Contacts of the strand formed by residues 646 - 652 (chain B) in PDB entry 5MJA
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 ILE 646 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637B ARG* 3.4 5.5 - - - +
638B LEU* 2.8 54.7 + - + +
640B LEU* 6.5 0.2 - - + -
644B ARG* 3.8 12.1 - - + +
645B GLU* 1.3 81.3 - - - +
647B PTR 1.3 67.2 + - - +
648B VAL* 3.9 13.5 - - + -
682B ARG* 6.0 0.7 - - - +
684B GLU* 3.8 33.4 - - + +
698B GLU* 5.7 0.7 - - - -
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Residues in contact with PTR 647 (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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622B GLU* 4.4 4.0 - - - -
635B LYS* 3.5 37.5 + - + -
636B GLY 3.4 11.7 - - - +
637B ARG* 3.1 53.5 + - + -
646B ILE* 1.3 82.1 - - - +
648B VAL* 1.3 63.6 + - - +
698B GLU* 4.8 0.3 - - - -
699B PHE* 3.6 35.5 + + + +
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Residues in contact with VAL 648 (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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619B VAL* 4.4 0.9 - - + -
635B LYS* 3.5 8.0 - - - +
636B GLY* 2.8 50.2 + - - -
637B ARG 3.8 5.2 - - - +
638B LEU* 3.7 24.9 - - + +
646B ILE* 3.9 14.6 - - + -
647B PTR 1.3 78.6 - - - +
649B ALA* 1.3 58.6 + - - +
650B ILE* 4.0 9.0 - - + -
684B GLU* 4.1 6.1 - - + -
696B ILE* 3.6 28.5 - - + -
697B THR 3.3 16.2 - - - +
698B GLU* 4.9 0.2 - - - -
699B PHE* 3.8 9.9 - - - -
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Residues in contact with ALA 649 (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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625B ILE* 4.1 8.5 - - + -
633B VAL* 4.3 0.4 - - + -
634B TYR 3.3 7.6 - - - +
648B VAL* 1.3 74.9 - - - +
650B ILE* 1.3 62.6 + - - +
695B ILE 3.8 0.5 - - - +
696B ILE* 3.5 4.3 - - - +
697B THR* 2.9 32.4 + - - +
698B GLU 4.3 0.4 - - - +
699B PHE* 4.0 3.0 - - - +
901B 7O3 3.3 55.6 - - + +
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Residues in contact with ILE 650 (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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619B VAL* 3.9 17.0 - - + -
620B LYS 4.1 1.1 - - - +
621B ILE* 3.9 25.4 - - + -
632B GLU 3.6 1.7 - - - +
633B VAL* 3.3 3.4 - - - -
634B TYR* 2.7 41.4 + - + +
635B LYS 4.4 1.8 - - - +
636B GLY* 3.7 28.9 - - - +
648B VAL* 4.0 8.7 - - + -
649B ALA* 1.3 79.9 - - - +
651B LYS* 1.3 62.9 + - - +
652B THR* 4.1 10.3 - - + -
694B MET* 3.9 35.4 - - + -
695B ILE 3.5 2.2 - - - -
696B ILE* 4.1 10.5 - - + -
901B 7O3 4.0 3.1 - - - +
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Residues in contact with LYS 651 (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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628B GLY* 5.1 12.1 - - - -
629B GLU 5.9 1.3 - - - +
630B PHE* 6.4 0.9 - - + -
631B GLY 5.9 0.7 - - - +
632B GLU 3.8 3.4 - - - +
633B VAL* 3.8 23.3 - - + +
650B ILE* 1.3 71.9 - - - +
652B THR* 1.3 60.8 + - - +
665B PHE* 3.4 22.7 - - + -
668B GLU* 2.8 29.0 + - - +
694B MET* 3.4 4.9 - - - -
695B ILE* 2.8 43.9 + - + +
762B ASP* 5.0 10.9 + - - +
901B 7O3 3.5 45.8 + - + +
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Residues in contact with THR 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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621B ILE* 4.9 9.2 - - + -
630B PHE 3.8 1.0 - - - -
631B GLY* 3.4 22.2 + - - -
632B GLU* 3.0 25.6 + - - -
634B TYR* 3.2 31.9 - - + -
650B ILE* 4.1 13.0 - - + -
651B LYS* 1.3 77.8 - - - +
653B LEU* 1.3 64.0 + - - +
654B LYS 4.0 0.2 - - - -
665B PHE* 3.8 9.2 - - - -
692B PRO* 5.2 8.7 - - + -
693B VAL 3.9 6.1 - - - +
694B MET* 4.5 10.5 - - + -
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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