Contacts of the strand formed by residues 698 - 704 (chain A) in PDB entry 6RUT
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 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A LYS* 5.2 13.0 - - - -
316A PHE* 6.6 0.2 - - + -
627A VAL* 3.7 33.0 - - + -
628A GLY* 3.7 22.0 - - - -
695A LEU 3.6 14.8 + - - +
696A THR 3.4 3.8 - - - +
697A THR* 1.3 75.4 - - - +
699A LYS* 1.3 66.9 + - - +
700A GLU* 3.4 22.4 - - - -
701A VAL* 3.4 30.5 - - + -
712A TYR* 3.8 18.6 - + - -
713A ILE 4.0 5.4 - - - -
714A PHE* 3.7 19.8 - + + -
718A LEU* 3.8 6.1 - - - +
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Residues in contact with LYS 699 (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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31A LYS* 5.1 9.7 + - - +
697A THR 3.2 1.0 + - - -
698A PHE* 1.3 80.8 - - - +
700A GLU* 1.3 67.0 + - + +
713A ILE* 2.7 22.4 + - + +
715A ASP* 4.1 22.9 - - + +
718A LEU* 4.0 18.6 - - + -
776A LEU* 4.1 22.8 + - + +
777A THR* 2.8 34.2 + - - +
778A GLY* 4.2 3.0 - - - +
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Residues in contact with GLU 700 (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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69A GLN* 2.7 32.0 + - - +
698A PHE* 3.4 11.4 - - - -
699A LYS* 1.3 88.6 - - + +
701A VAL* 1.3 66.7 + - - +
702A THR* 3.6 20.6 - - - +
713A ILE* 2.8 45.6 + - + +
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Residues in contact with VAL 701 (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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628A GLY* 3.7 14.1 - - - +
629A LEU 4.1 3.8 - - - +
630A LYS* 3.6 41.6 - - + +
698A PHE* 3.4 22.0 - - + -
700A GLU* 1.3 79.0 - - - +
702A THR* 1.3 75.1 + - - +
710A TRP* 4.4 0.7 - - + -
711A SER 3.4 2.2 - - - -
712A TYR* 3.4 39.7 - - + -
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Residues in contact with THR 702 (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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630A LYS* 4.4 6.1 - - - +
700A GLU* 3.6 25.6 - - + +
701A VAL* 1.3 77.9 - - - +
703A TYR* 1.3 62.1 + - - +
710A TRP* 3.2 12.0 - - - +
711A SER* 2.8 48.4 + - - +
713A ILE* 4.5 7.1 - - + +
779A VAL 5.9 2.7 - - - +
781A PRO* 5.9 9.0 - - + -
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Residues in contact with TYR 703 (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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630A LYS* 4.0 21.9 + - - +
631A ALA 4.5 0.9 - - - -
632A GLY* 3.5 22.9 - - - -
633A ILE 2.8 28.4 + - - -
702A THR* 1.3 76.5 - - - +
704A ASN* 1.3 59.9 + - - +
705A GLN* 3.8 32.4 + - + +
708A GLY* 3.2 29.3 - - - -
709A LEU 3.4 8.1 - - - -
710A TRP* 3.2 52.0 - + + +
742A ARG* 2.8 21.0 + - - -
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Residues in contact with ASN 704 (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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703A TYR* 1.3 72.3 - - - +
705A GLN* 1.3 54.3 + - - +
706A GLU* 3.0 29.3 + - - +
707A SER* 3.3 25.8 + - - -
708A GLY* 2.7 36.0 + - - -
709A LEU* 2.8 15.2 + - + +
781A PRO* 4.5 18.3 + - + +
783A SER 4.1 18.6 + - - -
784A GLU* 4.5 5.1 - - - +
804A ASN* 6.0 1.2 - - - +
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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