Contacts of the helix formed by residues 615 - 631 (chain A) in PDB entry 1LUF
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 SER 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A GLU 3.7 1.4 + - - -
614A ALA* 1.3 77.8 - - - +
616A ALA* 1.3 63.7 + - - +
617A ASP* 3.6 11.5 + - - +
618A MET* 3.1 34.5 + - - +
619A GLN* 3.1 22.5 + - - +
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Residues in contact with ALA 616 (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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614A ALA 3.9 0.2 + - - -
615A SER* 1.3 74.5 - - - +
617A ASP* 1.3 66.8 + - - +
619A GLN* 3.6 11.2 + - - +
620A ALA* 3.2 21.0 + - - +
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Residues in contact with ASP 617 (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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615A SER* 3.2 9.2 + - - +
616A ALA* 1.3 81.6 + - - +
618A MET* 1.3 63.5 - - - +
619A GLN 3.2 0.2 - - - -
620A ALA* 3.3 7.8 + - - +
621A ASP* 3.1 27.3 + - - +
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Residues in contact with MET 618 (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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584A ALA* 3.8 25.1 - - + +
585A PHE* 3.6 28.6 - - + +
610A LEU* 4.4 2.5 - - + -
611A LYS* 5.0 7.4 - - + +
614A ALA* 3.9 17.7 - - + -
615A SER* 3.1 36.5 + - - +
617A ASP* 1.3 77.5 - - - +
619A GLN* 1.3 62.2 + - - +
621A ASP* 3.3 10.1 + - - +
622A PHE* 3.1 19.4 + - - +
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Residues in contact with GLN 619 (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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610A LEU* 3.8 16.1 - - + +
614A ALA* 5.0 4.0 - - + +
615A SER 3.1 16.8 + - - +
616A ALA* 3.6 10.0 - - - +
617A ASP 3.2 0.2 - - - -
618A MET* 1.3 75.9 - - - +
620A ALA* 1.3 66.0 + - - +
622A PHE* 3.1 4.0 + - - +
623A GLN* 2.9 45.2 + - - +
648A LYS* 3.9 25.7 + - - +
650A MET* 3.8 25.0 - - - +
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Residues in contact with ALA 620 (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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616A ALA 3.2 12.4 + - - +
617A ASP* 3.3 11.2 + - - +
619A GLN* 1.3 79.3 - - - +
621A ASP* 1.3 60.2 + - - +
623A GLN* 3.8 10.0 - - - +
624A ARG* 2.8 31.4 + - - +
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Residues in contact with ASP 621 (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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585A PHE* 3.9 14.4 - - + -
617A ASP 3.1 14.4 + - - +
618A MET* 3.5 13.0 - - - +
619A GLN 3.2 0.2 - - - -
620A ALA* 1.3 77.4 - - - +
622A PHE* 1.3 52.1 + - - +
624A ARG* 3.2 6.8 + - - +
625A GLU* 2.8 43.7 + - + +
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Residues in contact with PHE 622 (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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585A PHE* 3.7 35.4 - + + -
608A LYS* 3.5 42.8 - - + -
610A LEU* 3.8 37.9 - - + -
618A MET 3.1 11.1 + - - +
619A GLN 3.3 8.1 - - - +
621A ASP* 1.3 78.1 - - - +
623A GLN* 1.3 60.3 + - - +
625A GLU* 3.2 5.8 + - + +
626A ALA* 2.9 28.3 + - + +
650A MET* 4.0 32.5 - - + -
652A LEU* 3.5 32.4 - - + +
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Residues in contact with GLN 623 (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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564A LEU* 4.3 8.9 - - + +
619A GLN* 2.9 41.5 + - - +
620A ALA* 4.0 7.5 - - - +
622A PHE* 1.3 74.4 - - - +
624A ARG* 1.3 61.5 + - - +
626A ALA* 3.3 8.0 + - - +
627A ALA* 2.9 30.5 + - - +
645A ALA* 5.4 5.1 + - - +
650A MET* 3.2 35.6 - - + +
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Residues in contact with ARG 624 (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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620A ALA 2.8 20.3 + - - +
621A ASP* 3.4 7.9 - - - +
623A GLN* 1.3 76.2 - - - +
625A GLU* 1.3 64.1 + - + +
627A ALA* 3.4 8.1 + - - +
628A LEU* 3.3 27.3 + - + +
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Residues in contact with GLU 625 (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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585A PHE* 2.8 36.7 - - + -
608A LYS* 3.4 15.9 + - - +
621A ASP* 2.8 29.8 + - + +
622A PHE* 3.5 5.4 - - + +
624A ARG* 1.3 75.2 - - + +
626A ALA* 1.3 64.4 + - - +
628A LEU* 3.2 12.2 + - + +
629A MET* 3.0 28.4 + - + +
652A LEU* 5.5 3.1 - - + -
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Residues in contact with ALA 626 (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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564A LEU* 3.9 17.8 - - + +
622A PHE* 2.9 13.4 + - + +
623A GLN* 3.3 11.6 + - - +
625A GLU* 1.3 74.9 - - - +
627A ALA* 1.3 57.5 - - - +
629A MET* 3.1 6.2 + - - +
630A ALA* 2.8 32.1 + - - +
640A LEU* 4.0 2.6 - - + +
643A VAL* 5.8 0.7 - - + -
652A LEU* 3.5 38.3 - - + +
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Residues in contact with ALA 627 (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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561A ASN* 3.7 22.8 + - - +
564A LEU* 4.0 13.1 - - + +
623A GLN 2.9 17.0 + - - +
624A ARG* 3.5 9.0 - - - +
626A ALA* 1.3 77.9 - - - +
628A LEU* 1.3 62.8 + - + +
630A ALA* 3.7 10.9 + - - +
631A GLU* 3.8 14.6 - - - +
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Residues in contact with LEU 628 (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 ARG* 3.3 15.0 + - + +
625A GLU* 3.2 12.0 + - + +
626A ALA 3.2 0.6 - - - -
627A ALA* 1.3 75.0 - - + +
629A MET* 1.3 67.6 + - + +
631A GLU* 3.4 14.6 + - - +
632A PHE* 3.8 20.6 - - + -
718A ARG* 5.1 0.2 + - - -
720A PHE* 4.2 31.6 - - + -
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Residues in contact with MET 629 (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 GLU* 3.0 20.2 + - + +
626A ALA* 3.6 10.1 - - - +
628A LEU* 1.3 78.9 - - + +
630A ALA* 1.3 62.3 + - - +
632A PHE* 2.9 52.2 + - + +
637A ILE* 4.7 3.4 - - + -
638A VAL* 3.5 25.1 - - + +
640A LEU* 4.4 13.0 + - + +
652A LEU* 6.0 0.4 - - + -
654A PHE* 3.9 31.9 - - + -
720A PHE* 5.6 4.0 - - - -
741A ALA* 6.3 3.6 - - - -
742A ASP* 6.3 1.8 - - - -
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Residues in contact with ALA 630 (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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561A ASN* 6.1 0.2 - - - +
563A LYS* 3.5 40.5 + - + -
564A LEU* 3.8 17.5 - - + -
567A LEU* 4.1 4.6 - - + +
626A ALA 2.8 16.3 + - - +
627A ALA* 3.7 7.9 - - - +
628A LEU 3.3 0.4 - - - -
629A MET* 1.3 76.5 - - - +
631A GLU* 1.3 62.7 + - - +
632A PHE 3.4 4.9 + - - +
640A LEU* 3.7 16.9 - - + +
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Residues in contact with GLU 631 (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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561A ASN* 5.1 3.3 + - - +
563A LYS* 3.6 31.5 - - - +
627A ALA 3.8 16.8 - - - +
628A LEU* 3.4 7.4 + - - +
629A MET 3.0 1.4 + - - -
630A ALA* 1.3 76.6 - - - +
632A PHE* 1.3 64.4 + - - +
633A ASP* 3.6 5.6 + - - +
714A TYR* 3.6 6.8 + - - -
718A ARG* 3.3 30.1 + - - +
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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