Contacts of the strand formed by residues 693 - 700 (chain A) in PDB entry 3K72
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 CYS 693 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A ASN* 3.7 11.4 + - - +
635A ILE 3.3 0.7 - - - -
636A CYS* 2.0 52.5 - - - -
691A ALA* 4.2 15.2 - - - -
692A HIS* 1.3 76.2 + - - +
694A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 694 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A ASN* 3.8 4.0 - - - -
635A ILE 3.0 26.3 + - - +
683A ARG* 4.5 13.2 + - - -
685A ARG* 2.9 36.9 + - - -
692A HIS* 3.9 12.8 + - + +
693A CYS* 1.3 75.8 - - - +
695A ASN* 1.3 69.6 + - - +
696A PHE* 3.1 46.5 - - + -
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Residues in contact with ASN 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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609A ILE* 4.0 22.1 - - + +
632A GLN* 4.3 18.2 + - - +
633A SER 3.2 7.0 - - - +
634A ASN* 3.6 32.2 - - + +
694A GLU* 1.3 82.6 - - - +
696A PHE* 1.3 63.7 + - - +
697A ASN* 5.4 0.5 - - - +
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Residues in contact with PHE 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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632A GLN* 3.5 6.1 - - - +
633A SER* 2.9 24.0 + - - +
635A ILE* 5.0 8.3 - - + -
658A LEU* 5.4 13.0 - - + -
660A LEU* 3.7 26.0 - - + -
673A PHE* 4.1 20.2 - - + -
675A GLU* 5.8 5.6 - - + -
681A LEU* 3.9 30.1 - - + -
683A ARG* 4.6 12.8 - - + -
685A ARG* 5.4 1.1 - - - -
694A GLU* 3.1 55.2 - - + -
695A ASN* 1.3 76.0 - - - +
697A ASN* 1.3 64.4 + - - +
698A LEU* 2.9 18.4 - - + +
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Residues in contact with ASN 697 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A LEU* 4.0 17.6 - - + +
631A VAL 4.0 1.8 - - - -
632A GLN* 3.5 27.4 + - - +
673A PHE* 3.2 10.9 - - - +
674A GLN* 3.0 57.6 + - + +
675A GLU 5.5 0.6 - - - +
695A ASN 5.4 0.6 - - - +
696A PHE* 1.3 76.3 - - - +
698A LEU* 1.3 61.4 + - - +
699A LEU* 4.4 0.2 - - - -
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Residues in contact with LEU 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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608A PHE* 4.5 8.1 - - + -
630A LEU* 3.3 12.8 - - - +
631A VAL* 2.9 53.0 + - + +
633A SER* 3.5 29.8 - - - +
662A LEU* 3.7 29.4 - - + -
671A ALA* 5.2 3.6 - - + -
672A THR 3.4 7.2 - - - +
673A PHE* 4.4 10.5 - - + -
696A PHE* 2.9 34.3 - - + +
697A ASN* 1.3 76.7 - - - +
699A LEU* 1.3 65.1 + - - +
700A LEU* 4.1 2.5 - - + -
711A ILE* 5.5 5.2 - - + -
713A LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 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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628A GLN* 3.5 31.4 - - + +
629A THR 3.6 5.4 - - - +
630A LEU* 4.5 7.6 - - + -
671A ALA* 3.7 3.2 - - - +
672A THR* 3.0 39.6 + - - +
673A PHE 4.3 0.7 - - - -
674A GLN* 3.4 53.4 - - + +
697A ASN 4.2 0.4 - - - +
698A LEU* 1.3 81.3 - - - +
700A LEU* 1.3 63.1 - - - +
701A PRO* 3.6 7.6 - - - +
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Residues in contact with LEU 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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613A ILE* 3.6 31.9 - - + -
617A ALA* 4.6 4.7 - - + +
628A GLN* 3.3 5.8 - - - -
629A THR* 3.1 42.7 + - + +
631A VAL* 3.3 36.1 - - + -
670A ARG* 3.4 24.5 - - + +
671A ALA* 3.7 12.6 - - + -
698A LEU* 5.6 1.6 - - + -
699A LEU* 1.3 71.4 - - - +
701A PRO* 1.3 73.3 - - + +
702A SER* 4.3 0.2 - - - -
704A VAL* 6.0 2.2 - - + -
711A ILE* 3.9 19.7 - - + -
748A PHE* 5.8 1.6 - - + -
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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