Contacts of the helix formed by residues 295 - 304 (chain A) in PDB entry 1YI3
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 LEU 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A VAL* 5.5 2.7 - - + +
294A LEU* 1.3 74.8 - - - +
296A PRO* 1.3 74.3 - - + +
297A GLN* 4.4 3.4 - - + +
298A GLU* 3.1 37.9 + - + +
299A THR* 2.7 29.1 + - - -
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Residues in contact with PRO 296 (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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150A GLN* 4.0 24.9 - - + +
179A ARG 3.2 16.4 - - - +
180A GLY* 3.3 21.6 - - - +
181A GLU* 3.9 16.6 - - + +
294A LEU 4.4 1.8 - - - +
295A LEU* 1.3 91.8 - - + +
297A GLN* 1.3 61.3 + - - +
299A THR* 3.2 8.4 + - - +
300A ALA 3.0 18.0 + - - -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASN 3.5 24.6 + - - +
179A ARG* 3.4 17.6 + - - +
295A LEU* 3.3 4.3 - - + +
296A PRO* 1.3 76.4 - - - +
298A GLU* 1.3 67.8 + - + +
300A ALA* 3.1 2.4 + - - +
301A GLU* 3.0 38.0 + - - +
305A HIS* 3.7 19.4 - - - -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL 5.0 0.3 - - - +
294A LEU* 3.4 25.1 - - + +
295A LEU* 3.1 50.5 + - + +
297A GLN* 1.3 77.8 - - + +
299A THR* 1.3 64.7 + - - +
301A GLU* 3.1 14.1 + - - +
302A ILE* 2.9 35.0 + - + +
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Residues in contact with THR 299 (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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143A LEU* 3.4 31.2 - - + -
146A SER* 2.6 34.4 + - - +
147A PHE* 3.9 11.9 - - + -
180A GLY 4.7 2.9 - - - +
294A LEU* 3.6 14.2 - - + +
295A LEU 2.7 17.9 + - - -
296A PRO* 3.3 10.3 - - - +
298A GLU* 1.3 77.7 - - - +
300A ALA* 1.3 56.2 + - - +
303A HIS* 2.9 33.9 + - + +
304A LEU* 3.6 3.6 + - + +
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Residues in contact with ALA 300 (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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178A ASN 3.6 24.2 - - - +
180A GLY* 3.7 18.8 - - - +
296A PRO 3.0 6.5 + - - +
297A GLN* 3.1 11.2 + - - +
299A THR* 1.3 77.6 - - - +
301A GLU* 1.3 58.3 + - - +
304A LEU* 2.7 38.4 + - + +
305A HIS* 2.8 23.3 + - + +
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Residues in contact with GLU 301 (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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297A GLN* 3.0 38.2 + - - +
298A GLU* 3.6 16.2 - - - +
300A ALA* 1.3 78.5 - - - +
302A ILE* 1.3 63.0 + - + +
305A HIS* 3.7 30.3 - - + +
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Residues in contact with ILE 302 (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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142A GLU* 3.8 8.5 - - - +
294A LEU* 3.8 27.4 - - + -
298A GLU* 2.9 21.1 + - + +
301A GLU* 1.3 83.0 - - + +
303A HIS* 1.3 83.9 + - + +
305A HIS* 5.4 1.9 - - - +
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Residues in contact with HIS 303 (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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136A ARG* 2.6 45.5 + - - +
140A GLN* 3.7 33.0 + - + -
142A GLU* 2.7 35.2 + - + +
143A LEU* 3.7 53.1 - - + +
294A LEU* 4.5 4.3 - - + -
299A THR* 2.9 16.9 + - + +
302A ILE* 1.3 93.3 + - + +
304A LEU* 1.3 55.3 - - + +
305A HIS* 4.0 1.3 - - - -
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Residues in contact with LEU 304 (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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132A PHE* 3.6 32.8 - - + -
136A ARG* 4.0 7.7 + - - +
147A PHE* 4.4 16.2 - - + -
175A ILE* 4.2 15.5 - - + -
177A LEU* 3.6 32.2 - - + +
180A GLY* 3.7 22.2 - - - -
299A THR* 3.9 5.2 - - + +
300A ALA* 2.7 35.1 + - - +
303A HIS* 1.3 86.0 - - + +
305A HIS* 1.3 66.6 + - - +
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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