Contacts of the helix formed by residues 549 - 564 (chain D) in PDB entry 1XMI
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 SER 549 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A TRP* 4.8 3.2 - - - -
543A GLU* 4.0 22.8 - - - -
548D LEU* 1.3 75.6 - - - +
550D GLY* 1.3 64.3 + - - +
551D GLY* 3.7 4.1 + - - -
552D GLN* 3.0 36.8 + - - +
553D ARG* 3.1 24.4 + - - +
660D SER 6.2 0.2 - - - -
663D THR* 4.1 21.7 + - - -
664D GLU* 4.4 5.4 + - - -
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Residues in contact with GLY 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D SER* 5.4 0.7 + - - -
549D SER* 1.3 72.9 - - - +
551D GLY* 1.3 59.6 + - - +
553D ARG* 3.6 23.5 + - - +
554D ALA* 3.1 24.1 + - - +
577D TYR* 4.0 13.0 - - - +
660D SER* 3.2 24.7 + - - +
663D THR* 6.1 0.2 - - - +
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Residues in contact with GLY 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D SER* 3.2 3.6 + - - -
550D GLY* 1.3 74.4 - - - +
552D GLN* 1.3 57.9 + - - +
554D ALA* 3.4 3.1 + - - +
555D ARG* 3.0 39.9 + - - +
577D TYR 4.2 0.4 - - - -
578D LEU* 3.7 17.6 - - - +
660D SER* 3.1 9.1 + - - -
664D GLU* 3.6 21.9 + - - +
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Residues in contact with GLN 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TRP* 5.8 3.4 - - - -
499A PRO* 5.8 3.8 - - - +
543A GLU* 4.6 4.0 - - - +
526D LEU* 4.6 1.3 - - + +
529D ASP* 3.0 33.3 + - - +
532D LYS* 6.3 0.6 - - - +
533D PHE* 3.9 20.0 - - - -
547D THR 4.8 1.4 - - - +
548D LEU* 3.6 28.1 - - + +
549D SER* 3.0 38.6 + - - +
551D GLY* 1.3 73.4 - - - +
553D ARG* 1.3 58.7 + - - +
555D ARG* 3.2 18.5 + - - +
556D ILE* 2.9 37.8 + - + +
667D ARG* 6.1 0.2 - - - -
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Residues in contact with ARG 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D SER* 3.9 21.8 + - - -
497D ILE* 3.7 35.9 - - + +
546D ILE* 4.2 18.5 + - - +
548D LEU* 2.8 42.5 + - + +
549D SER 3.1 12.6 + - - +
550D GLY* 3.8 22.9 - - - +
552D GLN* 1.3 77.3 - - - +
554D ALA* 1.3 58.6 + - - +
556D ILE* 3.4 2.5 + - - +
557D SER* 2.9 31.9 + - - -
577D TYR* 5.9 2.0 - - - -
656D GLU* 4.9 13.5 + - - -
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Residues in contact with ALA 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D CYS* 5.4 0.9 - - - -
495D SER* 3.4 18.1 + - - +
550D GLY 3.1 16.8 + - - +
551D GLY 3.6 5.2 - - - +
553D ARG* 1.3 78.6 - - - +
555D ARG* 1.3 58.4 + - - +
557D SER* 3.9 1.4 - - - -
558D LEU* 3.1 29.5 + - - +
574D PRO 4.0 20.6 - - - +
577D TYR* 4.6 11.0 - - + +
578D LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D CYS* 2.9 31.5 - - + +
525D GLN* 3.3 13.3 + - - +
526D LEU* 3.6 11.5 - - + +
529D ASP* 3.0 29.5 + - - -
551D GLY* 3.0 27.5 + - - +
552D GLN* 3.2 27.1 + - - +
554D ALA* 1.3 75.4 - - - +
556D ILE* 1.3 59.5 + - - +
558D LEU* 3.5 6.1 + - - +
559D ALA* 2.9 28.4 + - - +
578D LEU* 4.0 8.4 - - + +
582D THR* 4.8 1.3 - - - +
586D ILE* 3.9 22.0 - - + -
664D GLU* 2.8 40.9 + - - -
667D ARG* 3.8 15.9 - - - +
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Residues in contact with ILE 556 (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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497D ILE* 4.1 13.5 - - + -
502D ILE* 4.2 23.6 - - + +
505D ASN* 4.0 27.1 - - + -
506D ILE* 4.2 10.0 - - + +
526D LEU* 3.9 25.8 - - + -
541D LEU* 5.0 1.1 - - + -
548D LEU* 4.0 30.1 - - + -
552D GLN* 2.9 28.8 + - + +
553D ARG* 3.8 4.7 - - - +
555D ARG* 1.3 71.8 - - - +
557D SER* 1.3 61.2 + - - +
559D ALA* 3.2 3.1 + - - +
560D ARG* 2.9 32.5 + - - +
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Residues in contact with SER 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D PHE 5.5 0.2 - - - +
491D CYS* 3.9 15.5 - - - +
492D SER 5.0 2.6 + - - -
494D PHE 4.3 3.1 + - - -
495D SER* 3.9 27.7 + - - -
496D TRP* 3.9 5.2 + - - +
497D ILE* 5.1 0.2 - - - +
553D ARG 2.9 18.4 + - - -
554D ALA 3.9 4.3 - - - -
556D ILE* 1.3 77.6 - - - +
558D LEU* 1.3 60.1 + - - +
560D ARG* 3.7 25.2 + - - +
561D ALA* 3.4 20.6 + - - +
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Residues in contact with LEU 558 (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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491D CYS* 3.9 20.3 - - + -
524D CYS* 4.1 14.8 - - + -
554D ALA 3.1 17.7 + - - +
555D ARG* 3.8 5.8 - - + +
556D ILE 3.2 0.2 - - - -
557D SER* 1.3 75.2 - - - +
559D ALA* 1.3 65.5 + - - +
561D ALA* 3.2 2.4 + - - +
562D VAL* 2.9 43.6 + - + +
571D LEU* 4.4 17.0 - - + -
574D PRO* 4.5 13.2 - - + +
575D PHE* 3.8 18.8 - - + -
578D LEU* 6.2 1.1 - - + -
586D ILE* 3.6 31.9 - - + -
590D CYS* 4.4 6.1 - - - -
591D VAL* 5.4 3.4 - - + -
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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
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506D ILE* 3.9 13.5 - - + -
520D VAL* 3.5 20.1 - - + +
524D CYS* 3.8 14.1 - - + -
526D LEU* 3.6 19.7 - - + -
555D ARG 2.9 18.3 + - - +
556D ILE 3.4 5.6 - - - +
558D LEU* 1.3 77.1 - - - +
560D ARG* 1.3 56.2 + - - +
562D VAL* 3.3 0.4 + - - -
563D TYR* 2.9 32.6 + - - +
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Residues in contact with ARG 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D TRP* 2.9 58.0 + - - +
497D ILE* 4.2 3.4 - - - +
498D MET* 4.0 4.8 - - - +
505D ASN* 2.7 58.8 + - - +
506D ILE* 3.4 17.0 - - - +
507D ILE 5.5 0.4 - - - +
508D ALA* 4.4 15.1 - - + +
556D ILE* 2.9 17.6 + - - +
557D SER* 3.8 27.9 + - - +
558D LEU 3.2 0.2 - - - -
559D ALA* 1.3 78.0 - - - +
561D ALA* 1.3 62.3 + - - +
562D VAL 3.3 0.3 + - - -
563D TYR* 3.5 8.5 + - - +
564D LYS* 3.5 12.8 + - - +
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Residues in contact with ALA 561 (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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489D SER* 2.5 30.3 + - - +
490D PHE 3.8 12.8 - - - +
491D CYS* 3.7 31.4 - - + +
557D SER 3.4 6.3 + - - +
558D LEU 3.2 7.9 + - - +
560D ARG* 1.3 81.2 - - - +
562D VAL* 1.3 59.6 + - - +
564D LYS* 3.7 4.0 + - - -
569D TYR* 3.2 12.8 - - - -
571D LEU* 4.8 7.9 - - + -
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Residues in contact with VAL 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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516D ARG* 3.2 15.4 + - - -
520D VAL* 4.0 8.8 - - + +
524D CYS* 4.9 0.4 - - - -
558D LEU* 2.9 30.4 + - + +
559D ALA* 3.8 5.6 - - - +
561D ALA* 1.3 77.3 - - + +
563D TYR* 1.3 64.6 + - - +
564D LYS 3.2 4.1 + - - +
569D TYR* 3.8 9.0 + - - -
571D LEU* 5.3 1.1 - - + -
590D CYS* 3.5 29.4 - - - -
594D LEU* 3.9 28.0 - - + -
595D MET* 3.7 28.0 - - + -
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Residues in contact with TYR 563 (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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506D ILE* 4.0 20.4 - - + +
507D ILE* 3.5 30.9 - - + +
510D VAL* 4.2 19.0 - - + +
511D SER 2.7 27.8 + - - -
512D TYR* 3.4 2.4 - - - -
513D ASP* 2.8 23.6 + - - +
516D ARG* 2.5 48.8 + - + +
517D TYR* 3.7 33.9 - - + -
520D VAL* 3.9 12.5 - - + +
559D ALA 2.9 17.9 + - - +
560D ARG 3.8 4.7 - - - +
562D VAL* 1.3 78.0 - - - +
564D LYS* 1.3 59.1 + - - +
565D ASP 3.3 1.0 + - - -
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Residues in contact with LYS 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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487D ARG* 4.3 28.5 - - - +
488D ILE 2.9 29.2 + - - +
489D SER* 3.9 13.9 - - - +
510D VAL* 4.6 24.0 - - + -
516D ARG* 3.7 0.2 - - - -
560D ARG 3.5 8.9 + - - +
561D ALA* 3.9 9.9 - - - +
562D VAL 3.2 1.2 - - - -
563D TYR* 1.3 82.4 - - - +
565D ASP* 1.3 60.0 + - - +
566D ALA* 3.3 1.3 + - + -
569D TYR* 2.4 36.0 + - - -
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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
------------------------------------------------------------
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