Contacts of the helix formed by residues 568 - 583 (chain A) in PDB entry 1LMU
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 PRO 568 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PRO* 4.3 9.9 - - + -
205A LEU* 5.0 9.4 - - + -
208A ARG* 5.0 2.0 - - - +
503A ILE* 3.3 43.3 - - + -
506A PHE* 4.8 6.3 - - + -
507A VAL* 3.8 19.7 - - + -
516A LEU* 5.0 4.9 - - + +
522A LEU* 3.9 14.5 - - + +
566A ALA 4.2 3.1 - - - +
567A ARG* 1.3 95.7 - - + +
569A ASP* 1.3 62.6 + - - +
570A MET 3.3 1.8 - - - -
571A THR* 3.1 22.1 + - - +
572A ALA* 3.3 5.0 + - - +
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Residues in contact with ASP 569 (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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507A VAL* 3.7 26.0 - - - +
508A GLN* 5.2 4.0 - - - +
509A ASP* 5.4 2.9 - - - +
512A LEU* 3.3 25.8 - - + +
516A LEU* 6.2 0.2 - - - -
564A MET* 5.9 3.6 - - + +
567A ARG* 3.2 26.7 + - + +
568A PRO* 1.3 72.9 - - - +
570A MET* 1.3 60.0 + - - +
572A ALA* 2.7 27.9 + - - +
573A HIS* 3.3 8.7 + - + +
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Residues in contact with MET 570 (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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172A TYR* 5.5 1.3 - - + +
197A ARG* 5.7 0.7 - - + -
564A MET* 2.9 65.4 + - + +
567A ARG 4.2 4.2 + - - +
568A PRO 3.3 0.8 - - - -
569A ASP* 1.3 77.1 - - - +
571A THR* 1.3 62.9 + - - +
573A HIS* 3.1 20.6 + - - +
574A TRP* 3.0 69.3 + - + -
598A THR* 3.9 23.1 - - + -
602A LEU* 4.7 1.6 - - + -
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Residues in contact with THR 571 (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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197A ARG* 3.5 29.3 + - - +
201A PRO* 5.0 0.9 - - - +
516A LEU* 5.2 2.7 - - + -
521A GLY 4.7 0.7 - - - +
522A LEU* 3.3 26.4 - - + +
567A ARG 5.2 0.4 + - - -
568A PRO* 3.1 15.3 + - - +
570A MET* 1.3 78.1 - - - +
572A ALA* 1.4 57.0 + - - +
574A TRP* 2.6 14.4 + - - +
575A GLU* 2.6 67.9 + - + +
576A SER 3.8 0.5 + - - -
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Residues in contact with ALA 572 (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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512A LEU* 3.1 46.2 - - + -
515A ILE* 3.3 35.3 - - + +
516A LEU* 4.1 13.2 - - + +
568A PRO 3.3 4.2 + - - +
569A ASP* 2.7 13.4 + - - +
571A THR* 1.4 72.7 - - - +
573A HIS* 1.3 68.2 + - + +
576A SER* 3.4 3.5 - - - -
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Residues in contact with HIS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 5.5 13.2 - - + +
569A ASP* 3.3 13.0 + - + -
570A MET* 3.1 17.6 + - - +
571A THR 3.0 0.6 - - - -
572A ALA* 1.3 85.2 - - - +
574A TRP* 1.4 71.2 + - + +
576A SER* 4.1 0.9 - - - -
577A VAL* 3.4 21.6 + - - +
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Residues in contact with TRP 574 (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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172A TYR* 3.8 30.1 - + + -
197A ARG* 3.0 62.1 - - + +
570A MET* 3.0 53.6 + - + +
571A THR* 2.6 11.9 + - - +
573A HIS* 1.4 75.1 - - + +
575A GLU* 1.4 63.7 + - - +
576A SER 3.2 1.8 - - - -
577A VAL* 2.7 27.6 - - + +
578A LEU* 2.9 8.2 + - - +
591A PHE* 4.0 20.4 - + + -
594A PRO 5.6 0.6 - - - -
595A LEU* 2.9 37.8 - - + +
598A THR* 3.8 14.5 - - - +
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Residues in contact with GLU 575 (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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165A ARG* 2.9 39.7 + - - -
197A ARG* 3.5 15.2 + - - +
198A VAL* 4.6 0.9 - - - +
516A LEU* 5.6 2.5 - - + -
519A THR* 4.0 10.8 - - + +
521A GLY 3.5 20.0 - - - +
523A GLY* 3.3 28.5 + - - +
571A THR* 2.6 39.9 + - + +
574A TRP* 1.4 73.0 - - - +
576A SER* 1.3 63.1 + - - +
578A LEU* 3.1 3.5 + - - +
579A THR* 2.9 23.4 + - - -
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Residues in contact with SER 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ILE* 2.9 43.1 - - - +
519A THR* 3.6 14.8 + - - -
571A THR 3.8 2.0 + - - -
572A ALA 3.4 9.4 - - - -
573A HIS 4.1 1.1 - - - -
574A TRP 3.2 0.4 - - - -
575A GLU* 1.3 80.4 - - - +
577A VAL* 1.3 56.4 + - - +
579A THR* 2.7 29.7 - - - +
580A GLN* 2.9 28.3 + - - +
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Residues in contact with VAL 577 (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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573A HIS 3.4 14.5 + - - +
574A TRP* 2.7 24.7 + - + +
576A SER* 1.3 79.0 - - - +
578A LEU* 1.3 57.9 + - - +
580A GLN* 2.8 36.0 + - - +
581A ILE* 2.9 19.2 + - + +
586A CYS* 3.6 29.2 - - - -
590A ASP 5.7 0.2 - - - -
591A PHE* 2.9 41.3 - - + -
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Residues in contact with LEU 578 (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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106A ARG* 4.2 3.7 + - - +
161A SER* 3.0 45.9 + - - +
164A ALA* 3.6 13.5 - - + -
165A ARG* 2.9 68.4 - - + +
197A ARG* 3.9 14.6 - - - +
574A TRP 2.9 8.5 + - - +
575A GLU* 3.4 13.2 - - - +
577A VAL* 1.3 83.4 - - + +
579A THR* 1.3 63.4 + - - +
581A ILE* 3.4 12.7 + - + +
591A PHE* 4.7 6.7 - - + -
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Residues in contact with THR 579 (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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106A ARG* 4.0 15.1 + - - +
519A THR* 4.5 21.6 + - + +
575A GLU* 2.9 12.8 + - - +
576A SER* 2.7 25.1 + - - +
578A LEU* 1.3 78.6 - - - +
580A GLN* 1.4 58.7 + - + +
582A SER* 2.6 25.8 + - - -
583A GLU* 2.5 41.4 + - - +
585A GLN* 4.9 0.2 - - - +
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Residues in contact with GLN 580 (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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515A ILE* 5.2 3.6 - - - +
576A SER* 2.9 38.8 + - - +
577A VAL* 3.1 24.7 - - - +
579A THR* 1.4 76.8 - - + +
581A ILE* 1.3 62.5 + - - +
583A GLU* 3.2 8.3 + - - -
584A LYS 3.0 3.5 + - - -
585A GLN* 2.8 53.5 + - + +
586A CYS* 3.5 22.6 - - + +
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Residues in contact with ILE 581 (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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157A PRO* 3.6 10.4 - - - +
160A VAL* 2.9 38.8 - - + -
161A SER* 3.3 8.7 - - - +
164A ALA* 3.8 28.5 - - + -
577A VAL 2.9 20.3 + - - +
578A LEU* 3.6 15.9 - - + +
579A THR 3.1 0.2 - - - -
580A GLN* 1.3 77.2 - - - +
582A SER* 1.4 56.4 + - - +
584A LYS* 3.1 17.7 + - - +
586A CYS* 3.7 28.1 - - + +
587A ARG* 4.6 6.1 - - - +
588A TYR* 4.9 7.4 - - - +
591A PHE* 4.2 18.4 - - + -
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Residues in contact with SER 582 (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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106A ARG* 4.2 7.6 + - - -
157A PRO* 3.5 21.5 - - - +
158A LEU* 4.4 19.8 + - - -
161A SER* 2.7 25.3 + - - -
579A THR* 2.6 25.3 + - - -
581A ILE* 1.4 75.6 - - - +
583A GLU* 1.3 71.0 + - - +
584A LYS* 4.7 0.7 - - - +
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Residues in contact with GLU 583 (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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579A THR* 2.5 53.7 + - - +
580A GLN 3.7 0.4 - - - +
581A ILE 3.2 0.2 - - - -
582A SER* 1.3 91.8 + - - +
584A LYS* 1.4 70.3 + - - +
585A GLN* 2.8 42.9 + - - +
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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