Contacts of the helix formed by residues 696 - 702 (chain B) in PDB entry 1SER
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 GLU 696 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B ARG* 1.3 72.4 - - - +
697B LYS* 1.3 64.2 + - - +
699B PHE* 2.9 16.9 + - - +
700B LEU* 2.9 29.4 + - + +
705B PHE* 3.7 15.3 - - + -
709B ARG* 2.8 33.5 + - - -
719B ASP 4.1 2.5 + - - +
721B TYR* 3.7 27.2 + - + +
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Residues in contact with LYS 697 (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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695B ARG* 2.9 7.7 + - + +
696B GLU* 1.3 77.5 - - - +
698B ALA* 1.3 58.6 + - - +
700B LEU* 3.0 18.3 + - + +
701B GLY* 2.9 26.7 + - - -
732B ALA* 5.9 1.8 - - - +
735B SER* 3.5 29.9 + - - -
859B ARG 4.6 4.2 + - - -
860B ALA* 4.1 17.6 + - - +
861B ASN* 5.9 0.2 - - - +
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Residues in contact with ALA 698 (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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153A VAL* 4.4 7.2 - - + +
694B ALA* 4.0 12.1 - - + -
695B ARG* 3.0 12.1 + - - +
697B LYS* 1.3 78.4 - - - +
699B PHE* 1.3 61.4 + - - +
701B GLY* 3.2 10.7 + - - +
702B THR* 3.4 17.3 + - - +
728B VAL* 3.8 33.4 - - + +
732B ALA* 4.1 17.9 - - + -
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Residues in contact with PHE 699 (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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694B ALA* 3.6 22.2 - - + -
695B ARG 3.4 16.4 - - - -
696B GLU* 2.9 10.0 + - - +
698B ALA* 1.3 75.7 - - - +
700B LEU* 1.3 63.6 + - - +
702B THR* 3.2 7.1 + - - -
704B HIS* 3.1 24.4 + + + -
705B PHE* 3.0 52.3 + + + +
712B VAL* 3.9 19.5 - - + -
721B TYR* 3.5 32.3 - + + -
722B LEU 4.0 0.4 - - - -
723B THR* 3.6 34.8 - - + -
724B GLY 5.2 0.4 - - - -
728B VAL* 4.0 14.6 - - + -
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Residues in contact with LEU 700 (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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599B LEU* 4.3 29.2 - - + +
696B GLU* 2.9 39.0 + - + +
697B LYS* 3.2 16.4 - - + +
699B PHE* 1.3 78.0 - - - +
701B GLY* 1.3 57.1 + - - +
703B GLY 3.4 4.2 + - - -
705B PHE* 3.7 33.1 - - + +
706B PRO* 4.3 3.4 - - + -
709B ARG* 5.4 3.4 - - - +
859B ARG* 3.1 28.7 + - - +
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Residues in contact with GLY 701 (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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697B LYS* 2.9 14.3 + - - -
698B ALA* 3.2 6.5 + - - -
700B LEU* 1.3 76.8 - - - +
702B THR* 1.3 56.8 + - - +
731B ASN* 3.1 16.4 - - - +
856B GLN* 3.4 23.4 - - - +
859B ARG* 3.8 16.3 - - - +
860B ALA* 4.0 14.5 - - - +
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Residues in contact with THR 702 (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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698B ALA 3.4 7.8 + - - +
699B PHE* 3.2 11.6 + - - -
701B GLY* 1.3 75.2 - - - +
703B GLY* 1.3 57.9 + - - +
704B HIS* 2.7 31.3 + - - +
727B GLU* 3.8 18.3 - - - +
728B VAL* 3.8 24.3 - - - +
731B ASN* 3.3 30.5 - - + +
852B LEU* 5.1 2.6 - - - +
855B TRP* 4.0 8.1 - - - -
856B GLN* 2.9 24.5 - - - +
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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