Contacts of the helix formed by residues 542 - 558 (chain D) in PDB entry 1M7X
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 ASP 542 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706B GLY 3.5 25.6 - - - +
707B ARG* 5.0 12.1 + - - +
708B GLN* 5.4 1.5 - - - +
541D GLY* 1.3 74.2 - - - -
543D ALA* 1.3 68.3 + - + +
544D TRP* 3.4 10.1 + - - +
545D GLN* 2.7 50.9 + - - +
546D LYS* 2.8 11.6 + - - -
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Residues in contact with ALA 543 (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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542D ASP* 1.3 73.7 - - + +
544D TRP* 1.3 62.8 + - - +
546D LYS* 3.3 13.5 + - - +
547D PHE* 3.1 33.0 + - + -
595D TRP* 3.5 29.4 - - + -
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Residues in contact with TRP 544 (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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542D ASP* 2.9 11.4 + - - +
543D ALA* 1.3 76.9 - - - +
545D GLN* 1.3 72.7 + - + +
547D PHE* 3.1 6.1 + - - +
548D ALA* 2.8 46.2 + - + +
551D ARG* 4.2 6.4 + - - -
595D TRP* 4.1 31.0 - + + -
659D PRO* 6.0 1.1 - - + -
682D ASP* 3.8 13.7 - - - -
687D HIS 3.5 16.0 + - - -
688D GLY* 4.1 8.8 + - - -
689D SER* 3.7 29.5 - - - +
717D PRO* 4.4 17.9 - - + -
718D LEU* 4.1 13.7 - - + -
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Residues in contact with GLN 545 (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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670B ASN* 5.6 2.8 - - - +
540D PRO 4.0 6.3 - - - +
541D GLY* 3.1 11.7 - - - -
542D ASP* 2.7 45.3 + - - +
544D TRP* 1.3 92.5 - - + +
546D LYS* 1.3 51.5 + - - +
548D ALA* 3.3 2.8 - - - +
549D ASN* 2.8 41.4 + - - +
659D PRO* 4.0 19.5 - - + +
718D LEU* 3.6 20.2 - - + -
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Residues in contact with LYS 546 (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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536D LEU* 3.5 35.4 + - + +
537D ASP* 3.6 22.6 + - - +
539D MET* 3.4 40.5 + - + +
540D PRO 3.8 7.6 - - - +
541D GLY 3.7 17.9 - - - +
542D ASP 2.8 16.5 + - - +
543D ALA* 3.5 16.8 - - - +
544D TRP 3.2 0.2 - - - -
545D GLN* 1.3 75.6 - - - +
547D PHE* 1.3 63.7 + - + +
550D LEU* 3.2 19.2 + - - +
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Residues in contact with PHE 547 (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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536D LEU* 4.0 17.9 - - + -
543D ALA* 3.1 23.7 + - + -
544D TRP 3.1 6.3 + - - +
546D LYS* 1.3 79.1 - - + +
548D ALA* 1.3 69.5 + - - +
550D LEU* 3.3 5.9 + - + +
551D ARG* 3.0 41.1 + - - +
573D ALA* 3.8 22.0 - - + -
595D TRP* 3.2 65.3 - + + -
596D HIS* 3.7 25.8 - + - -
599D VAL* 3.7 18.6 - - + +
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Residues in contact with ALA 548 (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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544D TRP* 2.8 44.9 + - + +
545D GLN* 3.3 9.0 - - - +
547D PHE* 1.3 79.3 - - - +
549D ASN* 1.3 64.8 + - - +
551D ARG* 3.0 20.1 + - - +
552D ALA 3.0 17.5 + - - -
718D LEU* 3.1 24.7 - - + +
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Residues in contact with ASN 549 (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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493D MET* 3.6 9.8 - - + +
497D PRO* 5.1 1.8 - - - +
500D ARG* 2.6 32.2 + - - +
539D MET* 3.6 17.5 - - + -
540D PRO* 3.5 31.5 + - - +
545D GLN* 2.8 30.1 + - - +
546D LYS 3.6 2.7 - - - +
548D ALA* 1.3 73.2 - - - +
550D LEU* 1.3 64.5 + - - +
552D ALA* 3.1 6.1 + - - +
553D TYR* 2.8 24.8 + - - +
657D PHE* 5.0 1.0 - - - -
718D LEU* 3.3 25.4 - - - +
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Residues in contact with LEU 550 (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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535D ILE* 3.5 34.3 - - + +
536D LEU* 4.0 20.6 - - + +
539D MET* 4.0 8.9 - - + -
546D LYS 3.2 11.9 + - - +
547D PHE* 3.3 8.3 + - + +
549D ASN* 1.3 78.3 - - - +
551D ARG* 1.3 62.9 + - + +
553D TYR* 3.4 8.7 + - + +
554D TYR* 3.0 60.3 + - + +
573D ALA* 3.5 35.2 - - + -
599D VAL* 4.6 8.3 - - + -
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Residues in contact with ARG 551 (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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544D TRP* 4.2 7.7 + - - +
547D PHE* 3.0 49.5 + - - +
548D ALA* 3.0 28.0 + - - +
550D LEU* 1.3 75.6 - - - +
552D ALA* 1.3 66.5 + - - +
554D TYR* 2.8 15.8 + - - +
555D GLY 2.9 11.3 + - - -
595D TRP* 5.0 2.6 + - - -
599D VAL* 4.4 19.6 - - + +
602D LEU* 3.5 23.7 - - + +
681D THR* 2.8 35.3 + - - +
682D ASP* 4.8 2.2 + - - +
686D TYR* 3.6 40.4 + - - +
687D HIS 3.8 5.4 + - - -
688D GLY* 3.6 24.6 - - - -
718D LEU 5.5 0.8 + - - -
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Residues in contact with ALA 552 (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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548D ALA 3.0 5.3 + - - -
549D ASN* 3.5 8.7 - - - +
551D ARG* 1.3 75.9 - - - +
553D TYR* 1.3 62.4 + - - +
556D TRP* 3.1 12.6 + - - +
657D PHE* 4.1 19.2 - - + -
681D THR* 3.8 2.5 + - - -
718D LEU 3.2 32.3 - - - +
719D ALA 3.6 11.4 - - - +
720D THR* 3.1 29.7 - - - +
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Residues in contact with TYR 553 (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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485D TRP* 3.6 20.5 - + - -
489D THR* 3.2 35.3 + - + -
490D LEU* 3.1 36.8 - - + +
493D MET* 3.9 28.0 - - + -
507D LEU* 6.4 0.9 - - + -
523D LEU* 3.6 28.7 - - + +
535D ILE* 4.4 10.3 - - + -
539D MET* 4.6 3.4 - - + -
549D ASN 2.8 16.6 + - - +
550D LEU* 3.4 7.9 - - + +
552D ALA* 1.3 76.3 - - - +
554D TYR* 1.3 69.4 + + - +
556D TRP* 3.1 11.1 + + - +
557D MET* 2.8 26.2 + - + +
657D PHE* 4.2 7.5 - + - -
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Residues in contact with TYR 554 (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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523D LEU* 3.8 24.2 - - + +
535D ILE* 4.4 5.0 - - + +
550D LEU* 3.0 44.3 + - + +
551D ARG* 2.8 12.5 + - - +
553D TYR* 1.3 79.9 - + - +
555D GLY* 1.3 58.0 + - - +
557D MET* 2.9 5.8 + - - -
558D TRP* 2.8 47.4 + + + +
566D LEU* 4.0 9.3 - - + +
570D ASN* 3.0 40.2 + - - +
599D VAL* 4.1 15.5 - - + -
602D LEU* 4.5 6.7 - - + -
603D VAL* 4.0 26.9 - - + -
606D LEU* 3.5 17.7 - - + -
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Residues in contact with GLY 555 (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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551D ARG 2.9 10.3 + - - -
554D TYR* 1.3 77.4 - - - +
556D TRP* 1.3 59.5 + - - +
559D ALA* 3.5 3.5 + - - +
606D LEU* 4.0 19.6 - - - +
679D LEU* 4.4 0.4 - - - -
681D THR* 4.3 2.4 - - - +
720D THR* 3.2 24.9 + - - -
722D TRP* 3.0 32.8 + - - -
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Residues in contact with TRP 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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485D TRP* 4.4 11.3 - + - +
489D THR* 4.3 11.9 - - + +
507D LEU* 3.6 39.8 - - + +
552D ALA 3.1 13.0 + - - +
553D TYR* 3.4 16.8 - + - +
554D TYR 3.1 0.2 - - - -
555D GLY* 1.3 75.1 - - - +
557D MET* 1.3 65.9 + - - +
559D ALA* 3.4 3.5 + - - +
560D PHE* 2.9 52.1 + + + +
628D TRP* 3.9 15.0 - + - -
639D LEU* 3.7 42.2 - - + -
641D PHE* 3.6 24.8 - + - -
653D VAL* 5.3 2.5 - - + -
655D SER* 3.3 26.0 - - - +
657D PHE* 4.1 14.1 - + + -
720D THR* 3.8 2.9 + - - -
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Residues in contact with MET 557 (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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485D TRP* 3.7 31.0 - - + -
521D LEU* 3.1 42.7 - - + +
523D LEU* 3.5 32.5 - - + +
553D TYR* 2.8 15.3 + - + +
554D TYR* 2.9 10.7 + - - +
556D TRP* 1.3 78.7 - - - +
558D TRP* 1.3 81.9 + - + +
559D ALA 3.2 0.9 + - - -
560D PHE 3.6 1.0 + - - -
564D LYS* 3.1 26.5 + - + -
565D LEU 3.6 23.1 - - - +
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Residues in contact with TRP 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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244D SER* 3.9 10.9 + - - -
281D PHE* 5.1 0.7 - + - -
554D TYR* 2.8 49.1 + + + +
557D MET* 1.3 102.3 - - + +
559D ALA* 1.3 57.0 + - - +
564D LYS* 3.4 31.9 - - + +
566D LEU* 3.8 35.9 - - + -
603D VAL* 4.4 14.6 - - + -
606D LEU* 3.4 43.3 + - + -
607D ASN* 2.9 28.9 + - - +
610D TYR* 3.6 28.1 - + + -
616D MET* 4.1 3.1 - - - +
722D TRP* 3.6 25.2 - - + -
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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