Contacts of the helix formed by residues 573 - 592 (chain A) in PDB entry 3UGM
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 GLY 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A ILE 5.6 0.2 - - - -
571A HIS* 2.6 8.1 + - - +
572A ASP* 1.3 73.2 - - - +
574A GLY* 1.3 52.5 + - - -
575A LYS 3.8 0.4 - - - -
576A GLN* 3.3 7.1 - - - +
577A ALA* 2.8 38.6 + - - +
605A ASN 6.1 0.7 - - - -
606A ILE* 5.0 8.4 - - - +
607A GLY 5.5 4.9 - - - -
608A GLY 5.7 0.5 + - - -
8B C 3.9 13.0 - - - -
9B C 3.6 19.1 + - - -
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Residues in contact with GLY 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLY* 5.4 1.0 - - - -
543A ALA* 4.1 9.2 - - - -
568A ILE 4.4 8.8 - - - +
569A ALA* 3.9 16.8 - - - -
571A HIS 3.0 11.1 + - - -
572A ASP 3.2 4.8 + - - -
573A GLY* 1.3 71.8 - - - +
575A LYS* 1.3 68.7 + - - +
577A ALA* 3.0 2.9 + - - +
578A LEU* 2.8 29.0 + - - +
8B C 4.6 1.8 + - - -
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Residues in contact with LYS 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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542A GLN* 3.7 33.6 - - + +
543A ALA* 4.0 8.7 - - - +
546A THR* 3.1 35.4 - - + +
574A GLY* 1.3 71.2 - - - +
576A GLN* 1.3 61.2 - - - +
578A LEU* 3.3 1.6 + - - +
579A GLU* 2.8 53.0 + - - +
8B C 3.2 28.3 + - - +
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Residues in contact with GLN 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY 3.3 9.6 - - - +
574A GLY 3.0 0.2 - - - -
575A LYS* 1.3 99.0 - - - +
577A ALA* 1.3 62.2 + - - +
579A GLU* 3.5 13.8 + - - +
580A THR* 2.5 36.1 + - - -
609A LYS* 4.1 22.8 - - + +
8B C 3.6 29.8 + - - +
9B C 3.4 29.6 + - - +
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Residues in contact with ALA 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ILE* 3.9 15.2 - - + +
573A GLY 2.8 21.3 + - - +
574A GLY 3.7 2.2 - - - +
576A GLN* 1.3 76.0 - - - +
578A LEU* 1.3 65.2 + - - +
580A THR* 3.8 3.5 - - - -
581A VAL* 2.9 22.0 + - - +
603A ALA* 3.8 25.0 - - + +
605A ASN 5.2 2.0 - - - +
608A GLY* 4.0 15.7 - - - +
609A LYS 4.4 8.2 - - - +
612A LEU* 5.1 0.9 - - - +
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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
----------------------------------------------------------
543A ALA* 6.2 0.4 - - + -
546A THR* 3.7 28.5 - - + +
547A VAL* 3.7 31.2 - - + -
550A LEU* 4.9 6.3 - - + +
554A LEU* 3.7 27.2 - - + +
565A VAL* 4.2 15.9 - - + +
568A ILE* 4.0 32.4 - - + +
569A ALA* 4.7 8.1 - - + +
574A GLY 2.8 16.9 + - - +
575A LYS 3.6 6.3 - - - +
577A ALA* 1.3 70.6 - - - +
579A GLU* 1.3 65.6 + - - +
581A VAL* 2.9 25.9 - - + +
582A GLN* 3.0 4.0 + - - +
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Residues in contact with GLU 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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546A THR* 4.7 10.7 - - + +
550A LEU* 4.5 9.6 - - + +
575A LYS* 2.8 45.2 + - - +
576A GLN* 3.5 17.5 + - - +
578A LEU* 1.3 70.6 - - - +
580A THR* 1.3 59.0 + - - +
582A GLN* 2.8 30.8 + - - +
583A GLN* 3.0 31.6 + - - +
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Residues in contact with THR 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLN* 2.5 25.7 + - - -
577A ALA 3.9 2.0 - - - -
579A GLU* 1.3 74.5 - - - +
581A VAL* 1.3 67.0 + - - +
583A GLN* 2.8 11.3 + - + +
584A LEU* 2.8 53.9 + - + +
609A LYS* 3.7 33.1 - - + +
612A LEU* 4.6 8.7 - - + -
613A ALA* 5.7 2.5 - - + +
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Residues in contact with VAL 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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554A LEU* 3.5 29.4 - - + -
560A LEU* 4.7 5.2 - - + -
568A ILE* 4.1 22.0 - - + -
577A ALA 2.9 17.2 + - - +
578A LEU* 2.9 19.7 + - + +
580A THR* 1.3 70.7 - - - +
582A GLN* 1.3 61.6 + - - +
585A LEU* 2.9 44.6 + - + +
599A VAL* 4.0 25.6 - - + +
600A VAL* 5.3 1.3 - - + -
603A ALA* 4.2 11.4 - - + -
612A LEU* 4.2 9.2 - - + +
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Residues in contact with GLN 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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550A LEU* 4.2 20.6 - - + +
553A VAL* 4.5 16.0 - - + +
554A LEU* 3.4 31.9 - - + -
558A HIS* 3.2 27.7 + - + +
578A LEU 3.7 4.5 - - - +
579A GLU* 2.8 14.2 + - - +
581A VAL* 1.3 81.8 - - - +
583A GLN* 1.3 65.9 + - + +
584A LEU 3.4 1.2 + - - -
586A PRO* 4.3 2.4 - - - +
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Residues in contact with GLN 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 GLU* 3.0 40.6 + - - +
580A THR* 2.8 12.4 + - + +
582A GLN* 1.3 86.3 + - + +
584A LEU* 1.3 71.4 + - + +
587A VAL* 3.8 10.7 - - - +
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Residues in contact with LEU 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A THR* 2.8 35.2 + - + +
581A VAL 5.2 0.2 - - - -
582A GLN 3.3 0.6 - - - -
583A GLN* 1.3 88.1 - - + +
585A LEU* 1.3 55.1 + - - +
586A PRO* 3.6 4.3 - - - -
587A VAL* 3.2 25.4 + - + -
588A LEU* 2.7 48.9 + - + +
599A VAL* 5.9 0.2 - - - -
612A LEU* 3.9 31.0 - - + +
613A ALA* 4.7 5.8 - - + +
616A GLN* 4.6 18.8 - - + -
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Residues in contact with LEU 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU* 5.1 0.7 - - + -
558A HIS* 3.2 53.2 - - + +
560A LEU* 4.2 20.9 - - + -
581A VAL* 2.9 25.7 + - + +
584A LEU* 1.3 75.9 - - - +
586A PRO* 1.4 69.3 - - + +
588A LEU* 3.4 3.3 + - - +
589A CYS* 3.0 44.8 + - - -
596A PRO* 5.5 11.2 - - + -
599A VAL* 4.7 22.1 - - + +
600A VAL* 6.2 0.4 - - + -
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Residues in contact with PRO 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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558A HIS* 3.4 28.0 - - + +
582A GLN 4.3 4.7 - - - +
584A LEU 3.6 1.6 - - - -
585A LEU* 1.4 96.0 - - + +
587A VAL* 1.3 69.7 + - + +
588A LEU 3.4 0.2 - - - -
589A CYS* 3.6 9.3 - - + +
590A GLN* 2.9 46.7 + - - +
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Residues in contact with VAL 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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583A GLN 3.8 9.9 - - - +
584A LEU* 3.3 36.1 - - + +
586A PRO* 1.3 82.5 - - + +
588A LEU* 1.3 59.7 + - - +
590A GLN* 5.0 1.8 - - - -
591A ALA* 2.9 35.5 + - + +
616A GLN* 3.7 16.8 - - + +
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Residues in contact with LEU 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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584A LEU* 2.7 41.1 + - + +
585A LEU 3.8 4.5 - - - +
587A VAL* 1.3 73.1 - - - +
589A CYS* 1.3 63.5 + - - +
590A GLN 3.2 0.6 + - - -
592A HIS* 2.6 47.4 - - + +
594A LEU* 3.9 28.3 - - + +
599A VAL* 4.5 17.5 - - + -
602A ILE* 5.5 0.9 - - + -
612A LEU* 4.4 22.9 - - + +
615A VAL* 3.0 37.5 - - + -
616A GLN* 4.4 6.7 - - - +
619A LEU* 5.6 0.9 - - + -
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Residues in contact with CYS 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 LEU* 3.0 42.9 + - - +
586A PRO* 3.6 9.9 - - + +
588A LEU* 1.3 76.5 - - - +
590A GLN* 1.3 59.9 + - + +
592A HIS 2.9 11.2 - - - +
593A GLY* 3.9 6.2 - - - -
594A LEU 3.4 24.7 - - - +
595A THR* 3.8 14.1 - - - -
596A PRO* 4.7 8.1 - - - -
599A VAL* 5.1 1.8 - - - -
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Residues in contact with GLN 590 (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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586A PRO* 2.9 28.5 + - - +
587A VAL* 4.5 2.2 - - - +
589A CYS* 1.3 84.5 - - + +
591A ALA* 1.3 65.1 + - - +
592A HIS 3.1 6.6 + - - +
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Residues in contact with ALA 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A VAL* 2.9 22.1 + - + +
590A GLN* 1.3 77.2 - - - +
592A HIS* 1.3 70.7 + - + +
616A GLN* 3.4 20.4 - - - +
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Residues in contact with HIS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LEU* 2.6 54.8 + - + +
589A CYS 2.9 18.5 - - - +
590A GLN 3.2 7.8 - - - +
591A ALA* 1.3 82.8 + - + +
593A GLY* 1.3 60.7 + - - +
594A LEU* 4.3 11.4 - - + -
616A GLN* 2.8 30.5 + - - -
619A LEU* 3.0 45.7 - - + +
620A PRO* 5.0 5.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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