Contacts of the helix formed by residues 616 - 628 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350M ALA* 4.5 23.8 - - + -
353M MLY 3.7 23.8 - - + -
354M LEU* 5.0 5.6 - - + -
389M LEU 5.0 3.6 - - - +
390M MET 3.4 33.4 - - - +
391M GLY* 3.6 7.0 - - - +
614M SER* 3.0 3.4 + - - -
615M SER* 1.3 80.0 - - - +
617M MLY 1.3 54.9 + - - +
618M THR 4.7 0.4 - - - +
619M LEU* 2.7 39.1 + - + +
620M ALA 3.0 8.4 + - - -
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Residues in contact with MLY 617 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346M ASP* 5.4 9.9 - - - +
614M SER 5.0 1.8 - - - +
615M SER 3.5 8.5 + - - +
616M VAL* 1.3 69.8 + - - +
618M THR* 1.3 53.9 + - - +
620M ALA* 2.9 11.7 + - - +
621M LEU* 2.6 48.9 + - + +
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Residues in contact with THR 618 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346M ASP* 5.1 4.5 + - - -
347M GLU* 4.0 18.2 + - - +
350M ALA* 3.7 29.2 - - + +
354M LEU* 4.4 7.2 - - + -
437M MET* 6.3 0.2 - - + -
440M TRP* 3.6 36.9 - - + -
616M VAL* 4.5 1.8 - - - -
617M MLY 1.3 79.6 + - - +
619M LEU* 1.3 63.3 + - - +
621M LEU* 2.9 14.4 + - - +
622M LEU* 2.8 31.0 + - + +
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Residues in contact with LEU 619 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354M LEU* 4.6 13.0 - - + +
390M MET* 3.6 41.7 - - + +
392M LEU* 4.8 0.9 - - + -
433M VAL* 4.5 11.7 - - + -
611M TYR* 3.9 28.0 - - + +
614M SER* 3.9 9.4 - - - +
616M VAL* 2.7 23.4 + - + +
618M THR* 1.3 76.7 - - - +
620M ALA* 1.3 65.4 + - - +
622M LEU* 3.5 30.4 + - + +
623M PHE* 3.7 24.5 + - + +
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Residues in contact with ALA 620 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611M TYR 3.5 19.7 + - - +
612M GLN* 4.2 15.5 - - - +
614M SER 4.4 11.4 - - - +
616M VAL 3.0 5.7 + - - +
617M MLY 2.9 21.3 + - - +
619M LEU* 1.3 79.8 - - - +
621M LEU* 1.3 66.2 + - + +
623M PHE* 3.2 12.6 + - - +
624M ALA* 3.6 7.6 + - - +
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Residues in contact with LEU 621 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440M TRP* 5.2 15.0 - - + +
617M MLY 2.6 29.0 + - + +
618M THR* 2.9 12.0 + - - +
620M ALA* 1.3 77.7 - - + +
622M LEU* 1.3 57.3 + - + +
623M PHE 2.8 11.8 + - - -
624M ALA* 3.0 27.0 + - + +
625M THR* 5.3 0.5 - - - +
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Residues in contact with LEU 622 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354M LEU* 4.9 7.9 - - + -
433M VAL* 4.3 11.7 - - + +
436M MLY 3.5 34.2 - - + +
437M MET* 4.0 27.8 - - + +
440M TRP* 4.2 22.9 - - + -
618M THR* 2.8 36.8 + - + +
619M LEU* 3.7 26.7 - - + +
621M LEU* 1.3 80.4 - - + +
623M PHE* 1.5 57.2 + - + +
625M THR* 4.1 8.6 - - - +
626M TYR* 4.0 5.4 - - - -
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Residues in contact with PHE 623 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429M LEU* 5.4 0.4 - - + -
432M ALA* 4.2 7.4 - - + -
433M VAL* 3.7 39.5 - - + -
436M MLY 4.0 13.2 - - + -
603M LEU* 4.6 0.4 - - + -
608M ILE* 3.7 36.6 - - + -
611M TYR* 3.2 38.6 - + + -
612M GLN* 3.2 20.3 + - + +
619M LEU* 4.1 13.0 - - + +
620M ALA 3.2 9.3 + - - +
621M LEU 2.8 6.7 + - - -
622M LEU* 1.5 72.0 - - + +
624M ALA* 1.3 61.9 + - - +
625M THR 3.2 2.7 - - - -
626M TYR* 2.9 53.1 + + - +
627M GLY 3.2 8.3 + - - -
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Residues in contact with ALA 624 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612M GLN* 4.4 7.2 - - - +
620M ALA 3.6 5.7 + - - +
621M LEU* 3.0 22.3 + - + +
622M LEU 3.7 0.2 - - - -
623M PHE* 1.3 76.5 - - - +
625M THR* 1.3 55.9 + - + +
627M GLY* 3.1 3.0 + - - -
628M GLY* 2.8 31.5 + - - -
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Residues in contact with THR 625 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621M LEU 5.3 0.2 - - - +
622M LEU 4.1 19.3 - - - +
624M ALA* 1.3 73.9 - - + +
626M TYR* 1.3 74.6 + - + +
628M GLY* 3.8 2.1 + - - +
629M GLU* 3.5 35.0 + - - +
644M SER* 4.0 0.2 + - - -
646M PHE* 4.9 12.1 - - - -
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Residues in contact with TYR 626 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436M MLY 0.8 128.9 + - + -
603M LEU* 4.5 9.0 - - + -
605M GLU* 6.6 0.9 - - + -
608M ILE* 4.5 17.3 - - + -
612M GLN* 4.3 2.7 - - - +
622M LEU 4.0 6.1 - - - -
623M PHE* 2.9 39.9 + + - +
625M THR* 1.3 87.4 - - + +
627M GLY* 1.3 62.6 + - - +
628M GLY 3.4 0.3 + - - -
629M GLU* 3.5 12.8 + - - +
630M ALA* 3.6 12.3 + - - +
645M SER* 5.8 3.0 - - - -
646M PHE* 5.2 15.3 - + - -
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Residues in contact with GLY 627 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612M GLN* 2.3 39.0 - - - +
624M ALA 3.1 4.9 + - - -
626M TYR* 1.3 76.3 - - - +
628M GLY* 1.4 59.3 - - - +
629M GLU 3.8 0.2 + - - -
630M ALA* 4.0 13.9 + - - +
631M GLU* 5.2 3.5 + - - +
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Residues in contact with GLY 628 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624M ALA 2.8 17.3 + - - -
625M THR* 3.8 3.3 + - - -
626M TYR 3.2 0.4 - - - -
627M GLY* 1.4 75.0 - - - +
629M GLU* 1.4 56.6 + - - +
630M ALA 3.5 0.4 - - - -
631M GLU* 4.3 19.6 - - - -
643M GLY* 3.0 6.4 - - - +
644M 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