Contacts of the strand formed by residues 695 - 701 (chain A) in PDB entry 4L11
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 695 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A THR 3.4 0.3 - - - +
629A HIS* 3.0 7.4 - - - +
630A ALA* 2.7 52.1 + - + -
649A ILE* 5.6 0.4 - - - -
651A ARG* 3.6 6.7 - - - +
652A GLY 3.9 2.2 - - - -
653A SER 3.4 36.6 - - - -
654A ILE* 3.5 23.3 - - + -
691A ALA* 4.1 3.4 - - - -
693A THR 3.8 8.1 - - - -
694A TYR* 1.3 78.3 - - - +
696A ASP* 1.3 61.9 + - - +
697A LEU* 4.0 13.2 - - + -
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Residues in contact with ASP 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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554A HIS* 3.6 24.7 - - - -
627A THR* 5.6 3.1 - - + -
628A THR 3.4 2.0 - - - -
629A HIS* 3.2 32.7 + - + +
650A ALA* 2.8 45.1 + - + +
651A ARG* 3.2 26.4 + - - +
695A CYS* 1.3 73.4 - - - +
697A LEU* 1.3 66.0 + - - +
698A HIS* 6.4 0.2 - - + -
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Residues in contact with LEU 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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627A THR* 3.3 5.5 - - - +
628A THR* 2.6 52.8 + - + +
630A ALA* 4.0 24.0 - - + -
636A LEU* 3.6 26.9 - - + -
647A TYR* 4.3 14.6 - - + -
648A PHE 3.4 4.3 - - - +
649A ILE* 3.4 36.3 - - + -
654A ILE* 4.0 13.0 - - + -
672A PHE* 4.3 10.8 - - + -
695A CYS* 4.0 9.0 - - + -
696A ASP* 1.3 78.4 - - - +
698A HIS* 1.3 63.3 + - - +
699A LYS* 3.9 1.3 + - + -
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Residues in contact with HIS 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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599A LEU* 3.1 31.2 + - + -
600A ASN* 4.0 7.1 + - - -
602A ASN* 4.6 5.6 - - + +
603A LEU* 3.4 49.5 + - + +
625A PHE* 4.0 7.4 - - + -
626A LYS 3.3 3.8 - - - -
627A THR* 3.3 25.1 + - + -
647A TYR* 3.4 1.6 - - - -
648A PHE* 2.8 48.4 + - + +
650A ALA* 3.9 27.6 - - + +
669A ASP* 5.4 2.7 - - - -
696A ASP* 6.4 0.2 - - + -
697A LEU* 1.3 72.5 - - - +
699A LYS* 1.3 58.9 + - - +
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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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625A PHE* 3.8 3.5 - - - -
626A LYS* 2.9 62.7 + - + +
628A THR* 3.8 24.0 + - - +
645A TYR* 3.5 36.1 - - + -
646A LEU 3.3 9.6 - - - +
647A TYR* 3.8 35.7 + - + +
697A LEU* 3.9 2.8 + - + +
698A HIS* 1.3 76.3 - - - +
700A ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 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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621A LEU* 4.4 10.1 - - + +
624A LYS* 4.2 17.3 - - + +
625A PHE* 3.7 42.7 - - + -
645A TYR* 3.3 5.5 - - - -
646A LEU* 3.0 43.7 + - + +
648A PHE* 4.8 0.2 - - + -
699A LYS* 1.3 72.6 - - - +
701A HIS* 1.3 72.4 - - - +
702A ARG* 3.7 0.7 + - - -
704A ASP* 4.1 12.1 - - + -
705A LEU* 4.1 48.7 - - + +
708A VAL* 5.5 0.7 - - + -
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Residues in contact with HIS 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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624A LYS 5.1 0.8 + - - -
626A LYS* 5.9 1.3 - - - -
644A THR* 3.7 15.8 + - - -
645A TYR* 3.4 46.1 - + + +
700A ILE* 1.3 78.1 - - - +
702A ARG* 1.3 91.0 + - + +
703A ASP* 3.1 37.3 + - + +
704A ASP* 3.0 24.7 + - - +
705A LEU* 3.0 18.6 + - - +
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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