Contacts of the helix formed by residues 594 - 601 (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 594 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547P ASP* 2.9 14.2 + - - -
593P SER* 1.3 73.3 - - - +
595P TRP* 1.3 66.2 + - - +
596P LEU 3.2 2.0 - - - -
597P GLU* 3.1 11.5 + - - +
598P MLY 2.7 48.9 + - - +
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Residues in contact with TRP 595 (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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473P ASN 4.5 2.0 - - - -
474P SER* 2.8 20.5 + - - -
475P PHE* 3.0 41.1 - + + +
478P LEU* 4.0 28.0 - - + -
532P ILE* 5.3 1.6 - - + -
536P LEU* 3.9 26.9 - - + -
547P ASP* 4.0 0.8 + - - +
550P PHE* 4.1 22.4 - + + -
579P PHE* 4.4 15.5 - + - -
590P TYR* 4.3 16.4 - - + -
591P ASN 2.8 32.6 + - - -
592P ILE* 3.5 9.4 - - + -
593P SER 3.1 17.0 - - - +
594P GLY* 1.3 82.8 - - - +
596P LEU* 1.3 56.2 + - - +
598P MLY 3.6 6.6 - - - +
599P ASN* 2.6 41.2 + - - +
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Residues in contact with LEU 596 (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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536P LEU* 3.8 18.8 - - + -
539P GLU* 4.6 11.7 - - + +
540P CYS* 3.8 12.2 - - - -
545P ALA* 3.8 27.8 - - + +
546P THR 3.5 30.7 - - - +
547P ASP* 3.4 13.5 + - - +
550P PHE* 3.8 27.4 - - + -
594P GLY 3.2 0.2 - - - -
595P TRP* 1.3 80.2 - - - +
597P GLU* 1.3 63.8 + - + +
599P ASN* 3.4 3.3 + - - +
600P MLY 3.2 41.2 + - - +
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Residues in contact with GLU 597 (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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547P ASP* 4.9 0.2 + - - -
594P GLY* 3.1 13.4 + - - +
596P LEU* 1.3 76.0 - - + +
598P MLY 1.3 60.0 + - - +
599P ASN 2.9 1.8 - - - -
600P MLY 2.5 32.5 + - - -
601P ASP 3.2 8.8 + - - -
602P PRO* 3.3 33.0 - - + +
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Residues in contact with MLY 598 (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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272P MLY 4.8 11.4 - - - -
431P MLY 6.4 2.2 - - - -
472P PHE* 5.8 3.6 - - - -
474P SER* 4.2 16.2 + - - -
475P PHE* 3.9 23.0 - - + +
476P GLU* 2.7 40.7 + - + +
593P SER 3.6 24.2 - - - -
594P GLY* 2.7 31.7 + - - +
595P TRP* 3.6 5.4 - - - +
597P GLU* 1.3 73.6 - - - +
599P ASN* 1.3 61.8 + - - +
600P MLY 3.4 0.3 + - - -
601P ASP* 3.7 6.1 + - - +
602P PRO* 5.5 0.2 - - - -
649P VAL* 3.2 17.7 - - - +
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Residues in contact with ASN 599 (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* 3.6 8.5 - - + -
536P LEU* 3.6 25.9 + - + +
537P GLU* 4.4 0.6 - - - +
540P CYS* 4.0 10.9 - - - -
595P TRP 2.6 19.8 + - - +
596P LEU* 3.6 5.4 - - - +
598P MLY 1.3 76.5 + - - +
600P MLY 1.3 58.3 + - - +
647P GLN 4.6 0.5 - - - +
648P THR* 2.8 18.3 + - - +
649P VAL* 2.0 83.8 + - + +
650P SER* 2.7 23.4 + - - -
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Residues in contact with MLY 600 (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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539P GLU 3.8 3.4 - - - -
540P CYS* 3.3 44.0 - - + +
541P MET 4.7 0.4 - - - -
542P PHE 2.8 34.5 - - - -
543P PRO* 4.1 13.5 - - - -
545P ALA* 4.7 13.7 - - - -
596P LEU* 3.2 28.7 - - - +
597P GLU* 2.5 25.1 + - - +
599P ASN* 1.3 75.0 + - - +
601P ASP* 1.3 68.0 + - - +
602P PRO* 3.9 11.4 - - + -
640P LYS* 3.2 29.9 + - - +
646P PHE 5.3 1.6 - - - +
647P GLN 5.4 4.0 - - - +
649P VAL* 4.8 0.4 - - - -
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Residues in contact with ASP 601 (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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272P MLY 3.5 38.8 + - - -
432P ALA* 5.5 0.5 - - - +
436P MLY 3.6 19.8 - - - -
597P GLU 3.2 2.0 + - - -
598P MLY 3.7 3.8 + - - +
599P ASN 3.5 1.4 - - - -
600P MLY 1.3 80.6 + - - +
602P PRO* 1.3 73.0 - - - +
603P LEU* 3.4 25.0 + - - +
640P LYS* 5.0 1.2 + - - -
646P PHE* 6.6 0.2 - - + -
649P VAL* 4.0 15.7 - - + -
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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