Contacts of the strand formed by residues 627 - 634 (chain B) in PDB entry 5MJ6
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 GLU 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622B GLN 4.0 0.3 - - - +
623B LYS* 3.7 4.2 - - - +
624B LYS* 2.7 41.6 + - + +
626B LYS* 1.3 85.3 - - + +
628B LEU* 1.3 59.2 + - - +
629B PHE* 3.7 22.8 - - + -
680B VAL* 3.7 29.3 - - + +
681B ILE 3.7 3.8 - - - +
682B ASN* 4.7 11.1 + - - +
683B LEU* 4.5 1.8 - - - -
1122B NAG 5.1 7.8 - - - +
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Residues in contact with LEU 628 (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 VAL* 3.6 24.0 - - + -
622B GLN 3.9 0.9 - - - -
623B LYS* 4.1 19.5 - - + +
626B LYS 4.1 0.2 + - - -
627B GLU* 1.3 74.0 - - - +
629B PHE* 1.3 60.7 + - - +
630B ILE* 3.8 15.3 + - + +
658B TYR* 4.9 8.1 - - + -
680B VAL* 3.5 1.4 - - - -
681B ILE* 2.8 72.3 + - + +
683B LEU* 4.3 12.1 - - + -
690B VAL* 4.2 35.7 - - + -
692B VAL* 4.7 9.2 - - + -
708B ASP* 6.0 0.2 - - - -
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Residues in contact with PHE 629 (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 THR 3.6 0.9 - - - +
621B VAL* 3.4 4.7 - - - -
622B GLN* 2.8 54.6 + - + +
624B LYS* 3.9 40.2 - - + +
627B GLU* 3.7 33.4 - - + -
628B LEU* 1.3 74.6 - - - +
630B ILE* 1.3 60.0 + - - +
679B GLY 3.8 5.4 - - - -
680B VAL* 3.8 22.2 - - + -
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Residues in contact with ILE 630 (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* 4.7 3.1 - - + -
620B THR 3.1 3.4 - - - +
621B VAL* 3.5 25.8 - - + -
628B LEU* 4.2 22.4 - - + +
629B PHE* 1.3 82.0 - - - +
631B GLN* 1.3 60.7 + - - +
656B LEU* 3.7 33.9 - - + -
672B SER* 4.7 1.8 - - - +
674B LEU* 4.3 22.1 - - + +
678B SER* 3.3 5.1 - - - -
679B GLY* 2.9 45.6 + - - +
681B ILE* 3.7 20.6 - - + -
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Residues in contact with GLN 631 (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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618B LEU 3.6 0.5 - - - +
619B VAL* 3.4 3.7 - - - +
620B THR* 2.7 51.5 + - + +
630B ILE* 1.3 77.2 - - - +
632B GLN* 1.3 62.1 + - - +
633B GLU* 4.1 12.8 - - - +
674B LEU* 4.5 4.9 - - - +
677B LYS* 3.3 44.5 + - - +
678B SER* 4.1 11.4 - - - +
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Residues in contact with GLN 632 (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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617B PRO* 4.5 2.9 - - + -
618B LEU 3.4 7.4 - - - +
619B VAL* 4.8 0.7 - - + -
631B GLN* 1.3 75.2 - - - +
633B GLU* 1.3 55.8 + - - +
650B TYR 4.2 0.5 - - - +
651B LEU* 3.6 15.4 - - + +
652B TRP* 2.7 59.8 + - - +
654B ILE* 4.0 20.3 - - + +
674B LEU* 4.0 15.5 + - + +
675B ASP 4.3 0.2 - - - -
676B LYS 3.0 24.0 + - - +
677B LYS* 2.7 58.1 + - - +
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Residues in contact with GLU 633 (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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617B PRO* 3.3 4.9 - - - +
618B LEU* 2.7 61.5 + - + +
620B THR* 4.1 8.3 + - - +
631B GLN* 4.1 10.9 - - - +
632B GLN* 1.3 76.8 - - - +
634B ARG* 1.3 68.0 + - - +
650B TYR 5.9 0.9 - - - -
652B TRP* 4.4 6.7 - - - -
677B LYS* 3.5 15.3 + - - +
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Residues in contact with ARG 634 (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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523B SER 4.5 5.7 + - - -
524B LEU 4.6 1.0 + - - -
525B ASN* 3.6 21.8 + - - +
613B GLN* 4.6 12.3 - - - +
614B LYS* 3.3 43.3 + - - +
615B GLY* 5.5 3.6 - - - -
616B PHE 4.8 1.6 - - - +
618B LEU* 4.7 0.5 - - - +
633B GLU* 1.3 86.4 - - - +
635B PHE* 1.3 65.9 + - - +
636B PHE* 3.1 67.8 + - + +
650B TYR* 5.6 10.1 + - + +
652B TRP* 3.9 26.3 - - + -
743B LYS* 5.1 2.8 + - - -
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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