Contacts of the helix formed by residues 269 - 277 (chain A) in PDB entry 3Q7I
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 GLY 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 4.5 1.8 - - - -
264A LEU* 3.2 23.9 + - - -
266A SER 2.9 12.6 + - - -
268A ILE* 1.3 75.6 - - - +
270A MET* 1.3 63.6 + - - +
271A SER 3.2 3.8 - - - -
272A ILE* 2.9 33.7 + - - +
273A ALA* 3.2 4.2 + - - +
281A PHE* 3.8 10.3 - - - -
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Residues in contact with MET 270 (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 VAL* 3.8 28.3 - - + -
120A LEU* 3.7 28.3 - - + -
121A VAL* 4.6 0.2 - - - +
142A ASN* 5.7 0.2 - - - +
195A ILE* 3.8 23.1 - - + -
232A VAL* 4.0 10.1 - - + -
234A ILE* 3.6 21.1 - - + -
252A TYR* 3.6 42.2 - - + -
267A SER* 2.9 16.0 + - - +
268A ILE 3.1 1.0 - - - -
269A GLY* 1.3 76.4 - - - +
271A SER* 1.3 59.5 + - - +
273A ALA* 3.0 7.5 + - - +
274A PHE* 2.9 35.7 + - + -
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Residues in contact with SER 271 (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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140A ILE* 4.9 0.4 - - - -
142A ASN* 4.0 20.2 + - - -
152A PRO* 3.3 27.7 - - - +
156A VAL* 3.9 5.5 - - - +
169A VAL* 3.9 22.3 - - - +
171A PHE* 3.5 11.2 - - - -
195A ILE* 4.3 7.2 - - - -
268A ILE 4.1 2.5 + - - -
270A MET* 1.3 80.5 - - - +
272A ILE* 1.3 60.1 + - - +
274A PHE* 3.4 13.5 + - - +
275A ALA* 3.3 20.1 + - - +
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Residues in contact with ILE 272 (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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152A PRO* 3.8 32.8 - - + +
155A VAL* 3.8 33.0 - - + -
156A VAL* 3.8 10.8 - - + +
264A LEU* 4.1 22.7 - - + +
269A GLY* 2.9 22.8 + - - +
271A SER* 1.3 76.9 + - - +
273A ALA* 1.3 62.2 + - - +
275A ALA* 2.9 5.9 + - - +
276A ILE* 2.9 47.5 + - + +
281A PHE* 3.9 15.5 - - + -
284A LEU* 4.3 2.2 - - + -
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Residues in contact with ALA 273 (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 VAL* 4.9 0.2 - - + -
121A VAL* 3.8 17.3 - - + +
165A THR* 4.0 0.5 - - - +
269A GLY 3.2 6.0 + - - +
270A MET* 3.0 12.6 + - - +
272A ILE* 1.3 79.2 - - - +
274A PHE* 1.3 59.1 + - - +
277A GLY* 2.8 38.4 + - - -
278A TYR* 3.8 33.7 - - + -
281A PHE* 4.1 13.2 - - + -
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Residues in contact with PHE 274 (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 LEU* 3.9 22.7 - - + -
121A VAL* 3.8 26.7 - - + -
124A VAL* 3.8 27.1 - - + -
140A ILE* 3.9 31.0 - - + -
165A THR* 2.6 31.2 + - - +
167A LEU* 3.6 27.5 - - + +
169A VAL* 4.1 5.1 - - + +
193A LEU* 3.9 16.8 - - + -
195A ILE* 4.1 8.3 - - + -
270A MET* 2.9 47.9 + - - -
271A SER* 3.7 8.3 - - - +
272A ILE 3.2 0.4 - - - -
273A ALA* 1.3 77.7 - - - +
275A ALA* 1.3 51.5 + - - +
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Residues in contact with ALA 275 (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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156A VAL* 4.0 13.7 - - + -
163A HIS* 3.3 33.9 - - + +
164A CYS 3.0 23.4 + - - -
165A THR* 3.5 8.4 + - - -
167A LEU 5.1 3.3 - - - +
169A VAL* 4.0 15.5 - - + +
271A SER 3.3 10.0 + - - +
272A ILE 2.9 8.7 + - - +
274A PHE* 1.3 77.3 - - - +
276A ILE* 1.3 62.3 + - + +
277A GLY 3.6 0.4 - - - -
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Residues in contact with ILE 276 (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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155A VAL 5.5 0.9 - - - +
156A VAL* 5.4 1.6 - - - +
159A LEU* 3.7 40.6 - - + +
162A TYR* 3.7 13.5 - - + +
163A HIS* 3.7 25.8 - - + +
164A CYS* 3.1 13.7 - - - -
272A ILE* 2.9 39.3 + - + +
273A ALA* 4.6 0.2 - - - -
275A ALA* 1.3 77.9 - - + +
277A GLY* 1.3 67.4 + - - +
280A ASN* 3.0 52.4 + - + +
281A PHE* 3.9 2.2 - - - +
284A LEU* 5.3 1.3 - - + -
470A PRO* 4.7 0.4 - - + -
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Residues in contact with GLY 277 (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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121A VAL* 5.0 2.2 - - - -
164A CYS* 4.4 4.0 - - - -
165A THR* 3.7 13.1 - - - +
273A ALA* 2.8 24.2 + - - +
275A ALA 3.6 1.6 - - - -
276A ILE* 1.3 78.5 - - - +
278A TYR* 1.3 66.9 + - - -
279A ASP 3.3 3.1 - - - -
280A ASN 3.4 0.5 + - - -
281A PHE* 3.1 18.4 + - - +
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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