +
231A VAL* 3.6 39.0 - - + -
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Residues in contact with TYR 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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211A GLY* 3.3 22.8 - - - +
212A LYS 5.0 1.1 - - - -
214A ILE* 3.8 2.7 - - + -
215A ASN* 4.0 26.6 + - - -
216A ASN 3.1 31.2 - - - +
217A PRO* 3.7 16.2 - - + -
219A SER* 3.2 14.1 + - - +
220A VAL 3.3 0.2 - - - -
221A TYR* 1.3 75.0 - - - +
223A TRP* 1.3 98.0 + + - +
225A GLN* 2.6 45.4 + - - +
226A LYS* 3.1 32.4 + - + +
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Residues in contact with TRP 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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117A ARG* 3.7 14.9 - - + +
120A VAL* 4.0 6.3 - - + -
121A GLN* 3.3 56.4 - - + +
217A PRO* 2.7 37.4 + - + -
219A SER 3.2 19.3 + - - -
220A VAL 3.3 7.7 + - - +
221A TYR 3.3 0.2 - - - -
222A TYR* 1.3 96.1 - + - +
224A ALA* 1.3 57.0 + - - +
226A LYS* 3.0 32.6 + - + +
227A ASN* 2.8 51.9 + - - -
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Residues in contact with ALA 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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120A VAL* 3.5 17.5 - - + +
128A LEU* 4.4 4.7 - - + -
220A VAL 2.9 14.8 + - - +
221A TYR* 3.5 15.3 - - - +
222A TYR 3.2 0.4 - - - -
223A TRP* 1.3 75.9 - - - +
225A GLN* 1.3 60.5 + - - +
227A ASN 3.4 0.7 + - - -
228A HIS 3.1 3.5 + - - -
229A ILE* 2.7 47.7 + - - +
231A VAL* 4.1 15.7 - - + -
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Residues in contact with GLN 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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208A ALA* 3.4 40.4 - - + +
212A LYS* 3.6 35.8 + - - +
221A TYR 3.2 10.3 + - - +
222A TYR* 2.6 44.5 + - - +
224A ALA* 1.3 76.4 - - - +
226A LYS* 1.3 84.5 + - - +
228A HIS* 3.0 21.9 + - - +
229A ILE 4.8 1.6 - - - +
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Residues in contact with LYS 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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222A TYR* 3.1 41.4 + - + +
223A TRP* 3.0 36.8 + - + +
225A GLN* 1.3 90.6 - - - +
227A ASN* 1.3 65.6 + - - +
228A HIS* 3.5 14.2 + - - -
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Residues in contact with ASN 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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92A ARG* 3.4 16.6 + - - -
93A PRO* 5.6 0.3 - - - +
120A VAL 2.7 27.7 + - - -
121A GLN* 2.9 19.8 + - - +
123A ASN* 3.0 29.5 + - - +
223A TRP* 2.8 30.5 + - - +
226A LYS* 1.3 84.5 + - - +
228A HIS* 1.3 72.7 + - - +
229A ILE* 3.3 9.9 + - + +
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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