Contacts of the helix formed by residues 531 - 540 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524P GLU 4.7 0.9 - - - -
525P LEU* 3.1 18.8 - - - -
526P ILE 3.9 2.2 - - - -
528P MLY 3.0 15.9 + - - +
530P MET* 1.3 80.3 - - - +
532P ILE* 1.3 55.1 - - - -
533P PHE 3.3 2.2 - - - -
534P SER* 2.8 29.2 + - - -
535P ILE* 3.2 9.3 + - - -
558P HIS* 3.6 8.5 - - - -
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Residues in contact with ILE 532 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478P LEU* 4.4 17.9 - - + -
525P LEU* 3.1 22.9 + - + +
526P ILE* 4.4 10.1 - - + +
531P GLY* 1.3 69.2 - - - +
533P PHE* 1.3 60.0 + - + +
535P ILE* 3.4 2.1 + - - +
536P LEU* 2.7 30.7 + - + +
550P PHE* 4.4 7.0 - - + -
554P LEU* 4.1 24.7 - - + -
558P HIS* 4.1 6.0 + - + -
565P PHE* 4.1 19.7 - - + -
579P PHE* 3.7 39.9 - - + -
581P LEU* 4.2 14.1 - - + -
595P TRP* 5.3 1.8 - - + -
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Residues in contact with PHE 533 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475P PHE* 4.3 11.7 - + - -
478P LEU* 3.5 37.9 - - + -
479P CYS* 4.3 17.0 - - - -
482P PHE* 4.0 19.1 - + - -
526P ILE* 3.4 35.6 + - + +
527P GLU* 5.1 0.4 - - - -
531P GLY 3.0 1.2 + - - -
532P ILE* 1.3 79.4 - - + +
534P SER* 1.3 51.5 + - - +
536P LEU* 2.8 13.5 + - + +
537P GLU* 2.5 43.0 + - - +
650P SER* 4.1 20.4 - - - -
653P PHE* 4.8 4.5 - + - -
654P ARG* 3.5 42.2 - - + +
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Residues in contact with SER 534 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3501 SER 2.6 20.4 + - - -
3511 THR* 1.6 55.0 + - - +
3531 GLN* 3.3 12.4 - - - +
3541 GLN* 1.4 68.5 + - - -
526P ILE 4.8 0.4 + - - -
528P MLY 4.4 1.9 + - - -
531P GLY 2.8 8.7 + - - -
533P PHE* 1.3 71.5 - - - +
535P ILE* 1.3 45.5 - - - -
537P GLU* 2.7 2.3 + - - +
538P GLU 2.7 3.1 + - - -
654P ARG* 4.9 5.5 + - - +
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Residues in contact with ILE 535 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3511 THR* 1.5 52.6 + - + +
3541 GLN* 4.7 5.2 - - + +
530P MET* 3.1 34.8 - - + +
531P GLY 3.2 2.7 + - - +
532P ILE 3.9 2.0 - - - +
534P SER* 1.3 68.7 - - - +
536P LEU* 1.3 59.8 + - - +
538P GLU* 4.8 2.0 - - - +
539P GLU* 3.4 15.0 + - - +
550P PHE* 3.9 12.0 - - + -
553P MLY 3.9 37.2 - - + +
554P LEU* 3.4 32.1 - - + -
557P GLU* 4.2 8.1 - - + -
558P HIS* 3.8 14.6 - - + +
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Residues in contact with LEU 536 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475P PHE* 4.2 16.2 - - + -
532P ILE* 2.7 16.5 + - + +
533P PHE* 2.8 23.4 + - + +
535P ILE* 1.3 81.5 - - - +
537P GLU* 1.3 58.4 + - - +
538P GLU 3.3 0.9 + - - -
539P GLU* 4.3 1.0 - - - +
540P CYS* 3.3 19.4 + - - -
550P PHE* 3.2 34.1 - - + -
595P TRP* 3.9 32.8 - - + -
596P LEU* 3.8 18.2 - - + +
599P ASN* 3.6 22.4 - - - +
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Residues in contact with GLU 537 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3491 LEU* 1.7 31.3 - - - +
3501 SER* 0.4 129.9 + - - +
3511 THR 2.5 1.8 - - - -
533P PHE* 2.5 32.1 + - - +
534P SER 2.7 0.6 + - - -
536P LEU* 1.3 72.4 - - - +
538P GLU* 1.3 47.7 - - - +
540P CYS* 3.8 4.8 - - - +
599P ASN* 4.4 0.4 - - - +
641P LYS* 5.1 3.1 + - - -
648P THR* 3.2 11.9 - - - +
650P SER* 2.6 31.8 + - - +
651P ALA* 3.5 6.4 + - - +
654P ARG* 2.9 34.8 + - - -
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Residues in contact with GLU 538 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431 TYR* 3.7 2.1 + - - -
3461 LEU* 4.2 6.7 - - + +
3491 LEU* 1.8 47.0 - - + +
3511 THR* 1.3 104.5 + - - +
3521 PHE* 2.8 18.7 - - + +
3551 MET* 1.9 42.6 - - - +
530P MET* 4.7 2.1 - - - +
534P SER 2.7 0.2 + - - -
535P ILE* 4.8 2.1 - - - +
537P GLU* 1.3 62.3 - - - +
539P GLU* 1.3 54.8 - - - +
541P MET* 2.4 19.9 + - + +
542P PHE* 4.4 4.6 - - + -
553P MLY 4.3 21.9 - - - +
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Residues in contact with GLU 539 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3511 THR* 2.4 6.9 + - - -
535P ILE 3.5 14.4 - - - +
536P LEU 4.3 2.7 - - - +
538P GLU* 1.3 78.0 - - - +
540P CYS* 1.3 58.1 + - - +
541P MET 2.8 5.2 + - - -
542P PHE* 3.0 28.9 + - - +
545P ALA* 3.5 19.7 - - + +
549P SER* 2.8 30.9 + - - +
550P PHE* 4.1 12.3 - - + -
553P MLY 3.0 59.7 + - - +
596P LEU* 4.6 11.6 - - + +
600P MLY 3.8 1.7 - - - -
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Residues in contact with CYS 540 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3491 LEU* 3.3 3.0 - - - +
536P LEU* 3.3 19.5 + - - -
537P GLU* 3.8 13.0 - - - +
538P GLU 2.7 3.6 + - - -
539P GLU* 1.3 76.0 - - - +
541P MET* 1.3 57.2 + - - +
542P PHE 3.4 0.2 - - - -
596P LEU* 3.8 32.8 - - - -
599P ASN* 4.0 22.4 - - - -
600P MLY 3.3 35.6 - - + +
640P LYS* 6.1 0.7 - - - -
647P GLN 3.9 15.6 - - - +
648P THR* 4.4 2.2 - - - -
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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
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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