Contacts of the helix formed by residues 616 - 628 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350G ALA* 4.5 23.3 - - + -
353G MLY 3.7 22.9 - - + -
354G LEU* 5.0 5.4 - - + -
389G LEU 4.4 4.7 - - - +
390G MET 3.4 32.8 - - - +
391G GLY* 3.6 7.0 - - - +
614G SER* 3.0 3.5 + - - -
615G SER* 1.3 80.8 - - - +
617G MLY 1.3 54.9 + - - +
618G THR* 3.2 1.6 - - - +
619G LEU* 2.7 39.4 + - + +
620G ALA 3.0 7.7 + - - -
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Residues in contact with MLY 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346G ASP* 5.4 10.5 - - - +
614G SER 5.0 1.8 - - - +
615G SER 3.5 8.3 + - - +
616G VAL* 1.3 71.5 + - - +
618G THR* 1.3 53.8 + - - +
620G ALA* 2.8 12.6 + - - +
621G LEU* 2.6 47.6 + - + +
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Residues in contact with THR 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G ASP* 5.1 4.5 + - - -
347G GLU* 4.0 18.7 - - - +
350G ALA* 3.7 28.7 - - + +
354G LEU* 4.4 7.0 - - + -
437G MET* 6.3 0.4 - - + -
440G TRP* 3.6 36.5 - - + -
616G VAL* 3.2 1.8 - - - -
617G MLY 1.3 80.1 + - - +
619G LEU* 1.3 63.6 + - - +
621G LEU* 2.9 14.3 + - - +
622G LEU* 2.8 31.3 + - + +
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Residues in contact with LEU 619 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G LEU* 4.6 13.4 - - + +
390G MET* 3.6 41.3 - - + +
392G LEU* 4.9 0.9 - - + -
433G VAL* 4.5 11.7 - - + -
611G TYR* 3.9 28.0 - - + +
614G SER* 3.9 9.4 - - - +
616G VAL* 2.7 24.5 + - + +
618G THR* 1.3 78.0 - - - +
620G ALA* 1.3 65.7 + - - +
622G LEU* 3.5 28.6 + - + +
623G PHE* 3.7 24.5 + - + +
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Residues in contact with ALA 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611G TYR 3.5 20.6 + - - +
612G GLN* 4.2 15.7 - - - +
614G SER* 4.4 11.4 - - - +
616G VAL 3.0 5.5 + - - +
617G MLY 2.8 22.1 + - - +
619G LEU* 1.3 79.1 - - - +
621G LEU* 1.3 66.9 + - + +
623G PHE* 3.2 12.6 + - - +
624G ALA* 3.6 8.1 + - - +
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Residues in contact with LEU 621 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440G TRP* 5.2 14.8 - - + +
617G MLY 2.6 28.2 + - + +
618G THR* 2.9 12.2 + - - +
620G ALA* 1.3 78.3 - - + +
622G LEU* 1.3 57.8 - - + +
623G PHE 2.8 11.5 + - - -
624G ALA* 3.0 26.7 + - + +
625G THR* 5.3 0.5 - - - +
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Residues in contact with LEU 622 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G LEU* 4.9 8.1 - - + -
433G VAL* 4.3 12.3 - - + +
436G MLY 3.5 35.4 - - + +
437G MET* 4.0 28.9 - - + +
440G TRP* 4.2 23.3 - - + -
618G THR* 2.8 36.3 - - + +
619G LEU* 3.7 25.8 - - + +
621G LEU* 1.3 80.0 - - + +
623G PHE* 1.5 57.1 + - + +
625G THR* 4.1 8.7 - - - +
626G TYR* 4.0 5.4 - - - -
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Residues in contact with PHE 623 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429G LEU* 5.4 0.4 - - + -
432G ALA* 4.2 8.1 - - + -
433G VAL* 3.7 39.5 - - + -
436G MLY 4.0 12.6 - - + -
603G LEU* 4.6 0.4 - - + -
608G ILE* 3.7 36.3 - - + -
611G TYR* 3.2 39.3 - + + -
612G GLN* 3.2 19.7 + - + +
619G LEU* 3.7 12.5 + - + +
620G ALA 3.2 8.6 + - - +
621G LEU 2.8 5.9 + - - -
622G LEU* 1.5 72.9 - - + +
624G ALA* 1.3 62.6 - - - +
625G THR 3.2 3.1 - - - -
626G TYR* 2.9 52.7 + + - +
627G GLY 3.2 8.3 + - - -
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Residues in contact with ALA 624 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612G GLN* 4.4 7.6 - - - +
620G ALA 3.6 5.9 + - - +
621G LEU* 3.0 22.2 + - + +
623G PHE* 1.3 76.1 - - - +
625G THR* 1.3 55.0 + - + +
627G GLY* 3.1 2.6 + - - -
628G GLY* 2.8 31.9 + - - -
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Residues in contact with THR 625 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622G LEU 4.1 18.8 - - - +
623G PHE 4.3 0.2 - - - -
624G ALA* 1.3 74.4 - - + +
626G TYR* 1.3 75.6 + - + +
628G GLY* 3.8 1.9 + - - +
629G GLU* 3.5 35.0 + - - +
644G SER* 4.0 0.2 + - - -
646G PHE* 4.9 11.4 - - - -
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Residues in contact with TYR 626 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436G MLY 0.8 129.1 + - + -
603G LEU* 4.5 8.5 - - + -
605G GLU* 6.6 0.4 - - + -
608G ILE* 4.5 17.9 - - + -
612G GLN* 3.6 2.7 - - - +
622G LEU 4.0 6.5 - - - -
623G PHE* 2.9 38.7 + + - +
625G THR* 1.3 87.0 - - + +
627G GLY* 1.3 61.7 + - - +
628G GLY 3.4 0.3 + - - -
629G GLU* 3.5 12.6 + - - +
630G ALA* 3.6 12.0 + - - +
645G SER* 5.8 2.5 - - - -
646G PHE* 5.2 15.7 - + - -
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Residues in contact with GLY 627 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612G GLN* 2.3 39.9 - - - +
624G ALA 3.1 4.0 + - - -
626G TYR* 1.3 75.3 - - - +
628G GLY* 1.4 59.4 + - - +
629G GLU 3.8 0.2 + - - -
630G ALA* 4.0 15.2 + - - +
631G GLU* 5.2 3.3 + - - +
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Residues in contact with GLY 628 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624G ALA 2.8 17.7 + - - -
625G THR* 3.8 2.8 + - - -
626G TYR 3.2 0.6 - - - -
627G GLY* 1.4 75.9 - - - +
629G GLU* 1.4 56.1 + - - +
630G ALA 3.5 0.4 - - - -
631G GLU* 4.3 20.2 - - - +
643G GLY* 3.0 6.0 - - - +
644G SER* 3.5 3.6 + - - -
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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