Contacts of the strand formed by residues 649 - 655 (chain B) in PDB entry 5M5X
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 MET 649 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 4.4 6.1 - - - -
397B THR* 6.1 3.6 - - - +
400B GLN* 4.2 18.1 + - - +
401B GLU* 5.0 2.4 + - - +
402B VAL* 3.8 28.7 - - + -
503B VAL* 5.8 0.7 - - + -
527B PHE* 3.7 40.6 - - + -
528B LEU* 3.8 18.2 - - + -
545B PHE* 3.6 27.8 - - + -
550B ARG 4.1 3.6 - - - +
551B ILE* 5.0 2.2 - - + -
625B GLU* 4.2 1.0 - - - +
647B SER 4.7 1.8 - - - +
648B ARG* 1.3 77.1 - - - +
650B LEU* 1.3 72.4 + - - +
665B GLY* 3.4 0.2 - - - -
666B PRO* 3.2 32.5 - - + +
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B PHE* 3.5 5.6 - - - -
549B CYS* 3.2 8.1 - - - +
550B ARG* 2.8 40.1 + - + +
552B SER* 3.7 27.6 - - - +
623B ASP* 3.7 15.5 - - - +
625B GLU* 3.4 29.4 - - + +
648B ARG* 3.2 30.5 - - - +
649B MET* 1.3 84.6 - - - +
651B ARG* 1.3 61.5 + - - +
663B ILE* 3.6 18.2 - - + -
664B VAL 3.2 18.4 - - - +
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Residues in contact with ARG 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLY* 3.3 38.0 + - - +
527B PHE* 3.5 26.2 - - + -
548B LYS 4.3 1.3 - - - +
549B CYS* 4.0 12.3 - - + -
550B ARG 4.1 1.3 - - - +
650B LEU* 1.3 77.6 - - - +
652B PRO* 1.3 86.5 + - + +
653B VAL* 4.8 3.1 - - - -
663B ILE* 3.4 5.2 - - - -
664B VAL* 2.8 42.8 + - + +
669B GLN* 3.6 12.0 - - - +
674B ILE* 5.5 0.2 - - - +
690B GLU* 3.1 33.0 + - - +
695B ASN* 3.0 38.6 + - - +
696B ILE* 4.7 2.6 - - - +
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Residues in contact with PRO 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LYS* 3.1 35.2 - - + +
550B ARG* 4.6 14.1 - - + -
651B ARG* 1.3 105.1 + - + +
653B VAL* 1.3 58.8 - - - +
661B GLU* 3.1 30.5 - - + +
662B ASP 3.2 14.4 - - - +
663B ILE* 4.1 10.8 - - + -
690B GLU* 5.6 1.6 - - - +
691B PHE* 4.3 15.4 - - + -
695B ASN* 4.9 3.6 + - - -
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Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B ARG* 4.8 3.1 - - - -
652B PRO* 1.3 76.8 - - - +
654B ARG* 1.3 65.4 + - - +
661B GLU* 4.9 0.4 - - - -
662B ASP* 2.8 39.0 + - + +
664B VAL* 3.7 40.6 - - + -
674B ILE* 4.7 8.5 - - + -
688B HIS* 4.1 16.2 - - + -
689B VAL 3.2 29.6 - - - +
690B GLU* 4.1 13.2 - - + +
691B PHE* 4.4 6.3 - - - -
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Residues in contact with ARG 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B VAL* 1.3 73.5 - - - +
655B TYR* 1.3 58.7 + - - +
656B LEU* 3.6 11.3 - - - +
659B ASP* 2.7 55.0 + - - +
660B LYS 3.6 9.0 - - - +
661B GLU* 4.8 1.6 - - - +
662B ASP* 4.9 0.2 - - - -
678B PRO* 3.9 19.2 - - - +
681B ILE* 4.9 0.2 - - - +
688B HIS* 3.6 4.5 - - - +
689B VAL* 2.8 66.3 + - + +
691B PHE* 3.6 40.6 - - + +
153N VAL* 3.4 25.1 - - - +
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Residues in contact with TYR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B ASP* 4.5 18.4 + - - +
609B ARG* 5.1 9.6 - - + +
610B TYR* 4.8 11.1 - + - +
613B VAL* 4.5 23.3 - - + -
653B VAL 3.7 0.2 + - - -
654B ARG* 1.3 72.9 - - - +
656B LEU* 1.3 60.9 + - - +
657B PRO* 3.1 48.5 - - + +
658B LEU 4.8 0.7 - - - -
659B ASP* 3.0 31.0 - - - +
660B LYS 3.1 13.8 + - - +
662B ASP* 3.0 31.2 - - - +
687B THR* 3.5 22.3 - - + +
688B HIS* 3.3 34.3 - + - -
145N ILE* 5.5 5.9 - - - +
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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