Contacts of the strand formed by residues 619 - 627 (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 VAL 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B ILE* 3.4 24.9 - - + -
616B VAL* 3.1 25.9 + - - +
617B SER* 4.3 4.5 - - - +
618B PHE* 1.4 77.3 - - - +
620B LYS* 1.3 60.0 + - - +
621B ILE* 4.1 3.8 + - + +
637B ARG 3.4 11.4 - - - +
638B LEU* 4.2 11.0 - - + -
648B VAL* 4.4 5.8 - - + -
650B ILE* 3.9 23.8 - - + -
687B VAL* 4.6 0.4 - - + -
694B MET* 4.1 19.5 - - + -
696B ILE* 4.0 21.8 - - + -
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Residues in contact with LYS 620 (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* 1.3 73.2 - - - +
621B ILE* 1.3 66.7 + - - +
622B GLU* 4.4 16.6 - - + +
636B GLY* 3.1 6.1 - - - -
637B ARG* 2.9 47.8 + - + +
645B GLU* 5.8 1.1 - - - +
650B ILE* 4.1 1.9 - - - +
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Residues in contact with ILE 621 (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* 4.1 3.3 - - + +
620B LYS* 1.3 78.3 - - - +
622B GLU* 1.3 67.2 + - - +
634B TYR* 3.6 43.1 - - + -
635B LYS 4.2 2.0 - - - -
650B ILE* 3.9 18.6 - - + -
652B THR* 4.9 11.4 - - + -
692B PRO* 5.0 6.1 - - + -
694B MET* 3.8 32.1 - - + -
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Residues in contact with GLU 622 (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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620B LYS* 3.8 14.1 + - + +
621B ILE* 1.3 80.9 - - - +
623B GLU* 1.3 80.8 + - - +
634B TYR* 3.5 15.1 - - - -
635B LYS* 2.8 22.7 + - - +
636B GLY* 4.7 4.4 - - - -
637B ARG* 2.8 48.0 + - - +
647B PTR 4.4 6.8 - - - -
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Residues in contact with GLU 623 (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* 1.3 93.1 - - - +
624B VAL* 1.3 69.9 + - + +
625B ILE* 4.1 9.1 - - + +
634B TYR* 3.3 2.4 - - - -
635B LYS* 2.8 60.1 + - - +
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Residues in contact with VAL 624 (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 4.0 0.2 + - - -
623B GLU* 1.3 78.3 - - + +
625B ILE* 1.3 63.8 + - - +
626B GLY* 3.5 24.2 - - - +
632B GLU* 4.3 14.4 - - + -
633B VAL 3.5 7.2 - - - +
634B TYR* 4.0 16.8 - - + -
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Residues in contact with ILE 625 (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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623B GLU* 3.5 13.0 + - + +
624B VAL* 1.3 77.5 - - - +
626B GLY* 1.3 57.8 + - - +
633B VAL* 2.8 27.3 + - + +
634B TYR 3.6 20.9 - - - +
635B LYS* 3.7 22.9 - - + +
649B ALA* 4.1 6.7 - - + -
699B PHE* 3.9 19.1 - - + -
901B 7O3 3.8 58.1 + - + +
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Residues in contact with GLY 626 (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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624B VAL* 3.5 15.4 - - - +
625B ILE* 1.3 80.8 - - - +
627B ALA* 1.3 61.0 + - - -
632B GLU* 3.7 2.8 - - - +
633B VAL* 3.0 33.3 + - - +
901B 7O3 5.0 5.4 - - - -
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Residues in contact with ALA 627 (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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626B GLY* 1.3 74.4 - - - -
628B GLY* 1.3 61.3 + - - +
631B GLY 4.2 3.8 - - - +
632B GLU* 4.5 4.3 - - + +
633B VAL* 4.2 8.9 - - - +
654B LYS* 6.2 1.8 - - - +
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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