Contacts of the helix formed by residues 555 - 574 (chain D) 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 THR 555 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D TYR* 2.5 20.6 + - - -
553D LEU* 4.6 0.2 - - - +
554D PRO* 1.3 85.7 + - - +
556D PHE* 1.3 63.4 + - + +
557D HIS* 3.7 20.6 - - + +
558D MET* 2.4 44.6 + - + +
559D ALA 2.8 10.7 + - - -
669D PRO 5.3 7.9 + - - +
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Residues in contact with PHE 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C ASN* 3.8 33.0 - - - -
465D LEU* 4.6 12.6 - - + -
468D ILE* 3.6 19.4 - - + +
469D SER* 3.7 33.7 - - - -
472D TYR* 2.9 33.4 - - + -
555D THR* 1.3 72.6 - - + +
557D HIS* 1.3 69.3 + + + +
559D ALA* 4.1 0.5 - - - +
560D SER* 2.8 50.2 + - - -
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Residues in contact with HIS 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 6.5 0.7 - - + -
440C ASN* 4.8 13.2 + - - -
528C ASN* 3.1 33.6 + - - -
531C ASN* 5.7 5.8 - - + -
555D THR* 2.8 15.3 + - + +
556D PHE* 1.3 86.3 - + + +
558D MET* 1.3 57.9 + - + +
560D SER* 3.3 5.1 - - - -
561D PHE* 2.8 27.4 + - - +
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Residues in contact with MET 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LEU* 3.2 25.1 - - + +
554D PRO* 4.1 19.7 - - + -
555D THR* 2.4 34.2 + - + +
557D HIS* 1.3 76.9 - - + +
559D ALA* 1.3 57.1 + - - +
561D PHE* 2.8 26.9 + - + +
562D PHE 2.8 13.3 + - - -
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Residues in contact with ALA 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 4.3 7.6 - - + -
472D TYR* 3.9 16.4 - - + -
549D ALA* 3.7 9.1 - - - +
550D ALA* 3.7 30.5 - - - +
553D LEU* 3.3 14.4 - - + +
555D THR 2.8 9.5 + - - +
556D PHE 4.1 2.2 - - - +
558D MET* 1.3 71.5 - - - +
560D SER* 1.3 52.4 + - - +
562D PHE* 3.8 1.4 - - - +
563D SER* 2.7 42.9 + - - -
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Residues in contact with SER 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 4.9 0.2 - - - +
465D LEU* 3.4 29.5 - - - +
468D ILE* 4.4 12.9 - - - +
556D PHE* 2.8 37.3 + - - -
557D HIS* 3.3 6.3 - - - -
559D ALA* 1.3 75.7 - - - +
561D PHE* 1.3 57.2 + - - +
563D SER* 4.4 6.1 - - - -
564D ASN* 3.0 24.7 + - - +
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Residues in contact with PHE 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LEU* 5.7 0.9 - - + -
557D HIS 2.8 9.5 + - - +
558D MET* 2.8 20.0 + - + +
560D SER* 1.3 76.6 - - - +
562D PHE* 1.3 94.5 + + + +
563D SER 2.9 1.8 - - - -
564D ASN* 2.8 15.5 + - + -
565D ALA* 2.8 35.8 + - + -
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Residues in contact with PHE 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D ALA* 4.0 23.8 - - + -
552D LEU* 4.9 14.6 - - + -
553D LEU* 3.7 39.3 - - + -
558D MET 2.8 6.2 + - - +
559D ALA 3.8 2.2 - - - +
561D PHE* 1.3 90.4 - + + +
563D SER* 1.3 59.6 + - - +
565D ALA* 3.4 2.0 + - - +
566D LEU* 2.8 58.9 + - + +
657D LEU* 5.5 5.2 - - + -
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Residues in contact with SER 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 3.6 29.0 - - - +
468D ILE* 4.2 4.7 - - - +
545D MET* 3.5 21.3 - - - +
546D ALA* 4.7 0.9 - - - -
549D ALA* 3.3 20.3 - - - +
559D ALA 2.7 24.9 + - - -
560D SER* 4.4 2.0 - - - -
561D PHE 2.9 0.4 + - - -
562D PHE* 1.3 76.3 - - - +
564D ASN* 1.3 58.5 + - - -
566D LEU* 2.9 6.2 + - - +
567D TYR* 2.8 29.8 + - - +
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Residues in contact with ASN 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C TYR* 5.1 6.2 + - + +
461D PHE* 3.2 38.5 - - + -
464D ILE* 4.6 14.3 - - - +
465D LEU* 3.8 23.0 - - - +
560D SER* 3.0 24.3 + - - +
561D PHE* 2.8 10.6 + - + +
563D SER* 1.3 75.5 - - - +
565D ALA* 1.3 53.9 + - - +
567D TYR* 3.9 13.0 - - + +
568D ASN* 2.8 31.4 + - - +
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Residues in contact with ALA 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C PHE* 4.0 9.5 - - + -
561D PHE* 2.8 48.5 + - + +
562D PHE 3.6 3.8 - - - +
564D ASN* 1.3 69.1 - - - +
566D LEU* 1.3 53.3 + - - +
567D TYR 3.1 1.6 - - - -
568D ASN* 3.7 4.9 - - - +
569D SER* 2.7 39.9 + - - -
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Residues in contact with LEU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D MET* 3.7 30.5 - - + -
562D PHE* 2.8 52.4 + - + +
563D SER 3.4 4.0 - - - +
565D ALA* 1.3 67.6 - - - +
567D TYR* 1.3 55.5 + - - +
569D SER* 2.3 25.4 + - - +
570D PHE* 3.3 44.3 + - + -
654D PHE* 4.6 9.6 - - + -
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Residues in contact with TYR 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ALA 2.7 24.3 + - - -
458D LEU* 4.2 6.6 + - - -
460D PRO* 3.2 38.1 - - + -
461D PHE* 4.2 23.5 - + + +
464D ILE* 5.3 7.6 - - + -
545D MET* 5.1 7.2 - - + -
563D SER 2.8 14.7 + - - +
564D ASN* 3.9 20.4 - - + +
566D LEU* 1.3 74.9 - - - +
568D ASN* 1.3 82.6 + - + +
569D SER 2.9 1.3 - - - -
570D PHE* 2.8 19.4 + - - +
571D TYR* 2.8 29.3 + + - +
595D PHE* 5.3 5.2 - + + -
596D LEU* 3.8 23.6 - - + -
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Residues in contact with ASN 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C MET* 4.2 23.2 - - - +
399C PHE* 3.5 27.1 - - + -
400C LEU* 5.7 0.8 - - - +
425C GLN* 3.1 27.1 + - - +
564D ASN 2.8 23.6 + - - +
565D ALA* 4.0 5.2 - - - +
567D TYR* 1.3 80.2 - - + +
569D SER* 1.3 59.6 + - - +
571D TYR* 3.6 14.6 - - - +
572D LEU* 3.4 26.5 - - - +
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Residues in contact with SER 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C PHE* 3.7 14.5 - - - -
403C PHE* 3.2 37.8 - - - -
565D ALA 2.7 10.5 + - - -
566D LEU* 2.3 43.7 + - - +
568D ASN* 1.3 74.5 - - - +
570D PHE* 1.3 61.6 + - - -
572D LEU 4.3 0.2 - - - -
573D ALA 3.7 5.0 + - - -
590D ILE* 3.7 16.0 - - - +
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Residues in contact with PHE 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D LEU* 3.3 35.7 - - + -
567D TYR* 2.8 11.5 + - - +
569D SER* 1.3 76.7 + - - +
571D TYR* 1.3 64.5 + - - +
572D LEU 3.3 0.2 - - - -
573D ALA* 3.3 2.2 + - - +
574D GLY* 3.0 19.6 + - - -
590D ILE* 4.2 14.8 - - + -
593D VAL* 3.0 45.5 - - + -
594D SER* 3.1 31.7 + - - +
595D PHE* 3.4 37.9 - + - -
596D LEU* 3.6 13.3 - - + +
654D PHE* 4.1 13.2 - + - -
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C TYR* 3.1 31.0 - - - -
425C GLN* 3.0 33.6 + - - -
549C LEU* 5.6 0.2 - - - +
453D PHE* 3.9 31.0 - + - -
454D MET* 5.4 7.9 - - + +
457D ALA* 4.3 13.0 - - + -
567D TYR* 2.8 34.7 + + + +
568D ASN* 3.6 12.3 - - - +
569D SER 3.4 0.2 - - - -
570D PHE* 1.3 75.4 - - - +
572D LEU* 1.3 73.8 + - + +
574D GLY* 3.2 14.7 + - - +
577D MET* 3.5 29.7 - - + +
596D LEU* 3.5 12.7 - - + +
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Residues in contact with LEU 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C PHE* 4.2 9.4 - - + +
400C LEU* 3.7 33.4 - - + -
403C PHE* 3.5 49.4 - - + -
404C VAL* 5.7 1.1 - - + -
425C GLN* 4.3 9.9 - - + +
568D ASN* 3.4 18.6 - - - +
571D TYR* 1.3 89.5 - - + +
573D ALA* 1.3 55.1 + - - +
574D GLY 2.8 22.2 - - - +
577D MET* 5.2 3.8 - - + -
578D ILE* 2.8 40.1 + - + +
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Residues in contact with ALA 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C PHE* 4.3 5.0 - - - -
569D SER 3.7 9.5 + - - +
570D PHE* 3.3 11.1 + - - +
572D LEU* 1.3 76.9 - - - +
574D GLY* 1.3 64.2 + - - +
575D GLY 3.6 0.7 + - - -
578D ILE* 4.9 5.4 - - - +
580D LEU* 4.0 9.5 - - - +
583D LEU* 5.1 4.3 - - - +
588D ALA* 6.2 0.2 - - - +
590D ILE* 3.8 18.8 - - + -
591D SER* 3.4 44.4 - - - -
594D SER* 4.1 7.0 - - - -
597D ARG* 4.1 1.8 - - - +
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Residues in contact with GLY 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D PHE* 4.2 11.2 - - - -
570D PHE 3.0 13.3 + - - -
571D TYR 3.6 10.9 - - - +
572D LEU 2.8 20.8 + - - +
573D ALA* 1.3 76.5 - - - +
575D GLY* 1.3 69.0 + - - +
576D PHE 3.8 0.7 - - - -
577D MET 4.3 0.2 + - - -
578D ILE* 3.9 5.0 + - - +
580D LEU 5.5 0.2 + - - -
596D LEU* 4.8 0.4 - - - -
597D ARG* 3.6 23.9 - - - +
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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
------------------------------------------------------------
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