Contacts of the helix formed by residues 527 - 546 (chain A) in PDB entry 5DO7
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 527 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 3.6 27.4 - - + +
443A PRO* 4.0 23.6 - - + -
446A ARG* 4.1 11.2 - - - +
521A LEU* 3.9 16.2 - - + -
525A GLN 3.8 7.2 - - - +
526A ASN* 1.3 86.8 - - - +
528A ASN* 1.3 59.4 + - - +
529A ILE 3.1 0.4 - - - -
530A VAL* 2.8 23.5 + - + +
531A ASN 2.8 11.8 + - - -
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Residues in contact with ASN 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 5.1 1.1 - - - -
526A ASN* 2.5 10.3 + - - +
527A PRO* 1.3 77.1 - - - +
529A ILE* 1.3 57.2 + - - +
531A ASN* 3.5 12.6 + - - +
532A SER* 3.1 25.8 + - - +
465B LEU* 4.9 6.3 - - - +
556B PHE* 3.8 23.5 - - - -
557B HIS* 3.4 32.1 + - - +
672B ASP 5.6 0.2 - - - +
673B TRP* 3.9 38.1 - - + +
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Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL* 3.9 20.2 - - + -
526A ASN* 2.8 20.6 + - + +
528A ASN* 1.3 73.6 - - - +
530A VAL* 1.3 69.8 + - - +
531A ASN 3.0 1.6 - - - -
532A SER* 2.8 13.7 + - - +
533A VAL* 2.8 28.1 + - + +
673B TRP* 4.6 21.2 - - + +
557C ILE* 4.5 22.2 - - + -
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 4.7 2.7 - - + -
517A THR* 3.7 31.9 - - + +
520A LEU* 3.8 21.5 - - + -
521A LEU* 3.9 24.2 - - + -
524A VAL* 3.7 30.9 - - + +
526A ASN 4.1 0.4 + - - -
527A PRO* 2.8 16.7 + - + +
529A ILE* 1.3 75.8 - - - +
531A ASN* 1.3 57.3 + - - +
533A VAL* 2.9 10.4 + - - +
534A VAL* 2.8 37.4 + - + +
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Residues in contact with ASN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 4.1 18.3 + - - -
435A MET* 2.8 47.1 - - - +
436A LEU* 4.6 1.2 + - - -
439A VAL* 3.6 23.7 - - + +
527A PRO 2.8 15.0 + - - +
528A ASN* 3.9 15.4 + - - +
529A ILE 3.0 0.2 - - - -
530A VAL* 1.3 71.8 - - - +
532A SER* 1.3 64.7 + - - +
535A ALA* 3.8 7.3 - - - +
557B HIS* 5.7 6.4 - - + -
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Residues in contact with SER 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ASN* 3.1 22.7 + - - -
529A ILE* 2.8 21.5 + - - +
531A ASN* 1.3 70.5 - - - +
533A VAL* 1.3 67.8 + - - +
535A ALA* 2.8 17.8 + - - +
536A LEU* 3.1 10.9 + - - +
461B PHE* 4.2 9.4 - - - -
465B LEU* 4.2 22.6 - - - +
673B TRP* 5.9 1.6 - - - -
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 3.6 27.8 - - + -
524A VAL* 6.3 0.9 - - + -
529A ILE* 2.8 20.1 + - + +
530A VAL* 2.9 24.5 - - + +
532A SER* 1.3 72.4 - - - +
534A VAL* 1.3 74.8 + - - +
536A LEU* 2.8 23.6 + - + +
537A LEU* 2.8 35.5 + - + +
558C PRO* 6.4 1.8 - - + -
561C ILE* 5.2 11.2 - - + -
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO 5.4 0.2 - - - +
435A MET* 3.4 24.2 - - + -
513A GLY* 4.8 6.3 - - - +
516A LEU* 4.1 16.6 - - + -
517A THR* 3.6 29.4 - - - +
520A LEU* 3.9 23.8 - - + -
530A VAL* 2.8 33.7 + - + +
533A VAL* 1.3 73.8 - - - +
535A ALA* 1.3 56.7 + - - +
537A LEU* 3.3 10.1 - - + +
538A SER* 2.8 35.0 + - - +
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 4.1 21.1 - - + +
435A MET* 3.7 7.4 - - + +
531A ASN 3.8 11.3 + - - +
532A SER 2.8 11.0 + - - +
534A VAL* 1.3 78.5 - - - +
536A LEU* 1.3 65.0 + - - +
538A SER* 2.8 9.2 + - - -
539A ILE* 2.8 32.9 + - + +
461B PHE* 3.6 24.7 - - + -
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Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A SER 3.1 6.3 + - - +
533A VAL* 2.8 13.8 + - + +
535A ALA* 1.3 76.9 - - - +
537A LEU* 1.3 72.5 + - + +
539A ILE* 3.3 12.6 - - + +
540A ALA* 2.8 32.3 + - + +
427B MET* 4.3 20.4 - - + -
461B PHE* 3.7 27.8 - - + -
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 3.8 26.0 - - + -
520A LEU* 4.4 11.4 - - + -
533A VAL* 2.8 34.1 + - + +
534A VAL* 3.3 23.8 - - - +
536A LEU* 1.3 85.9 - - + +
538A SER* 1.3 58.7 + - - +
539A ILE 2.9 0.3 + - - -
540A ALA* 3.6 3.8 - - - +
541A GLY* 2.8 30.1 + - - -
568A GLN* 4.2 0.8 + - - -
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Residues in contact with SER 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 4.0 12.2 + - - +
431A PRO* 3.9 27.8 - - - +
432A TYR* 4.5 8.1 + - - +
435A MET* 4.2 6.1 - - - +
516A LEU* 6.2 1.3 - - - -
534A VAL* 2.8 27.9 + - - -
535A ALA* 2.8 11.7 + - - -
537A LEU* 1.3 73.2 - - - +
539A ILE* 1.3 60.5 - - - +
542A VAL* 3.9 10.0 - - - +
567A PHE* 4.9 3.4 - - - -
568A GLN* 3.4 22.1 + - - +
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Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY 4.9 9.2 - - - +
432A TYR* 5.5 6.3 - - + -
535A ALA* 2.8 25.8 + - + +
536A LEU* 3.3 19.7 - - + +
538A SER* 1.3 80.3 - - - +
540A ALA* 1.3 84.4 + - + +
541A GLY 3.1 0.4 - - - -
542A VAL* 2.8 30.7 + - + +
543A LEU* 3.4 3.1 + - + +
458B LEU* 5.1 19.1 - - + +
461B PHE* 4.8 26.2 - - + -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 2.8 22.0 + - + +
537A LEU* 3.6 3.8 - - - +
539A ILE* 1.3 81.2 - - + +
541A GLY* 1.3 67.3 - - - +
543A LEU* 2.8 27.1 + - - +
544A VAL* 3.4 10.6 + - + +
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Residues in contact with GLY 541 (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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537A LEU 2.8 11.1 + - - -
540A ALA* 1.3 78.0 - - - +
542A VAL* 1.3 56.0 + - - +
544A VAL* 3.2 9.1 - - - +
545A GLY* 2.8 29.1 + - - -
566A THR* 4.5 6.8 - - - +
568A GLN* 3.2 31.3 - - - +
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.1 39.7 - - + +
427A VAL* 3.6 9.9 - - + +
428A GLY* 3.4 36.6 - - - +
538A SER 3.9 3.8 - - - +
539A ILE* 2.8 33.8 + - + +
541A GLY* 1.3 70.2 - - - -
543A LEU* 1.3 63.0 + - - +
546A SER* 2.5 32.2 + - - +
568A GLN* 3.5 24.5 - - + +
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Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.8 18.4 - - - +
539A ILE* 4.3 3.6 - - + +
540A ALA* 2.8 16.5 + - - +
542A VAL* 1.3 82.3 - - - +
544A VAL* 1.3 59.8 + - + +
546A SER 3.7 7.3 - - - +
549A LEU* 4.3 20.4 + - + +
550A ARG* 4.8 6.2 + - - +
555A MET* 5.1 0.2 - - - +
431B ILE* 5.7 5.6 - - + -
434B LEU* 3.5 33.9 - - + -
435B TYR* 4.1 14.4 - - + +
454B MET* 4.0 31.6 - - + -
458B LEU* 4.5 9.9 - - + -
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA* 3.5 9.9 - - + +
541A GLY* 3.2 19.3 - - - +
543A LEU* 1.3 78.4 - - + +
545A GLY* 1.3 57.9 + - - +
546A SER 3.5 7.8 - - - +
552A ILE* 4.5 3.1 - - - +
555A MET* 3.5 23.6 - - + +
559A PHE* 4.1 23.3 - - + -
562A ILE* 4.6 18.2 - - + -
563A SER* 3.6 18.0 - - - +
566A THR* 4.8 4.5 - - + -
434B LEU* 3.1 32.1 - - + -
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Residues in contact with GLY 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLY 2.8 20.8 + - - -
542A VAL 3.9 0.9 - - - -
544A VAL* 1.3 72.6 - - - +
546A SER* 1.3 53.8 + - - +
552A ILE* 5.6 1.6 - - - -
563A SER* 4.0 10.5 - - - -
566A THR* 3.7 16.8 - - - -
568A GLN* 4.1 3.1 - - - -
569A LYS* 2.3 47.3 + - - +
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 4.1 6.8 - - - -
427A VAL* 5.5 0.9 - - - -
542A VAL* 2.5 29.6 + - - +
543A LEU 3.7 7.8 + - - +
544A VAL 3.5 10.9 - - - +
545A GLY* 1.3 77.0 - - - +
547A GLY* 1.3 68.0 + - - +
548A PHE* 3.1 25.5 + - - -
549A LEU 5.3 0.3 + - - -
552A ILE* 5.2 2.0 - - - -
568A GLN* 5.1 1.6 - - - -
569A LYS* 4.5 1.1 - - - +
572A SER* 3.0 31.4 - - - -
573A GLU* 5.6 1.3 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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