Contacts of the helix formed by residues 569 - 587 (chain A) in PDB entry 6P5C
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 GLU 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A ARG* 3.1 33.9 + - - -
521A LEU* 3.5 20.9 - - + +
568A HIS* 1.3 73.8 + - + +
570A ILE* 1.3 60.8 + - - +
571A VAL 3.2 1.7 + - - -
572A GLU* 3.5 31.0 - - - +
573A ASN* 3.0 25.0 + - - +
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Residues in contact with ILE 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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518A ILE* 3.8 22.4 - - + +
521A LEU* 3.8 21.0 - - + +
522A ALA* 3.7 32.5 - - + +
526A PHE* 4.9 0.2 - - + -
537A ILE* 3.9 16.6 - - + -
538A LEU* 3.7 22.4 - - + -
542A LEU* 3.8 11.2 - - + -
544A LEU* 4.8 0.4 - - + -
568A HIS* 3.1 22.8 + - + +
569A GLU* 1.3 77.1 - - - +
571A VAL* 1.3 74.7 + - + +
573A ASN* 3.5 3.3 + - - +
574A ILE* 3.1 29.8 + - + +
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Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LEU* 4.8 3.8 - - + -
544A LEU* 3.8 24.5 - - + -
561A LEU* 2.8 52.7 - - + +
564A LEU* 3.7 21.8 - - + +
565A ALA* 3.7 13.0 - - + +
568A HIS 3.4 6.5 + - - +
569A GLU 3.2 1.4 - - - -
570A ILE* 1.3 84.4 - - + +
572A GLU* 1.3 58.3 - - - +
574A ILE* 3.0 11.9 + - - +
575A LEU* 2.9 29.6 + - + +
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Residues in contact with GLU 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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565A ALA* 4.8 17.3 - - + +
568A HIS 4.8 1.2 + - - +
569A GLU* 3.5 35.0 - - - +
571A VAL* 1.3 74.4 - - - +
573A ASN* 1.3 69.4 + - - +
575A LEU* 3.2 13.7 + - + +
576A HIS* 3.0 30.6 + - - +
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Residues in contact with ASN 573 (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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514A VAL* 3.2 22.1 - - + +
517A ARG* 3.8 24.8 - - - +
518A ILE* 3.4 20.9 - - + -
521A LEU* 3.3 21.0 - - + +
569A GLU* 3.0 27.9 + - - +
570A ILE 3.5 4.9 + - - +
571A VAL 3.3 0.2 - - - -
572A GLU* 1.3 88.8 + - - +
574A ILE* 1.3 51.4 + - - +
576A HIS* 3.4 5.0 + - - +
577A TYR* 2.9 30.3 + - - +
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Residues in contact with ILE 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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518A ILE* 3.4 22.7 - - + -
528A ILE* 4.9 7.9 - - + -
534A LEU* 3.5 39.0 - - + -
538A LEU* 3.8 23.8 - - + -
561A LEU* 3.5 26.7 - - + -
570A ILE* 3.1 31.0 + - + +
571A VAL* 3.0 10.4 + - - +
573A ASN* 1.3 74.3 - - - +
575A LEU* 1.3 56.8 + - - +
577A TYR* 3.5 4.4 + - - +
578A ARG* 3.0 36.9 + - + +
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Residues in contact with LEU 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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558A ALA* 3.8 36.6 - - + +
561A LEU* 4.0 25.4 - - + -
562A GLU* 4.2 26.5 - - + +
565A ALA* 5.4 2.9 - - + -
571A VAL* 2.9 21.3 + - + +
572A GLU* 3.2 13.9 + - + +
574A ILE* 1.3 76.2 - - - +
576A HIS* 1.3 59.7 + - - +
578A ARG* 3.4 7.1 + - + +
579A GLN* 3.1 26.0 + - - +
26B A 4.9 4.0 - - - +
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Residues in contact with HIS 576 (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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510A GLN* 4.8 8.5 + - - -
514A VAL* 3.6 27.9 - - + +
572A GLU 3.0 16.2 + - - +
573A ASN* 3.7 7.6 - - - +
575A LEU* 1.3 72.0 - - - +
577A TYR* 1.3 54.8 + - - +
579A GLN* 3.1 22.1 + - - +
580A LEU* 2.9 63.6 + - + +
632A GLU* 4.7 9.6 - - + -
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Residues in contact with TYR 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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511A LEU* 3.5 35.4 - - + +
514A VAL* 3.8 11.1 - - + +
515A GLU* 3.5 44.1 + - + +
518A ILE* 4.6 2.2 - - + -
527A ASN* 5.6 0.7 + - - -
528A ILE* 3.4 41.4 - - + +
529A ASN* 3.5 30.0 + - - -
573A ASN 2.9 18.8 + - - +
574A ILE* 3.5 8.3 - - - +
576A HIS* 1.3 75.2 - - - +
578A ARG* 1.3 58.9 + - + +
580A LEU* 4.6 2.2 - - - -
581A GLY* 2.8 34.3 + - - -
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Residues in contact with ARG 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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528A ILE* 5.0 8.2 + - + +
529A ASN* 5.3 9.5 - - - +
531A PRO* 6.0 1.4 - - - +
534A LEU* 3.2 23.3 - - - +
556A THR* 2.7 46.9 + - - -
561A LEU* 3.9 11.0 - - - +
574A ILE* 3.0 24.4 + - + +
575A LEU* 3.6 11.2 - - + +
577A TYR* 1.3 80.8 - - + +
579A GLN* 1.3 60.8 + - - +
581A GLY* 3.8 1.2 - - - -
582A LYS* 2.9 32.6 + - - +
25B C 3.1 20.2 + - - -
26B A 3.0 41.8 + - - +
27B C 5.5 0.4 - - - -
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Residues in contact with GLN 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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575A LEU 3.1 13.7 + - - +
576A HIS* 3.1 27.7 + - - +
578A ARG* 1.3 77.9 - - - +
580A LEU* 1.3 66.5 + - - +
582A LYS* 3.2 3.3 + - - +
583A LEU* 3.2 32.2 + - + +
630A LEU* 3.7 28.2 - - + +
632A GLU* 3.6 43.7 + - - +
633A GLY* 4.6 2.8 - - - +
27B C 4.0 21.9 + - - +
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Residues in contact with LEU 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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507A LEU* 3.7 23.3 - - + +
510A GLN* 3.7 52.0 - - + +
511A LEU* 3.7 20.4 - - + +
514A VAL* 4.1 4.7 - - + -
576A HIS* 2.9 56.0 + - + +
577A TYR* 3.8 0.7 - - - +
579A GLN* 1.3 75.6 - - - +
581A GLY* 1.3 51.3 + - - +
583A LEU* 3.2 10.3 + - + +
584A GLN* 2.9 35.0 + - - +
632A GLU* 6.0 5.6 - - + -
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Residues in contact with GLY 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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511A LEU* 3.8 12.0 - - - +
577A TYR* 2.8 26.6 + - - -
578A ARG* 3.8 2.9 - - - -
580A LEU* 1.3 72.2 - - - +
582A LYS* 1.3 52.7 + - - +
584A GLN* 3.8 4.6 - - - +
585A SER* 2.9 41.3 + - - -
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Residues in contact with LYS 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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578A ARG 2.9 18.2 + - - +
579A GLN 3.2 5.1 + - - +
581A GLY* 1.3 73.4 - - - +
583A LEU* 1.3 67.8 + - + +
585A SER* 5.0 1.3 - - - -
586A THR* 3.0 63.5 + - - +
587A TYR* 3.7 11.2 + - + -
625A ASN* 5.8 0.4 - - - +
26B A 2.7 66.4 + - - +
27B C 3.5 30.3 - - - +
10C G 3.7 12.3 + - - +
11C A 5.6 0.8 + - - -
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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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503A MET* 6.0 1.3 - - + -
507A LEU* 4.1 25.1 - - + -
579A GLN* 3.2 22.3 + - + +
580A LEU* 3.4 10.5 - - + +
582A LYS* 1.3 78.5 - - + +
584A GLN* 1.3 54.5 + - - +
587A TYR* 3.1 17.3 + - + +
588A ILE* 2.8 34.9 + - - +
627A PRO* 3.9 19.3 - - + -
632A GLU* 4.0 16.4 - - + +
633A GLY* 3.7 38.1 - - - +
636A ILE* 4.6 11.9 - - + -
27B C 5.5 4.9 - - - +
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Residues in contact with GLN 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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504A GLY* 3.4 26.2 + - - -
507A LEU* 4.1 8.1 - - + +
508A ALA* 3.7 24.4 - - - +
511A LEU* 4.0 19.1 - - + +
580A LEU 2.9 19.1 + - - +
581A GLY 3.8 4.5 - - - +
582A LYS 3.2 0.2 - - - -
583A LEU* 1.3 73.2 - - - +
585A SER* 1.3 60.5 + - - +
588A ILE* 3.5 28.1 + - - +
589A GLU* 2.9 53.1 + - - +
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Residues in contact with SER 585 (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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581A GLY* 2.9 23.5 + - - -
582A LYS* 4.4 1.1 - - - -
584A GLN* 1.3 75.7 - - - +
586A THR* 1.3 59.3 + - - +
589A GLU* 3.6 16.2 + - - +
590A GLY* 3.2 23.6 + - - -
593A LYS* 5.9 0.2 + - - -
11C A 3.2 32.0 + - - +
12C T 3.0 19.2 + - - -
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Residues in contact with THR 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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582A LYS* 3.0 39.5 + - - +
585A SER* 1.3 77.4 - - - +
587A TYR* 1.3 88.7 + - + +
590A GLY* 3.5 17.7 - - - -
591A LEU* 4.2 2.1 + - - +
625A ASN* 5.2 4.7 - - - +
10C G 5.0 13.9 + - - +
11C A 3.6 29.6 + - - +
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Residues in contact with TYR 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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582A LYS* 3.7 27.7 - - + -
583A LEU* 3.1 18.5 + - + +
586A THR* 1.3 98.1 - - + +
588A ILE* 1.3 63.7 + - - +
591A LEU* 2.9 40.3 + - + +
622A ASN 5.3 0.7 - - - -
625A ASN* 2.5 49.1 + - - -
626A ILE* 4.0 19.7 - - + -
627A PRO* 3.6 33.4 - - + -
636A ILE* 4.3 17.9 - - + -
27B C 3.4 17.9 + - - +
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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