Contacts of the helix formed by residues 546 - 559 (chain J) in PDB entry 1MVW
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 546 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544J LYS 4.6 3.1 + - - -
545J ALA* 1.3 79.0 + - - +
547J ASP* 1.3 70.5 + - + +
548J THR* 3.0 27.6 - - - +
549J SER* 2.9 17.9 + - - -
550J PHE* 2.8 33.1 + - - +
596J LEU* 3.5 7.4 - - - +
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Residues in contact with ASP 547 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546J THR* 1.3 76.8 - - + +
548J THR* 1.3 53.6 + - - +
550J PHE* 3.0 12.9 - - - +
551J MLY 2.7 35.9 + - - +
592J ILE* 3.7 17.7 - - + +
593J SER* 3.3 8.2 - - - -
594J GLY* 2.9 29.3 + - - -
595J TRP* 4.5 0.6 - - - +
596J LEU* 3.4 32.9 + - - +
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Residues in contact with THR 548 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546J THR* 3.0 17.5 - - - +
547J ASP* 1.3 79.9 - - - +
549J SER* 1.3 62.9 + - - +
551J MLY 3.3 29.2 + - - +
552J ASN* 2.8 41.8 + - - +
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Residues in contact with SER 549 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539J GLU* 2.8 29.2 + - - +
544J LYS 5.6 0.2 - - - -
545J ALA* 3.6 3.5 - - - +
546J THR* 2.9 30.3 + - - -
548J THR* 1.3 85.5 - - - +
550J PHE* 1.3 79.5 + - - +
552J ASN* 3.0 15.7 + - - +
553J MLY 3.1 12.5 + - - +
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Residues in contact with PHE 550 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532J ILE* 4.4 3.6 - - + -
535J ILE* 3.9 20.2 - - + -
536J LEU* 3.2 52.5 - - + -
539J GLU* 4.1 10.8 - - + -
546J THR 2.8 9.7 + - - +
547J ASP* 3.0 8.1 - - - +
549J SER* 1.3 80.2 + - - +
551J MLY 1.3 64.4 + - - +
553J MLY 3.0 5.3 + - - +
554J LEU* 2.9 39.6 + - + +
592J ILE* 3.0 40.4 - - + -
595J TRP* 4.1 15.5 - + + -
596J LEU* 3.8 18.8 - - + -
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Residues in contact with MLY 551 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547J ASP 2.7 19.4 + - - +
548J THR* 3.5 28.9 + - - +
549J SER 3.1 0.2 - - - -
550J PHE* 1.3 76.1 + - - +
552J ASN* 1.3 70.5 + - - +
554J LEU* 2.7 32.2 + - + +
555J TYR* 3.0 42.0 + - + +
576J GLU* 5.3 4.9 - - - -
577J ALA* 5.0 2.9 - - - -
578J HIS* 3.8 33.7 - - + +
592J ILE* 4.4 17.9 - - + -
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Residues in contact with ASN 552 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548J THR* 2.8 36.4 + - - +
549J SER* 3.0 8.8 + - - +
551J MLY 1.3 90.2 + - - +
553J MLY 1.3 64.3 + - + +
555J TYR* 2.9 11.7 + - - -
556J ASP* 2.9 15.6 + - - +
47Y MET* 2.8 22.9 - - + +
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Residues in contact with MLY 553 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535J ILE* 3.9 14.7 - - + +
538J GLU* 4.3 7.9 - - - +
539J GLU* 3.0 41.9 + - - +
542J PHE* 3.3 47.1 - - - -
549J SER 3.1 8.0 + - - +
550J PHE* 3.0 10.1 + - - +
552J ASN* 1.3 79.7 + - + +
554J LEU* 1.3 62.9 + - - +
555J TYR 3.4 0.2 + - - -
148W THR* 5.0 6.7 - - - -
167W GLU* 5.2 13.9 - - - -
168W GLY* 6.4 0.4 - - - -
355W MET* 5.5 0.2 - - - -
45Y VAL* 2.8 62.4 - - + +
46Y GLY* 2.9 30.5 - - - +
47Y MET* 3.4 1.1 - - + +
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Residues in contact with LEU 554 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532J ILE* 4.1 22.9 - - + -
535J ILE* 3.4 35.9 - - + -
550J PHE* 2.9 36.9 + - + +
551J MLY 2.7 15.0 + - + +
553J MLY 1.3 79.2 + - - +
555J TYR* 1.3 60.8 + - + +
558J HIS* 3.1 31.6 + - + +
565J PHE* 4.1 17.1 - - + -
579J PHE* 3.9 31.6 - - + -
592J ILE* 4.4 5.2 - - + -
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Residues in contact with TYR 555 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551J MLY 3.0 52.8 + - + +
552J ASN* 2.9 16.5 + - - +
554J LEU* 1.3 75.7 - - + +
556J ASP* 1.3 57.9 + - - +
557J GLU 2.7 13.5 + - - -
558J HIS 2.7 0.2 + - - -
559J LEU* 2.7 62.7 + - + +
565J PHE* 3.8 17.0 - + - -
567J LYS* 4.4 11.9 - - + +
568J PRO* 4.5 4.3 - - - +
578J HIS* 2.9 31.4 + - - -
579J PHE* 4.9 0.4 - - + -
47Y MET* 2.1 5.4 - - - -
95Y ARG* 5.7 2.6 + - - -
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Residues in contact with ASP 556 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552J ASN* 2.9 10.8 + - - +
555J TYR* 1.3 57.9 - - - +
557J GLU* 1.3 45.9 - - - -
559J LEU 5.0 3.3 - - - +
44Y MET* 3.2 32.8 - - + +
47Y MET* 0.7 379.0 - - + +
48Y GLY 2.3 16.6 + - - +
50Y LYS* 5.2 1.7 - - - +
53Y TYR* 5.1 4.4 - - - -
57Y GLU* 4.2 15.3 - - - +
61Y LYS* 4.4 7.3 + - - -
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Residues in contact with GLU 557 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530J MET* 3.6 33.2 - - - +
535J ILE* 4.2 0.9 - - + -
554J LEU 4.2 0.4 - - - +
555J TYR 2.7 2.0 + - - -
556J ASP 1.3 57.3 - - - -
558J HIS* 1.3 82.9 + - - +
559J LEU 5.2 0.4 - - - -
561J LYS* 4.2 20.5 + - - +
43Y VAL* 5.7 0.9 - - - +
44Y MET 4.7 0.2 - - - +
46Y GLY* 0.7 75.4 + - - +
47Y MET* 1.9 51.8 - - - +
48Y GLY* 3.4 11.1 + - - -
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Residues in contact with HIS 558 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525J LEU* 3.6 25.5 - - + +
530J MET* 2.7 31.9 + - + -
531J GLY* 3.6 17.0 - - - -
532J ILE* 4.1 6.0 + - + -
535J ILE* 3.8 8.9 - - + +
554J LEU* 3.1 28.2 + - + +
555J TYR 2.7 4.6 + - - -
557J GLU* 1.3 89.3 + - + +
559J LEU* 1.3 64.1 + - - +
560J GLY 3.3 0.3 + - - -
561J LYS* 4.0 2.0 - - - -
562J SER* 2.8 39.9 + - - +
565J PHE* 3.7 25.5 - + + -
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Residues in contact with LEU 559 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555J TYR* 2.7 54.2 + - + +
556J ASP 5.0 3.3 - - - +
557J GLU 5.2 0.2 - - - -
558J HIS* 1.3 73.6 - - - +
560J GLY* 1.3 69.0 + - - +
561J LYS* 3.0 8.4 + - - +
565J PHE* 3.6 20.6 - - + +
566J GLN* 5.4 0.7 - - - -
567J LYS* 4.2 32.8 - - + +
47Y MET* 5.5 0.2 - - - +
48Y GLY* 5.7 0.3 + - - -
50Y LYS* 6.1 3.8 - - - +
92Y ASN* 6.1 2.5 - - - +
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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
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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