Contacts of the helix formed by residues 531 - 540 (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 GLY 531 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524J GLU 4.7 0.9 - - - -
525J LEU* 3.1 18.6 - - - -
526J ILE 3.9 2.7 - - - -
528J MLY 3.0 15.6 + - - +
530J MET* 1.3 81.4 - - - +
532J ILE* 1.3 56.1 + - - -
533J PHE 3.3 2.0 - - - -
534J SER* 2.8 28.6 + - - -
535J ILE* 3.2 9.2 + - - -
558J HIS* 3.6 8.3 - - - -
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Residues in contact with ILE 532 (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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478J LEU* 4.4 18.8 - - + -
525J LEU* 3.1 23.1 + - + +
526J ILE* 4.4 10.3 - - + +
531J GLY* 1.3 68.2 - - - +
533J PHE* 1.3 59.1 + - + +
535J ILE* 3.4 2.3 + - - +
536J LEU* 2.7 32.1 + - + +
550J PHE* 4.4 6.6 - - + -
554J LEU* 4.1 24.0 - - + -
558J HIS* 4.1 5.8 + - + -
565J PHE* 4.1 20.2 - - + -
579J PHE* 3.7 39.5 - - + -
581J LEU* 4.2 14.4 - - + -
595J TRP* 5.3 1.6 - - + -
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Residues in contact with PHE 533 (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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475J PHE* 4.3 12.3 - + - -
478J LEU* 3.5 38.4 - - + -
479J CYS* 4.3 16.4 - - - -
482J PHE* 4.0 18.6 - + - -
526J ILE* 3.4 37.3 + - + +
527J GLU* 5.1 0.2 - - - -
531J GLY 3.0 1.4 + - - -
532J ILE* 1.3 78.5 - - + +
534J SER* 1.3 51.2 + - - +
536J LEU* 2.8 12.8 + - + +
537J GLU* 2.5 42.6 + - - +
650J SER* 4.1 20.2 - - - -
653J PHE* 4.8 5.4 - + - -
654J ARG* 3.5 40.8 - - + +
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Residues in contact with SER 534 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526J ILE 4.8 0.2 + - - -
528J MLY 4.4 1.9 + - - -
531J GLY 2.8 8.6 + - - -
533J PHE* 1.3 70.2 - - - +
535J ILE* 1.3 46.2 - - - -
537J GLU* 2.7 2.5 + - - -
538J GLU 2.6 3.3 + - - -
654J ARG* 4.9 6.0 - - - +
350W SER 2.6 20.6 + - - -
351W THR* 1.6 56.0 + - - +
353W GLN* 3.3 12.4 - - - +
354W GLN* 1.4 67.4 + - - -
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Residues in contact with ILE 535 (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* 3.1 31.2 - - + +
531J GLY 3.2 3.1 + - - +
532J ILE 3.9 2.0 - - - +
534J SER* 1.3 68.9 - - - +
536J LEU* 1.3 58.6 + - - +
538J GLU* 5.3 2.0 - - - +
539J GLU* 3.4 15.5 + - - +
550J PHE* 3.9 11.5 - - + -
553J MLY 3.9 26.9 - - + +
554J LEU* 3.4 30.5 - - + -
558J HIS* 3.8 13.9 - - + +
351W THR* 1.5 50.8 + - + +
354W GLN* 4.7 5.2 - - + +
45Y VAL* 6.1 1.3 - - + -
46Y GLY* 3.9 28.0 - - - -
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Residues in contact with LEU 536 (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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475J PHE* 4.2 16.2 - - + -
532J ILE* 2.7 17.2 + - + +
533J PHE* 2.8 23.0 + - + +
535J ILE* 1.3 80.2 - - - +
537J GLU* 1.3 57.7 + - - -
538J GLU 3.3 0.9 + - - -
539J GLU* 3.9 1.4 + - - +
540J CYS* 3.3 19.4 + - - -
550J PHE* 3.2 33.8 - - + -
595J TRP* 3.9 33.0 - - + -
596J LEU* 3.8 17.9 - - + +
599J ASN* 3.6 23.1 - - - +
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Residues in contact with GLU 537 (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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533J PHE* 2.5 33.0 + - - +
534J SER 2.7 0.6 + - - -
536J LEU* 1.3 72.0 - - - +
538J GLU* 1.3 46.8 - - - +
540J CYS* 3.8 4.4 - - - +
599J ASN* 4.4 0.7 - - - +
641J LYS* 5.1 2.6 + - - -
648J THR* 3.2 11.8 - - - +
650J SER* 2.6 32.3 + - - +
651J ALA* 3.5 6.5 + - - +
654J ARG* 2.9 34.0 + - - -
349W LEU* 1.7 31.6 - - - +
350W SER* 0.4 131.2 + - - +
351W THR 2.5 1.6 - - - -
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Residues in contact with GLU 538 (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* 4.7 1.9 - - - +
534J SER 2.6 0.2 + - - -
535J ILE* 4.8 1.0 - - - +
537J GLU* 1.3 62.0 - - - +
539J GLU* 1.3 55.2 + - - +
541J MET* 2.4 20.5 + - + +
542J PHE* 3.9 5.0 - - + -
553J MLY 4.3 13.4 - - - +
143W TYR* 3.7 1.7 + - - -
346W LEU* 4.2 6.4 - - + +
349W LEU* 1.8 47.2 - - + +
351W THR* 1.3 105.5 + - - +
352W PHE* 2.8 18.1 - - + +
355W MET* 1.9 43.0 - - - +
45Y VAL* 4.1 13.7 - - - +
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Residues in contact with GLU 539 (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* 3.4 14.4 + - - +
536J LEU 4.3 3.6 - - - +
538J GLU* 1.3 77.1 - - - +
540J CYS* 1.3 57.1 + - - +
541J MET 2.8 5.9 + - - -
542J PHE* 3.0 29.8 + - - +
545J ALA* 3.5 20.1 - - + +
549J SER* 2.8 31.6 + - - +
550J PHE* 4.1 13.0 - - + -
553J MLY 3.0 58.4 + - - +
596J LEU* 4.6 12.9 - - + +
600J MLY 3.8 0.9 - - - -
351W THR* 2.4 6.5 + - - -
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Residues in contact with CYS 540 (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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536J LEU* 3.3 19.0 + - - -
537J GLU* 3.8 13.9 - - - +
538J GLU 2.7 3.2 + - - -
539J GLU* 1.3 75.8 - - - +
541J MET* 1.3 56.2 + - - +
542J PHE 3.4 0.2 - - - -
596J LEU* 3.8 32.5 - - - -
599J ASN* 4.0 21.8 - - - -
600J MLY 3.3 37.3 - - + +
640J LYS* 6.1 0.7 - - - -
647J GLN 3.9 15.6 - - - +
648J THR* 4.4 2.2 - - - -
349W LEU* 3.3 3.0 - - - +
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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
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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