Contacts of the helix formed by residues 718 - 723 (chain B) in PDB entry 4P3N
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 GLN 718 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B ASP* 5.2 3.3 - - - +
716B SER* 2.8 12.9 + - - -
717B LYS* 1.3 91.9 + - + +
719B ALA* 1.3 59.6 + - - +
720B GLU* 3.5 11.0 - - - +
721B GLU* 3.6 40.9 - - + +
722B GLU* 3.1 28.4 + - + +
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Residues in contact with ALA 719 (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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614B PHE* 3.6 32.3 - - + +
672B PHE* 4.1 5.4 - - + -
711B LEU* 3.4 33.8 - - + +
716B SER* 3.6 12.0 + - - +
717B LYS 3.8 2.8 + - - -
718B GLN* 1.3 72.3 - - - +
720B GLU* 1.3 75.4 + - - +
721B GLU 3.3 0.7 - - - -
722B GLU 3.3 0.3 + - - -
723B PHE* 3.0 21.7 + - - +
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Residues in contact with GLU 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B PRO* 5.7 0.3 - - - +
614B PHE 4.8 0.9 + - - -
671B ASN* 2.9 53.8 + - - +
672B PHE* 4.2 12.8 - - + -
690B THR* 4.0 21.1 - - + +
691B ARG* 3.6 25.4 + - + +
692B ASP* 4.7 15.3 - - + +
696B HIS* 2.9 32.6 + - - -
717B LYS 5.0 1.2 - - - +
718B GLN* 4.3 12.0 - - - +
719B ALA* 1.3 92.1 + - - +
721B GLU* 1.3 59.5 + - + +
723B PHE* 3.7 1.0 - - - +
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Residues in contact with GLU 721 (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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692B ASP* 4.6 11.9 - - + +
694B LYS* 5.9 8.6 - - - -
696B HIS* 4.9 3.1 - - - -
718B GLN* 3.6 42.2 + - + +
719B ALA 3.3 0.2 - - - -
720B GLU* 1.3 82.0 - - + +
722B GLU* 1.3 62.3 + - + +
723B PHE* 3.3 7.0 + - - +
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Residues in contact with GLU 722 (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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707B ARG* 2.5 34.9 + - - +
711B LEU* 4.3 10.2 - - + +
716B SER* 3.1 22.7 + - - -
717B LYS* 4.9 2.8 + - - +
718B GLN* 3.1 29.8 + - + +
719B ALA 3.3 3.9 + - - +
721B GLU* 1.3 77.2 - - + +
723B PHE* 1.3 58.8 + - - +
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Residues in contact with PHE 723 (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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672B PHE* 3.8 14.1 - + + -
688B ILE* 3.5 37.7 - - + -
696B HIS* 3.5 48.3 + + + +
699B ARG* 3.7 34.2 + - - -
704B THR* 3.9 14.1 - - + -
707B ARG* 3.2 53.0 + - + +
708B LEU* 3.7 22.0 - - + -
711B LEU* 3.8 13.7 - - + -
719B ALA 3.0 13.4 + - - +
720B GLU 3.7 2.0 - - - +
721B GLU 3.3 4.2 - - - +
722B GLU* 1.3 79.4 - - - +
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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