Contacts of the helix formed by residues 616 - 628 (chain A) 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 VAL 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ALA* 4.5 23.8 - - + -
353A MLY 3.7 23.8 - - + -
354A LEU* 5.0 5.4 - - + -
389A LEU 4.4 4.0 - - - +
390A MET 3.4 33.2 - - - +
391A GLY* 3.6 7.6 - - - +
614A SER* 3.0 3.3 + - - -
615A SER* 1.3 79.7 - - - +
617A MLY 1.3 53.7 + - - +
618A THR* 4.7 0.9 - - - +
619A LEU* 2.7 40.1 + - + +
620A ALA 3.0 8.0 + - - -
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Residues in contact with MLY 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 5.4 10.3 - - - +
614A SER 5.0 2.2 - - - +
615A SER 3.5 8.2 + - - +
616A VAL* 1.3 70.5 + - - +
618A THR* 1.3 54.1 + - - +
620A ALA* 2.8 11.8 + - - +
621A LEU* 2.6 47.0 + - + +
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Residues in contact with THR 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 5.1 4.5 + - - -
347A GLU* 4.0 18.7 - - - +
350A ALA* 3.7 28.9 - - + +
354A LEU* 4.4 7.4 - - + -
437A MET* 6.3 0.2 - - + -
440A TRP* 3.6 36.4 - - + -
616A VAL* 3.2 1.8 - - - -
617A MLY 1.3 78.8 + - - +
619A LEU* 1.3 65.2 + - - +
621A LEU* 2.9 13.8 + - - +
622A LEU* 2.8 30.7 + - + +
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 4.6 13.4 - - + +
390A MET* 3.6 40.6 - - + +
392A LEU* 4.8 1.1 - - + -
433A VAL* 4.5 11.4 - - + -
611A TYR* 3.9 27.4 - - + -
614A SER* 3.9 9.6 - - - +
616A VAL* 2.7 23.2 + - + +
618A THR* 1.3 77.5 - - - +
620A ALA* 1.3 67.6 + - - +
622A LEU* 3.5 28.9 + - + +
623A PHE* 3.7 25.0 + - + +
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A TYR 3.5 19.5 + - - +
612A GLN* 4.2 15.0 - - - +
613A MLY 5.4 0.2 - - - -
614A SER 4.4 11.4 - - - +
616A VAL 3.0 6.7 + - - +
617A MLY 2.8 21.7 + - - +
619A LEU* 1.3 78.7 - - - +
621A LEU* 1.3 65.8 + - + +
623A PHE* 3.2 12.8 + - - +
624A ALA* 3.6 7.8 + - - +
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Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A TRP* 5.2 14.1 - - + +
617A MLY 2.6 27.9 + - + +
618A THR* 2.9 12.8 + - - +
620A ALA* 1.3 76.8 - - + +
622A LEU* 1.3 58.0 + - + +
623A PHE 2.8 10.6 + - - -
624A ALA* 3.0 27.8 + - + +
625A THR* 5.3 0.3 - - - +
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Residues in contact with LEU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 4.9 7.9 - - + -
433A VAL* 4.3 11.0 - - + +
436A MLY 3.5 34.6 - - + +
437A MET* 4.0 28.7 - - + +
440A TRP* 4.2 23.6 - - + -
618A THR* 2.8 35.7 - - + +
619A LEU* 3.7 27.1 - - + +
620A ALA 3.4 0.2 - - - -
621A LEU* 1.3 79.4 - - + +
623A PHE* 1.5 57.1 + - + +
624A ALA 3.7 0.2 - - - -
625A THR* 4.1 9.3 - - - +
626A TYR* 4.0 5.2 - - - -
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Residues in contact with PHE 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A LEU* 5.4 0.4 - - + -
432A ALA* 4.2 7.2 - - + -
433A VAL* 3.7 39.9 - - + -
436A MLY 4.0 13.5 - - + -
603A LEU* 4.6 0.4 - - + -
608A ILE* 3.7 36.8 - - + -
611A TYR* 3.2 39.5 - + + -
612A GLN* 3.2 19.9 + - + +
619A LEU* 3.7 12.5 + - + +
620A ALA 3.2 8.8 + - - +
621A LEU 2.8 5.9 + - - -
622A LEU* 1.5 72.2 - - + +
624A ALA* 1.3 63.2 + - - +
625A THR 3.2 2.5 - - - -
626A TYR* 2.9 53.0 + + - +
627A GLY 3.2 8.0 + - - -
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A GLN* 4.4 7.4 - - - +
620A ALA 3.6 5.7 + - - +
621A LEU* 3.0 22.7 + - + +
623A PHE* 1.3 76.0 - - - +
625A THR* 1.3 54.3 + - + +
627A GLY* 3.1 2.9 + - - -
628A GLY* 2.8 31.4 + - - -
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Residues in contact with THR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A LEU 5.3 0.2 - - - +
622A LEU 4.1 18.8 - - - +
623A PHE 4.3 0.2 - - - -
624A ALA* 1.3 75.0 - - + +
626A TYR* 1.3 75.7 + - + +
628A GLY* 3.8 2.1 + - - +
629A GLU* 3.5 35.7 + - - +
644A SER* 4.0 0.3 + - - -
646A PHE* 4.9 11.8 - - - -
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Residues in contact with TYR 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A MLY 0.8 128.2 + - + -
603A LEU* 4.5 9.2 - - + -
605A GLU* 6.6 0.4 - - + -
608A ILE* 4.5 17.5 - - + -
612A GLN* 3.6 2.7 - - - +
622A LEU 4.0 6.3 - - - -
623A PHE* 2.9 39.9 + + - +
625A THR* 1.3 87.8 - - + +
627A GLY* 1.3 62.1 + - - +
628A GLY 3.4 0.7 + - - -
629A GLU* 3.5 12.9 + - - +
630A ALA* 3.6 11.8 + - - +
645A SER* 5.8 3.2 - - - -
646A PHE* 5.2 15.0 - + - -
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Residues in contact with GLY 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A GLN* 2.3 41.8 - - - +
624A ALA 3.1 4.5 + - - -
626A TYR* 1.3 75.9 - - - +
628A GLY* 1.4 58.6 - - - +
629A GLU 3.8 0.2 + - - -
630A ALA* 4.0 14.7 + - - +
631A GLU* 5.2 3.6 + - - +
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Residues in contact with GLY 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A ALA 2.8 17.0 + - - -
625A THR* 3.8 2.6 + - - -
626A TYR 3.2 0.8 - - - -
627A GLY* 1.4 73.9 - - - +
629A GLU* 1.4 57.8 + - - +
630A ALA 3.5 0.4 - - - -
631A GLU* 4.3 20.2 - - - +
643A GLY* 3.0 7.0 - - - +
644A SER* 3.5 3.8 + - - -
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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