Contacts of the strand formed by residues 579 - 582 (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 PHE 579 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478G LEU* 5.2 3.8 - - + -
532G ILE* 3.7 25.6 - - + -
554G LEU* 3.9 14.4 - - + -
555G TYR* 4.9 1.3 - - + -
565G PHE* 4.0 21.5 - + + -
566G GLN 3.5 12.1 - - - +
568G PRO* 3.3 6.7 - - - +
578G HIS* 1.3 82.9 - - - +
580G SER* 1.3 58.4 + - - +
581G LEU* 3.1 36.3 - - + -
588G VAL 3.7 0.2 - - - +
590G TYR* 2.6 61.8 + + + +
592G ILE* 3.3 40.4 - - + -
595G TRP* 4.4 12.3 - + - -
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Residues in contact with SER 580 (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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564G ASN 3.7 0.7 - - - +
565G PHE* 4.1 0.2 - - - -
566G GLN* 3.0 46.9 + - - +
567G LYS 3.6 1.6 + - - -
568G PRO* 3.6 18.2 - - - +
569G LYS 4.6 0.3 + - - -
579G PHE* 1.3 76.1 - - - +
581G LEU* 1.3 71.3 + - - +
582G VAL* 6.1 0.2 - - - -
587G THR* 3.7 15.7 - - - -
588G VAL 2.8 12.3 - - - -
589G ASP* 3.4 16.3 + - - -
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Residues in contact with LEU 581 (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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478G LEU* 4.6 3.6 - - + -
522G CYS* 4.2 8.1 - - - -
525G LEU* 4.3 11.0 - - + -
526G ILE* 4.0 32.8 - - + -
532G ILE* 4.2 10.3 - - + -
564G ASN 3.3 7.4 - - - +
565G PHE* 4.3 8.7 - - + -
579G PHE* 3.1 42.0 - - + -
580G SER* 1.3 77.7 - - - +
582G VAL* 1.3 66.3 + - - +
583G HIS* 3.6 25.8 + - + +
587G THR* 3.1 7.3 - - - +
588G VAL 2.9 27.6 + - - -
590G TYR* 3.9 10.1 - - + -
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Residues in contact with VAL 582 (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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485G GLU* 4.3 0.2 - - - +
522G CYS* 3.9 13.6 - - - +
563G ASN 4.7 1.1 - - - +
564G ASN* 3.1 46.9 + - - +
566G GLN* 4.1 25.4 - - + +
580G SER 5.5 0.2 - - - -
581G LEU* 1.3 80.8 - - - +
583G HIS* 1.3 65.4 + - - +
586G GLY* 3.9 4.7 - - - +
587G THR* 4.0 15.0 - - + +
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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