Contacts of the strand formed by residues 640 - 649 (chain A) in PDB entry 1LQF
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 LEU 640 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A TRP* 3.4 40.2 - - + +
597A GLU* 3.5 13.0 - - + +
600A TRP* 4.2 20.9 - - + -
634A ILE* 3.5 1.6 - - - -
635A PHE* 2.9 40.8 + - + -
638A THR* 3.7 20.9 - - - +
639A ASN* 1.3 82.5 - - - +
641A LYS* 1.3 61.4 + - - +
660A LEU* 4.1 18.8 - - + -
661A GLU 3.3 15.5 - - - +
662A ASN* 4.0 11.9 - - + -
663A LEU* 3.9 5.8 - - - +
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Residues in contact with LYS 641 (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 GLU* 3.4 35.6 + - + +
633A MET 3.2 18.8 - - - +
634A ILE* 3.7 12.3 - - + -
640A LEU* 1.3 75.0 - - - +
642A LEU* 1.3 60.7 + - - +
643A THR* 4.3 10.8 - - - +
659A GLU 3.6 1.3 - - - +
660A LEU* 3.4 7.5 - - - +
661A GLU* 2.9 60.2 + - + +
663A LEU* 3.9 21.9 - - + +
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Residues in contact with LEU 642 (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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596A TRP* 3.4 45.1 - - + +
624A TYR 3.4 4.7 - - - +
625A TRP* 4.0 1.6 - - + -
626A PRO* 3.7 18.3 - - + +
632A GLU* 3.3 2.9 - - - +
633A MET* 2.8 57.7 + - + +
635A PHE* 3.9 13.2 - - + -
640A LEU 4.3 0.2 + - - -
641A LYS* 1.3 74.6 - - - +
643A THR* 1.3 66.2 + - - +
658A LEU* 3.9 24.2 - - + -
659A GLU 3.6 5.8 - - - +
660A LEU* 4.2 20.9 - - + -
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Residues in contact with THR 643 (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 GLU* 3.6 24.5 - - - +
631A LYS 3.6 7.9 - - - +
632A GLU* 4.1 14.7 + - + +
641A LYS* 4.3 17.8 - - - -
642A LEU* 1.3 79.0 + - - +
644A LEU* 1.3 72.4 + - - +
645A ILE* 3.6 4.6 - - + +
658A LEU* 3.4 9.2 - - - -
659A GLU* 2.9 44.2 + - - +
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Residues in contact with LEU 644 (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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626A PRO* 3.3 38.7 - - + +
627A GLN 3.8 9.4 - - - +
629A GLU* 3.6 30.7 - - + +
630A GLU* 3.6 34.2 - - - +
631A LYS 2.9 10.0 + - - +
643A THR* 1.3 76.1 - - - +
645A ILE* 1.3 69.3 + - - +
646A SER 3.6 18.6 - - - +
647A GLU* 3.9 14.4 - - + +
656A ARG* 4.1 13.2 - - + -
657A GLN 3.8 6.7 - - - +
658A LEU* 3.9 15.0 - - + -
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Residues in contact with ILE 645 (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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629A GLU* 3.0 21.0 - - - +
630A GLU* 5.2 2.2 - - - +
643A THR* 3.6 9.6 - - + +
644A LEU* 1.3 81.2 - - - +
646A SER* 1.3 71.6 + - - +
657A GLN* 3.0 38.1 + - - +
658A LEU 3.8 6.1 - - - +
659A GLU* 3.7 38.4 - - + +
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Residues in contact with SER 646 (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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629A GLU* 5.6 1.1 - - - -
644A LEU* 3.6 6.7 - - - +
645A ILE* 1.3 83.2 + - - +
647A GLU* 1.3 67.5 + - - +
648A ASP 5.3 0.4 - - - -
655A VAL 5.1 1.6 - - - -
656A ARG* 3.3 7.3 - - - +
657A GLN* 2.8 52.5 + - - -
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Residues in contact with GLU 647 (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 GLN* 3.4 18.8 - - - +
628A LYS 4.1 12.8 - - - +
629A GLU* 4.9 8.4 - - + +
644A LEU* 3.9 12.6 - - + +
646A SER* 1.3 79.7 - - - +
648A ASP* 1.3 61.7 + - - +
649A ILE* 2.9 40.6 + - + +
654A THR* 4.3 2.5 - - + -
655A VAL 3.4 8.5 - - - -
656A ARG* 3.4 34.7 + - + +
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Residues in contact with ASP 648 (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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646A SER* 5.3 0.4 - - - -
647A GLU* 1.3 70.9 - - - +
649A ILE* 1.3 62.9 + - - +
650A LYS* 2.5 44.2 + - - +
653A TYR* 4.3 0.9 - - - +
654A THR* 3.4 2.6 - - - -
655A VAL* 3.0 46.1 + - + +
697A LYS* 5.3 0.3 + - - -
737D LYS* 4.4 12.3 - - - +
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Residues in contact with ILE 649 (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 GLU* 2.9 55.4 + - + +
648A ASP* 1.3 77.3 - - - +
650A LYS* 1.3 81.2 + - - +
654A THR* 3.9 23.1 - - + +
656A ARG* 5.5 2.0 - - - +
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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