Contacts of the strand formed by residues 647 - 654 (chain B) in PDB entry 1B70
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 647 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642B VAL 3.5 0.2 - - - +
643B LEU* 2.7 33.7 - - - -
644B VAL* 2.7 34.1 + - + -
645B GLU 2.9 6.0 + - - +
646B GLY* 1.3 80.8 - - - +
648B GLU* 1.3 70.8 + - - +
649B VAL* 3.9 1.8 - - + -
678B PRO* 5.1 8.1 - - + -
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Residues in contact with GLU 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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629B GLN* 4.4 8.7 + - - -
631B PHE* 5.3 2.3 - - - -
641B ARG* 3.4 44.0 + - - +
642B VAL 3.4 0.4 - - - -
643B LEU* 3.2 17.4 - - + +
647B GLU* 1.3 81.6 + - - +
649B VAL* 1.3 63.3 + - - +
650B GLY 3.9 11.4 + - - +
674B ARG* 3.9 12.1 + - - +
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Residues in contact with VAL 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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642B VAL* 3.0 16.4 + - + +
644B VAL* 4.0 34.8 - - + +
647B GLU* 4.1 4.3 - - + +
648B GLU* 1.3 79.1 - - - +
650B GLY* 1.3 71.6 + - - +
673B LEU* 3.2 19.6 - - + +
674B ARG* 3.2 56.5 - - + +
677B LEU* 5.4 4.7 - - + -
678B PRO* 5.7 1.6 - - + -
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Residues in contact with GLY 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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631B PHE* 4.9 2.5 - - - -
641B ARG* 3.9 1.4 - - - +
642B VAL 3.0 14.4 + - - -
648B GLU* 3.9 8.9 + - - +
649B VAL* 1.3 85.3 - - - +
651B PHE* 1.3 64.4 + - - +
672B GLU 2.8 20.0 - - - -
673B LEU* 3.4 8.3 - - - +
674B ARG* 4.6 2.4 - - - +
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Residues in contact with PHE 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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547B HIS* 4.8 4.7 - + - -
549B PHE* 3.7 26.0 - + + -
631B PHE* 3.5 31.9 - + + -
633B PHE* 4.2 23.3 - + - -
634B LEU* 3.5 32.1 - - + -
640B GLY 3.5 4.3 - - - +
642B VAL* 3.1 14.9 - - - +
650B GLY* 1.3 76.0 - - - -
652B LEU* 1.3 63.6 + - - +
670B LEU* 4.3 4.7 - - + -
671B PHE* 3.0 42.8 - - - +
672B GLU* 3.2 39.6 + - + +
673B LEU* 4.4 0.9 - - - +
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Residues in contact with LEU 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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606B TYR* 3.9 27.7 - - + +
609B LEU* 3.0 28.9 - - + -
610B LYS* 4.4 13.9 - - + -
613B LEU* 4.1 16.8 - - + -
624B PHE* 5.0 2.0 - - + -
626B VAL* 4.1 23.8 - - + -
634B LEU* 3.9 5.1 - - - +
639B SER 4.0 0.5 - - - -
640B GLY* 2.9 32.0 + - - +
642B VAL* 3.7 11.2 - - + -
651B PHE* 1.3 78.8 - - - +
653B GLY* 1.3 65.6 + - - +
669B HIS* 5.7 0.9 - - + -
670B LEU 2.8 28.0 - - - +
671B PHE* 3.9 5.2 - - + -
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Residues in contact with GLY 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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606B TYR* 4.3 8.5 - - - -
634B LEU* 4.1 10.3 - - - +
638B VAL 3.2 11.9 - - - -
652B LEU* 1.3 81.9 - - - +
654B ALA* 1.3 61.9 + - - -
655B LEU 3.8 0.2 + - - -
669B HIS* 3.4 6.4 - - - +
670B LEU* 2.6 47.8 + - - +
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Residues in contact with ALA 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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634B LEU* 3.7 6.3 - - - +
635B HIS* 3.0 29.8 + - + +
638B VAL* 3.0 40.5 + - + +
653B GLY* 1.3 72.8 - - - -
655B LEU* 1.3 62.2 + - - +
667B PRO* 6.6 0.2 - - + -
668B VAL 3.6 2.9 - - - +
669B HIS* 3.5 24.8 + - + -
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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