Contacts of the strand formed by residues 640 - 649 (chain M) in PDB entry 1M8V
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 640 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505L PRO* 4.5 0.4 - - - -
609M ILE* 5.4 3.8 - - + -
619M VAL* 4.2 15.5 - - + -
631M LEU* 3.9 17.3 - - + -
633M GLY 3.7 4.9 - - - -
634M TYR* 4.3 6.1 - - + +
638M LEU* 3.1 15.7 - - + +
639M ASN* 1.3 79.7 - - - +
641M VAL* 1.3 64.4 + - - +
642M LEU* 4.5 5.8 - - + -
660M ILE 3.6 1.0 - - - +
661M VAL* 3.5 3.3 - - - +
662M ILE* 2.9 60.5 + - + +
667M VAL* 5.2 1.3 - - + -
670M ILE* 3.6 24.0 - - + -
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Residues in contact with VAL 641 (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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503L GLU 3.5 10.3 - - - +
504L ARG 3.9 0.7 - - - -
505L PRO* 3.4 41.5 - - + -
508L VAL* 3.8 17.3 - - + -
631M LEU* 3.5 7.4 - - - +
632M ILE* 2.9 54.0 + - + -
633M GLY 3.0 8.2 + - - +
640M VAL* 1.3 76.3 - - - +
642M LEU* 1.3 63.6 + - - +
659M LYS* 4.1 9.2 - - + -
660M ILE 3.3 10.8 - - - +
661M VAL* 4.1 8.1 - - + -
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Residues in contact with LEU 642 (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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617M VAL* 3.5 29.4 - - + -
619M VAL* 4.0 11.9 - - + -
627M PHE* 3.9 19.7 - - + +
629M GLY 4.3 10.1 - - - +
630M ARG 3.1 7.4 - - - +
631M LEU* 3.8 19.5 - - + +
632M ILE* 4.2 3.1 - - - -
640M VAL* 4.5 2.7 - - + -
641M VAL* 1.3 81.2 - - - +
643M ALA* 1.3 62.5 + - - +
645M ALA* 4.0 20.4 - - + +
659M LYS* 3.3 6.1 - - - +
660M ILE* 3.0 34.7 + - + +
662M ILE* 3.8 29.6 - - + -
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Residues in contact with ALA 643 (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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629M GLY* 3.7 0.9 - - - -
630M ARG* 2.8 54.5 + - + +
632M ILE* 3.8 21.5 - - + -
642M LEU* 1.3 74.5 - - - +
644M ASP* 1.3 77.3 + - - +
645M ALA 3.0 4.0 + - - -
658M GLY 3.3 9.9 - - - +
659M LYS* 4.4 2.2 - - - +
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Residues in contact with ASP 644 (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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628M ARG 3.8 5.5 - - - +
629M GLY* 3.9 4.0 - - - -
630M ARG* 4.4 18.2 + - + +
643M ALA* 1.3 76.3 - - - +
645M ALA* 1.3 61.3 + - - +
646M GLU* 5.0 2.4 - - - +
656M ARG* 5.7 2.8 - - - -
657M TYR 3.6 5.2 - - - -
658M GLY* 2.9 25.5 + - - +
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Residues in contact with ALA 645 (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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627M PHE* 5.0 3.1 - - + -
628M ARG 3.1 13.2 - - - +
642M LEU* 4.0 28.9 - - + -
643M ALA 3.8 1.1 - - - -
644M ASP* 1.3 74.7 - - - +
646M GLU* 1.3 60.5 + - - +
647M MET 4.2 0.2 - - - -
656M ARG* 3.3 6.4 - - - -
657M TYR* 2.7 48.4 + - + +
660M ILE* 4.0 16.4 - - + -
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Residues in contact with GLU 646 (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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627M PHE* 4.4 2.5 - - - -
628M ARG* 2.9 56.9 + - + +
644M ASP 5.0 2.7 - - - +
645M ALA* 1.3 76.7 - - - +
647M MET* 1.3 62.3 + - - +
648M ILE* 3.5 8.6 + - + +
653M VAL* 3.7 26.0 - - + +
655M LYS 3.2 4.3 - - - -
656M ARG* 2.9 43.7 + - - +
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Residues in contact with MET 647 (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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520L ILE* 4.7 10.8 - - + -
568L LEU* 4.9 2.0 - - + -
625M PHE* 3.2 42.6 - - + -
626M GLU 3.6 4.3 - - - +
627M PHE* 3.3 38.6 - - + -
645M ALA 4.2 0.6 - - - -
646M GLU* 1.3 69.3 - - - +
648M ILE* 1.3 62.0 + - - +
649M GLN* 4.9 4.7 - - + -
653M VAL* 3.3 6.1 - - - -
654M VAL* 2.8 50.5 + - + -
655M LYS* 2.8 19.0 + - - +
657M TYR* 3.9 21.7 - - + +
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Residues in contact with ILE 648 (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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625M PHE* 3.0 23.8 - - - +
626M GLU* 2.7 43.2 + - + +
628M ARG* 3.2 55.0 - - + +
646M GLU* 3.5 13.5 - - + +
647M MET* 1.3 78.0 - - - +
649M GLN* 1.3 63.6 + - - +
650M ASP 4.2 0.2 - - - -
651M GLY* 3.8 15.5 - - - +
652M GLU 3.2 23.1 - - - +
653M VAL* 4.9 7.2 - - + -
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Residues in contact with GLN 649 (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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625M PHE* 3.4 38.6 - - + +
647M MET* 4.9 3.2 - - + -
648M ILE* 1.3 77.4 - - - +
650M ASP* 1.3 69.8 + - - +
651M GLY 3.0 0.4 - - - -
652M GLU* 2.7 43.0 + - - +
654M VAL* 3.6 34.7 - - + +
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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