Contacts of the helix formed by residues 368 - 372 (chain B) in PDB entry 6PSI
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 ASP 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B GLY* 4.4 2.1 - - - -
141B ALA* 3.3 24.8 + - + +
142B LEU* 3.0 33.9 + - - +
143B GLY 5.6 2.9 - - - +
144B VAL* 6.0 2.2 - - + -
364B THR* 3.0 37.6 + - + +
366B ASP 3.1 4.4 - - - +
367B LEU* 1.4 76.8 - - - +
369B GLU* 1.3 55.6 + - - +
370B ALA 3.0 12.0 + - - -
371B VAL* 3.1 34.0 + - - +
372B GLN* 4.0 0.7 + - - +
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 5.3 4.0 + - - +
145B ASP* 3.4 26.5 - - + +
201B PRO* 4.2 3.8 - - + -
202B GLY 3.0 24.1 + - - -
203B ASN* 2.8 26.0 + - - +
364B THR 3.7 0.6 + - - -
367B LEU* 3.1 29.4 + - + +
368B ASP* 1.3 75.8 - - - +
370B ALA* 1.4 52.7 + - - +
371B VAL 3.0 1.8 - - - -
372B GLN* 2.7 46.5 + - + +
160C ARG* 2.8 44.1 + - - -
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LYS 3.6 4.9 - - - +
137B THR* 3.0 22.3 + - - -
203B ASN* 3.1 20.2 + - - +
204B ALA* 4.0 11.2 - - - +
205B LEU* 6.4 0.2 - - + -
361B ILE 5.3 0.9 - - - +
362B GLY* 4.3 5.3 - - - -
363B GLU 3.8 8.3 - - - +
364B THR 3.4 35.2 + - - +
365B VAL* 3.7 16.2 - - + -
368B ASP 3.0 0.8 + - - -
369B GLU* 1.4 75.9 - - - +
371B VAL* 1.3 57.7 + - - +
372B GLN 3.5 0.2 - - - -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LYS* 2.7 44.3 + - - +
137B THR* 4.3 5.4 - - + -
138B TYR* 3.0 36.9 - - + +
139B ASN 4.0 2.2 - - - +
140B GLY* 3.5 23.1 - - - -
141B ALA 4.1 0.2 - - - +
142B LEU* 3.4 3.6 - - + +
321B LEU* 5.6 1.8 - - + -
363B GLU* 4.7 0.9 - - - -
364B THR* 3.8 24.9 - - - +
368B ASP* 3.1 35.9 + - - +
369B GLU 3.0 0.6 - - - -
370B ALA* 1.3 78.8 - - - +
372B GLN* 1.3 51.1 + - - +
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Residues in contact with GLN 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU* 2.8 31.9 + - - +
136B LYS* 3.9 10.3 - - - +
142B LEU* 3.3 46.3 - - + +
143B GLY 3.7 7.8 - - - +
145B ASP* 3.6 21.1 - - - +
201B PRO* 4.4 1.0 - - - +
204B ALA* 3.6 11.3 - - - +
368B ASP 4.5 1.6 - - - +
369B GLU* 2.7 38.1 + - - +
370B ALA 3.5 0.8 + - - -
371B VAL* 1.3 79.6 - - - +
373B ARG* 1.3 72.4 + - - +
374B ALA 3.3 22.6 + - - +
375B LEU* 4.2 0.6 - - - +
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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