Contacts of the helix formed by residues 580 - 592 (chain A) in PDB entry 3L4U
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 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A ALA 4.2 7.6 - - - +
547A TRP* 5.3 6.7 - - + +
578A ASP 3.6 8.5 - - - +
579A THR* 1.4 89.3 - - - +
581A GLU* 1.3 65.7 + - - +
582A GLU* 3.3 3.8 + - + +
583A LEU* 3.3 30.0 + - + +
584A CYS* 3.0 21.1 + - - +
606A LYS* 5.1 1.1 - - - +
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Residues in contact with GLU 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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579A THR 3.6 2.0 + - - -
580A PRO* 1.3 72.8 - - - +
582A GLU* 1.3 59.7 + - - +
584A CYS 3.4 0.3 + - - -
585A ARG* 2.9 68.8 + - - +
606A LYS* 4.9 4.1 - - - +
613A PHE* 4.0 33.3 - - + -
617A SER* 6.1 0.3 - - - -
618A LEU* 4.7 3.8 - - - +
619A LEU* 3.9 16.9 + - + +
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Residues in contact with GLU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A TRP* 3.8 16.3 - - + -
580A PRO* 3.2 4.4 - - + +
581A GLU* 1.3 86.6 + - - +
583A LEU* 1.3 64.5 + - - +
585A ARG* 3.4 25.5 + - - +
586A ARG* 3.1 29.4 + - + +
685A ASP 4.2 0.5 - - - +
686A GLU* 3.8 11.3 - - - +
687A GLY* 2.7 39.8 + - - -
688A ALA 4.1 5.0 + - - +
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Residues in contact with LEU 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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545A ALA* 3.4 41.1 - - - +
546A THR* 3.6 17.9 - - - +
547A TRP* 3.5 41.1 - - + +
550A LEU* 3.7 19.5 - - + -
579A THR* 4.0 9.0 - - - +
580A PRO* 3.3 21.0 + - + +
582A GLU* 1.3 78.8 - - - +
584A CYS* 1.3 57.7 + - - +
586A ARG* 3.2 2.4 + - - -
587A TRP* 2.8 46.2 + - + +
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Residues in contact with CYS 584 (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 CYS* 2.1 48.9 - - - -
579A THR* 3.6 22.6 + - + +
580A PRO 3.0 10.2 + - - +
581A GLU 4.0 0.4 - - - +
583A LEU* 1.3 77.0 - - - +
585A ARG* 1.3 58.4 + - - +
587A TRP* 4.3 0.7 - - - -
588A MET* 2.8 39.4 + - - +
608A GLN 4.0 5.6 - - - -
613A PHE* 3.8 25.8 - - + -
619A LEU* 3.8 11.9 - - + -
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Residues in contact with ARG 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLU* 2.9 51.8 + - - +
582A GLU* 3.6 24.1 - - - +
584A CYS* 1.3 78.3 - - - +
586A ARG* 1.3 68.1 + - - +
588A MET* 3.5 2.6 + - - +
589A GLN* 3.0 45.8 + - - +
618A LEU* 3.6 30.7 - - - +
619A LEU* 3.5 23.5 - - + +
622A SER* 4.7 4.0 - - - -
722A GLY* 3.0 38.1 + - - -
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Residues in contact with ARG 586 (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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547A TRP* 3.6 26.0 - - + -
550A LEU* 4.4 5.3 - - + +
582A GLU* 3.1 26.6 + - + +
583A LEU 3.8 2.7 - - - +
585A ARG* 1.3 84.8 - - - +
587A TRP* 1.3 62.0 + - - +
589A GLN* 2.9 26.0 + - - +
590A LEU* 3.1 23.2 + - - +
682A PRO* 5.6 0.7 - - - +
683A VAL* 3.6 40.3 - - + +
684A LEU* 6.1 0.2 - - - +
688A ALA 3.1 21.2 + - - -
689A GLU* 4.2 0.8 - - - +
720A LEU 3.1 21.8 + - - -
721A PRO 3.1 18.7 + - - -
722A GLY* 3.6 13.6 + - - +
724A LYS 2.9 19.4 + - - -
725A ILE* 5.6 0.2 - - - +
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Residues in contact with TRP 587 (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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543A ASN* 3.3 30.3 - - - -
544A THR 3.8 11.2 - - - -
546A THR 4.0 12.1 - - - -
549A ASP* 3.8 13.0 - - + -
550A LEU* 3.6 40.7 - - + +
553A SER* 4.9 0.2 - - - -
570A PRO* 3.9 9.6 - - + +
571A ASP 3.8 2.7 - - - -
572A ILE* 3.6 12.2 - - + +
573A CYS* 3.4 43.1 - - - +
574A GLY 3.7 2.5 - - - -
583A LEU* 2.8 41.5 + - + +
584A CYS 3.8 2.9 - - - +
586A ARG* 1.3 70.5 - - - +
588A MET* 1.3 56.2 + - - +
590A LEU* 3.9 0.4 - - + -
591A GLY* 2.6 32.3 + - - -
594A TYR* 2.9 33.9 + + - -
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Residues in contact with MET 588 (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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294A PHE* 3.9 24.7 - - + -
572A ILE* 3.6 20.6 - - + -
573A CYS* 3.9 9.4 - - - -
584A CYS* 2.8 24.5 + - - +
585A ARG* 3.9 4.5 - - - +
587A TRP* 1.3 74.6 - - - +
589A GLN* 1.3 63.2 + - - +
591A GLY* 3.8 0.4 - - - -
592A ALA* 3.0 24.8 + - - +
599A ASN* 3.8 17.0 - - - +
610A PRO* 3.6 23.1 - - + -
619A LEU* 4.8 4.9 - - + -
623A SER* 3.4 36.6 - - - +
626A TYR* 5.2 0.5 - - - +
627A LEU* 4.0 14.1 - - + +
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Residues in contact with GLN 589 (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 ARG* 3.0 26.5 + - - +
586A ARG* 2.9 36.2 + - - +
587A TRP 3.4 0.2 - - - -
588A MET* 1.3 79.7 - - + +
590A LEU* 1.3 60.9 - - - +
592A ALA* 3.6 4.5 - - - +
593A PHE* 3.4 23.4 - - - -
622A SER* 2.9 30.6 + - - +
623A SER* 6.1 0.2 - - - +
626A TYR* 4.0 15.5 - - + -
683A VAL 5.8 0.9 + - - -
722A GLY 2.9 25.7 + - - -
723A ASP 3.6 8.1 - - - -
724A LYS 3.4 9.7 - - - +
725A ILE* 3.6 20.7 - - + +
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Residues in contact with LEU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LEU* 3.9 17.9 - - + +
553A SER* 4.4 1.1 - - - +
554A ILE* 4.1 18.6 - - + -
586A ARG 3.1 13.7 + - - +
587A TRP 3.9 2.5 - - - +
589A GLN* 1.3 79.1 - - - +
591A GLY* 1.3 54.1 + - - +
593A PHE* 2.8 27.9 + - - +
594A TYR* 3.4 34.6 + - + +
672A PHE* 3.5 33.7 - - + -
680A ILE* 4.2 8.1 - - + -
682A PRO* 4.0 20.2 - - + -
684A LEU* 4.2 8.3 - - + -
725A ILE* 3.5 10.4 - - + +
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Residues in contact with GLY 591 (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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572A ILE* 3.5 12.8 - - - +
587A TRP 2.6 23.5 + - - -
588A MET* 3.8 1.3 - - - -
590A LEU* 1.3 69.4 - - - +
592A ALA* 1.3 57.0 + - - +
593A PHE 2.9 6.5 + - - -
594A TYR* 3.3 31.1 + - - +
597A SER* 2.7 28.6 + - - -
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Residues in contact with ALA 592 (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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588A MET* 3.0 12.5 + - - +
589A GLN 3.6 14.1 - - - +
590A LEU 3.1 0.2 - - - -
591A GLY* 1.3 76.1 - - - +
593A PHE* 1.3 61.6 + - + +
623A SER 5.4 0.2 - - - +
626A TYR* 3.7 35.9 - - + +
627A LEU* 4.0 22.7 - - + +
630A ARG* 2.8 33.7 + - - +
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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