Contacts of the strand formed by residues 669 - 675 (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 HIS 669 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588B LEU* 3.3 1.2 - - - -
589B LEU* 2.9 41.8 + - + +
590B PHE* 5.8 1.3 - - - -
605B GLY* 3.5 15.1 - - - -
606B TYR* 3.2 43.4 + - + +
609B LEU* 3.4 24.2 - - + +
638B VAL* 4.7 1.8 - - + -
652B LEU* 5.9 0.7 - - + -
653B GLY 3.4 3.5 + - - +
654B ALA* 3.5 32.1 + - + +
667B PRO* 5.2 8.9 - - + +
668B VAL* 1.3 78.3 + - - +
670B LEU* 1.3 73.4 + - - +
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Residues in contact with LEU 670 (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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549B PHE* 4.1 36.1 - - + -
553B VAL* 4.2 11.0 - - + -
587B GLY 3.5 7.9 - - - +
588B LEU* 3.7 20.0 - - + -
634B LEU* 4.9 8.5 - - + -
651B PHE* 4.3 10.3 - - + -
652B LEU* 2.8 18.0 - - - +
653B GLY 2.6 44.0 + - - +
655B LEU* 4.4 24.9 - - + -
668B VAL* 3.5 21.8 - - + -
669B HIS* 1.3 99.7 - - - +
671B PHE* 1.3 59.3 + - - +
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Residues in contact with PHE 671 (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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502B LEU* 6.1 2.9 - - + -
507B PHE* 4.4 19.1 - + - -
549B PHE* 5.4 1.1 - - - +
571B PHE* 5.3 1.6 - - + -
585B LEU* 4.0 15.5 - - + -
586B ALA* 3.0 9.7 - - - +
587B GLY* 2.9 74.2 + - - +
609B LEU* 3.5 22.9 - - + -
613B LEU* 3.9 28.0 - - + -
616B LEU* 6.2 1.3 - - + -
642B VAL* 5.5 0.4 - - + -
651B PHE* 3.0 23.8 - - - +
652B LEU* 3.8 11.4 - - + -
670B LEU* 1.3 80.2 - - - +
672B GLU* 1.3 59.5 + - - +
673B LEU* 3.0 28.9 - - + -
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Residues in contact with GLU 672 (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* 3.3 15.2 - - + -
548B LEU* 2.8 28.5 + - - +
549B PHE* 2.7 42.7 + - + +
584B HIS* 2.9 34.1 + - + +
585B LEU 3.2 6.1 - - - +
586B ALA* 3.6 6.3 - - + +
650B GLY* 2.8 30.8 - - - -
651B PHE* 3.2 29.5 + - + -
671B PHE* 1.3 75.2 - - - +
673B LEU* 1.3 55.9 + - - +
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Residues in contact with LEU 673 (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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584B HIS* 3.1 14.2 - - - -
585B LEU* 2.6 51.2 + - + +
613B LEU* 5.9 0.9 - - + -
617B PHE* 5.7 8.7 - - + -
642B VAL* 4.1 17.0 - - + -
649B VAL* 3.2 35.0 - - + +
650B GLY* 3.4 6.1 - - - -
651B PHE 4.0 2.5 - - - +
671B PHE* 3.0 42.2 - - + -
672B GLU* 1.3 80.0 - - - +
674B ARG* 1.3 65.0 + - - +
675B LEU* 5.4 0.7 - - + -
677B LEU* 5.1 9.9 - - + -
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Residues in contact with ARG 674 (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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582B GLU* 3.1 38.1 + - + +
583B THR 3.7 6.7 - - - +
584B HIS* 4.0 11.2 + - + +
648B GLU 3.9 20.0 + - - -
649B VAL* 3.2 29.5 - - + +
650B GLY 4.6 2.1 - - - +
673B LEU* 1.3 74.9 - - - +
675B LEU* 1.3 74.8 + - - +
676B PRO 4.2 3.3 - - - +
677B LEU* 3.8 15.2 - - - +
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Residues in contact with LEU 675 (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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495B GLU* 5.3 6.5 - - + +
498B LEU* 3.9 27.8 - - + -
573B VAL* 3.8 11.2 - - + -
582B GLU* 5.5 1.2 - - - +
583B THR* 2.7 52.2 + - + +
584B HIS 3.7 9.0 - - - +
585B LEU* 3.7 33.0 - - + +
673B LEU* 5.4 0.9 - - + -
674B ARG* 1.3 87.8 - - - +
676B PRO* 1.3 70.3 - - + +
677B LEU* 4.0 22.7 - - + +
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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