Contacts of the helix formed by residues 694 - 698 (chain A) in PDB entry 1SIW
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 PHE 694 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A VAL* 5.8 2.7 - - + +
650A GLU* 4.3 9.4 - - + -
651A ARG* 3.8 43.3 - - + -
657A SER* 4.2 16.4 - - - -
660A GLN* 3.5 14.4 - - + +
661A LEU* 4.5 9.6 - - + +
687A LEU* 3.9 30.5 - - + -
693A ARG* 1.3 75.5 - - - +
695A ALA* 1.3 65.5 + - - +
696A ALA* 3.1 11.2 + - + +
697A GLU* 3.1 36.1 + - + +
698A GLN* 4.4 1.4 + - - +
849A THR* 5.0 9.6 - - + -
869A TRP* 4.2 14.6 - + - -
882A ALA* 5.9 0.7 - - + -
883A PRO* 4.2 21.3 - - + -
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Residues in contact with ALA 695 (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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659A PRO* 3.5 26.5 - - + +
660A GLN 3.0 11.5 + - - +
661A LEU 3.8 9.4 - - - +
662A GLY* 4.0 3.1 - - - +
693A ARG 3.4 3.0 + - - -
694A PHE* 1.3 71.2 - - - +
696A ALA* 1.3 61.5 + - - +
698A GLN 3.1 23.5 + - - +
699A PRO* 3.4 3.8 - - - +
704A ASN* 3.5 39.5 - - + +
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Residues in contact with ALA 696 (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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613A ASN* 4.9 13.4 + - - +
643A ILE* 5.8 1.4 - - - +
647A VAL* 4.1 19.1 - - + +
650A GLU* 3.5 36.3 - - - +
657A SER* 5.6 0.4 - - - -
659A PRO 4.8 2.6 + - - -
660A GLN 4.8 0.6 + - - -
694A PHE* 3.1 8.1 - - + +
695A ALA* 1.3 79.6 - - - +
697A GLU* 1.3 60.7 + - - +
699A PRO* 3.4 13.8 - - - +
754A VAL* 3.7 13.2 - - - +
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Residues in contact with GLU 697 (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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647A VAL* 4.3 13.6 - - + +
651A ARG* 4.4 10.1 + - - +
693A ARG* 2.6 56.7 + - - +
694A PHE* 3.5 27.0 + - + +
695A ALA 3.1 1.2 - - - -
696A ALA* 1.3 77.9 - - - +
698A GLN* 1.3 62.1 + - + +
699A PRO* 3.5 1.1 - - - +
753A GLU* 3.7 21.0 - - - +
754A VAL* 3.4 3.7 - - - -
755A ASP* 3.1 27.5 + - - +
870A LYS* 3.4 29.0 + - - +
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Residues in contact with GLN 698 (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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693A ARG* 3.2 44.5 + - - +
694A PHE 4.4 1.5 + - - +
695A ALA 3.1 7.8 + - - -
697A GLU* 1.3 83.9 - - + +
699A PRO* 1.3 62.0 - - - +
700A GLU 3.1 6.5 + - - -
701A ASN* 3.4 32.6 + - + +
704A ASN* 2.9 20.6 + - - +
755A ASP* 3.0 33.2 + - + +
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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