Contacts of the helix formed by residues 549 - 564 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B TRP* 5.4 9.4 - - - -
548E LEU* 1.3 77.2 - - - +
550E GLY* 1.3 63.7 + - - +
551E GLY 3.6 2.9 + - - -
552E GLN* 3.1 37.5 + - - +
553E ARG* 3.0 23.3 + - - +
663E THR* 4.6 17.9 - - - -
664E GLU* 3.9 7.5 + - - -
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Residues in contact with GLY 550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495E SER* 5.3 0.5 + - - -
549E SER* 1.3 72.2 - - - +
551E GLY* 1.3 57.5 + - - +
553E ARG* 3.5 27.3 + - - +
554E ALA* 3.0 28.8 + - - +
577E TYR* 4.1 12.5 - - - +
660E SER* 3.3 22.9 + - - +
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Residues in contact with GLY 551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E SER* 3.2 3.8 + - - -
550E GLY* 1.3 76.2 - - - +
552E GLN* 1.3 55.1 + - - +
554E ALA* 3.4 2.8 + - - +
555E ARG* 3.1 40.4 + - - +
577E TYR 4.1 0.9 - - - -
578E LEU* 3.8 12.2 - - - +
660E SER* 3.1 9.5 + - - -
664E GLU* 3.3 27.5 + - - +
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Residues in contact with GLN 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B PRO* 5.8 3.8 - - - +
526E LEU* 4.5 1.7 - - + +
529E ASP* 2.7 39.8 + - + +
533E PHE* 4.8 12.9 - - - -
547E THR 4.7 1.4 - - - +
548E LEU* 3.6 26.8 - - + +
549E SER* 3.1 39.7 + - - +
551E GLY* 1.3 73.9 - - - +
553E ARG* 1.3 60.2 + - - +
555E ARG* 3.3 15.7 + - - +
556E ILE* 2.9 38.5 + - + +
667E ARG* 6.1 0.7 - - - -
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Residues in contact with ARG 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495E SER* 3.8 22.2 + - - -
497E ILE* 3.8 26.6 - - + +
544E GLY 3.5 22.5 + - - -
545E GLY* 2.8 25.1 + - - -
546E ILE* 5.0 0.6 - - - +
548E LEU* 2.8 39.2 + - + -
549E SER 3.0 12.2 + - - +
550E GLY* 3.6 26.2 - - - +
552E GLN* 1.3 74.7 - - - +
554E ALA* 1.3 57.8 + - - +
556E ILE* 3.9 1.8 - - - +
557E SER* 2.9 32.6 + - - -
577E TYR* 5.6 3.4 - - - -
656E GLU* 5.1 12.5 + - - +
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Residues in contact with ALA 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E SER* 3.5 16.1 + - - +
550E GLY 3.0 17.5 + - - +
551E GLY 3.5 6.7 - - - +
553E ARG* 1.3 77.3 - - - +
555E ARG* 1.3 56.0 + - - +
557E SER* 3.8 1.9 - - - -
558E LEU* 3.1 28.1 + - - +
574E PRO* 4.1 21.7 - - - +
577E TYR* 4.6 11.9 - - + +
578E LEU* 4.3 15.0 - - + -
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Residues in contact with ARG 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524E CYS* 3.0 30.1 - - - +
525E GLN* 3.3 20.0 + - - +
526E LEU* 3.8 9.8 - - + +
529E ASP* 2.8 25.1 + - - -
551E GLY* 3.1 25.8 + - - +
552E GLN* 3.5 23.2 - - - +
553E ARG 3.3 0.2 - - - -
554E ALA* 1.3 75.0 - - - +
556E ILE* 1.3 60.9 + - - +
558E LEU* 3.4 7.0 + - - +
559E ALA* 2.8 29.8 + - - +
578E LEU* 4.1 8.3 - - + +
582E THR* 4.8 2.7 - - - -
586E ILE* 3.7 23.1 - - + -
664E GLU* 2.7 33.8 + - - -
667E ARG* 3.8 20.4 - - - +
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Residues in contact with ILE 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497E ILE* 3.9 16.6 - - + -
502E ILE* 4.0 28.7 - - + +
505E ASN* 4.0 24.5 - - + -
506E ILE* 4.1 7.9 - - + +
526E LEU* 3.8 25.8 - - + -
541E LEU* 5.2 1.3 - - + -
548E LEU* 3.8 31.6 - - + -
552E GLN* 2.9 24.4 + - + +
553E ARG 3.9 2.9 - - - +
555E ARG* 1.3 75.6 - - - +
557E SER* 1.3 59.3 + - - +
559E ALA* 3.2 2.9 + - - +
560E ARG* 2.9 32.1 + - - +
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Residues in contact with SER 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E CYS* 4.0 15.2 - - - -
492E SER 5.0 2.6 + - - -
494E PHE 4.5 3.5 + - - -
495E SER* 3.9 26.5 + - - -
496E TRP 4.1 5.0 + - - -
553E ARG 2.9 19.7 + - - -
554E ALA 3.8 4.0 - - - -
555E ARG 3.3 0.2 - - - -
556E ILE* 1.3 77.5 - - - +
558E LEU* 1.3 59.5 + - - +
560E ARG* 3.5 26.8 + - - +
561E ALA* 3.3 20.4 + - - +
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Residues in contact with LEU 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E CYS* 3.8 22.5 - - - -
524E CYS* 3.9 15.3 - - + -
554E ALA 3.1 17.8 + - - +
555E ARG* 3.8 5.6 - - - +
557E SER* 1.3 72.2 - - - +
559E ALA* 1.3 60.6 + - - +
561E ALA* 3.1 2.9 + - - +
562E VAL* 2.9 47.4 + - + +
571E LEU* 4.4 18.8 - - + -
574E PRO* 4.3 14.8 - - + +
575E PHE* 4.0 15.7 - - + -
586E ILE* 3.7 30.7 - - + -
590E CYS* 4.0 8.3 - - + -
591E VAL* 5.3 2.5 - - + -
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Residues in contact with ALA 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E ILE* 3.9 13.7 - - + -
520E VAL* 3.5 25.0 - - + +
524E CYS* 3.9 8.2 - - - -
526E LEU* 3.7 21.3 - - + -
555E ARG 2.8 18.1 + - - +
556E ILE 3.4 5.2 - - - +
558E LEU* 1.3 76.3 - - - +
560E ARG* 1.3 53.1 + - - +
562E VAL* 3.2 0.7 + - - -
563E TYR* 2.8 37.6 + - - +
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Residues in contact with ARG 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E TRP* 2.7 64.3 + - - +
497E ILE* 4.0 0.6 - - - +
498E MET* 4.2 4.8 - - - +
505E ASN* 2.8 53.6 + - - +
506E ILE* 3.5 18.3 - - - +
508E ALA* 3.9 18.2 - - + +
556E ILE* 2.9 22.1 + - - +
557E SER* 3.6 26.8 + - - +
558E LEU 3.3 0.2 - - - -
559E ALA* 1.3 75.8 - - - +
561E ALA* 1.3 63.5 + - - +
563E TYR* 3.9 1.6 - - - +
564E LYS* 3.3 22.3 + - - +
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Residues in contact with ALA 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E SER* 2.5 30.9 + - - +
490E PHE 4.1 9.6 - - - +
491E CYS* 3.6 31.9 - - + +
557E SER 3.3 5.8 + - - +
558E LEU* 3.1 9.3 + - + +
560E ARG* 1.3 80.4 - - - +
562E VAL* 1.3 61.3 + - - +
564E LYS* 3.7 3.5 + - - +
569E TYR* 3.3 11.4 - - - -
571E LEU* 4.7 8.5 - - + -
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Residues in contact with VAL 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E ARG* 3.5 9.9 + - - -
520E VAL* 4.0 8.9 - - + +
524E CYS* 4.9 0.7 - - - -
558E LEU* 2.9 30.1 + - + +
559E ALA* 3.8 4.9 - - - +
561E ALA* 1.3 75.4 - - + +
563E TYR* 1.3 67.8 + - - +
564E LYS 3.2 9.1 - - - +
569E TYR* 3.9 9.6 + - + -
571E LEU* 5.5 0.7 - - + -
590E CYS* 3.5 25.8 - - - -
594E LEU* 3.7 30.7 - - + -
595E MET* 3.7 28.5 - - + -
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Residues in contact with TYR 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E ILE* 4.0 22.7 - - + +
507E ILE* 3.4 23.1 - - + +
510E VAL* 3.7 29.2 - - + -
511E SER 3.1 10.6 + - - -
512E TYR* 3.4 3.8 - - - -
513E ASP* 2.8 32.1 + - - +
516E ARG* 2.8 43.0 + - + +
517E TYR* 3.6 41.5 - + + -
520E VAL* 3.9 12.8 - - + +
559E ALA 2.8 21.8 + - - +
560E ARG 3.9 4.0 - - - +
562E VAL* 1.3 73.3 - - - +
564E LYS* 1.3 62.4 + - - +
565E ASP 3.3 0.7 + - - -
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Residues in contact with LYS 564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E ARG* 4.4 18.3 - - - +
488E ILE 2.9 31.1 + - - +
489E SER* 3.9 18.2 - - - +
510E VAL* 5.1 21.1 - - + -
560E ARG 3.3 10.4 + - - +
561E ALA 3.8 9.6 - - - +
562E VAL 3.2 6.5 - - - +
563E TYR* 1.3 81.9 - - - +
565E ASP* 1.3 67.1 + - - +
566E ALA* 4.8 0.2 - - - -
569E TYR* 2.6 32.2 + - - -
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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