Contacts of the strand formed by residues 568 - 577 (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 ALA 568 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.1 5.4 - - - -
340A LEU* 6.1 4.3 - - + -
556B LEU* 5.2 5.2 - - + -
565B PRO* 5.4 4.0 - - + -
567B ARG* 1.3 79.3 - - - +
569B LEU* 1.3 61.4 + - - +
570B LEU* 4.7 14.1 - - + -
588B LEU* 3.6 7.0 - - + +
589B LEU* 3.2 6.8 - - - +
590B PHE* 2.7 53.9 + - + +
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Residues in contact with LEU 569 (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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96A PHE* 3.8 41.7 - - + -
506B GLY 3.6 20.5 - - - +
507B PHE* 3.5 34.1 - - + -
508B GLN* 3.2 20.1 + - - +
568B ALA* 1.3 77.0 - - - +
570B LEU* 1.3 65.4 + - - +
588B LEU 3.4 13.9 - - - +
589B LEU* 4.1 17.0 - - + -
609B LEU* 5.1 5.8 - - + -
612B TYR* 3.9 26.0 - - + -
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.3 29.2 - - + -
507B PHE* 3.7 8.9 - - - -
508B GLN* 2.9 25.4 - - + +
510B VAL* 3.8 19.5 - - + -
552B LEU* 4.7 9.6 - - + -
555B VAL* 5.9 5.2 - - + -
568B ALA* 4.7 9.2 - - + -
569B LEU* 1.3 85.3 - - - +
571B PHE* 1.3 59.9 + - - +
587B GLY* 3.1 4.3 - - - -
588B LEU* 2.9 66.0 + - + +
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Residues in contact with PHE 571 (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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99A GLY 4.2 1.3 - - - -
100A LEU* 4.3 4.7 - - + -
499B ARG* 4.0 22.0 - - + -
502B LEU* 3.5 34.3 - - + -
503B SER 4.7 0.2 - - - -
507B PHE* 3.4 33.0 - - + -
508B GLN 2.9 12.9 + - - +
509B GLU* 3.0 47.8 - - + -
510B VAL* 2.9 29.2 + - - +
552B LEU* 4.6 3.6 - - - -
570B LEU* 1.3 78.4 - - - +
572B GLU* 1.3 65.6 + - - +
573B VAL* 4.2 12.1 - - + -
585B LEU* 3.8 12.3 - - + -
586B ALA 3.2 15.0 - - - +
587B GLY* 4.0 2.5 - - - -
671B PHE* 5.3 1.3 - - + -
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Residues in contact with GLU 572 (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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201A ARG* 4.6 2.6 + - - -
509B GLU* 4.9 0.9 - - - -
510B VAL* 2.9 29.7 - - - +
511B TYR* 4.1 1.3 - - - -
512B THR* 3.0 35.8 + - - +
545B ARG* 3.2 26.8 + - - -
548B LEU* 3.8 16.8 - - + +
552B LEU* 4.1 19.1 - - + +
571B PHE* 1.3 83.4 - - - +
573B VAL* 1.3 77.5 + - - +
585B LEU* 3.4 2.6 - - - +
586B ALA* 3.0 27.5 + - - +
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Residues in contact with VAL 573 (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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201A ARG* 5.2 1.7 + - - -
495B GLU* 4.5 17.5 - - + +
498B LEU* 5.9 3.6 - - + -
499B ARG* 4.0 38.2 + - - +
502B LEU* 5.2 2.5 - - + -
509B GLU* 4.7 5.3 + - - +
510B VAL 4.7 0.7 + - - +
511B TYR* 5.3 3.6 - - - -
571B PHE* 4.2 8.7 - - + -
572B GLU* 1.3 82.7 - - - +
574B GLY* 1.3 62.4 + - - +
583B THR* 4.0 11.2 - - + -
584B HIS 3.4 11.7 - - - +
585B LEU* 3.5 26.2 - - + -
675B LEU* 3.8 17.3 - - + -
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Residues in contact with GLY 574 (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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201A ARG* 4.6 6.3 - - - -
545B ARG* 3.8 12.1 - - - -
548B LEU* 3.7 10.9 - - - +
572B GLU* 4.7 1.8 - - - -
573B VAL* 1.3 76.6 - - - +
575B ARG* 1.3 64.2 + - - -
576B VAL 3.8 0.2 + - - -
583B THR* 3.7 5.3 - - - -
584B HIS* 2.8 35.6 + - - +
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Residues in contact with ARG 575 (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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123A GLU* 3.6 34.9 + - - +
124A GLY 2.6 31.1 + - - -
125A PRO* 4.4 0.8 - - - +
126A GLU* 3.4 29.0 + - - +
176A ARG* 4.4 7.9 - - - +
201A ARG* 4.7 1.6 - - - +
495B GLU* 4.4 7.5 + - - -
545B ARG* 2.8 29.6 + - - +
574B GLY* 1.3 72.0 - - - -
576B VAL* 1.3 59.9 + - - +
577B PHE* 3.3 12.5 - - + -
581B GLU* 3.1 39.7 - - + +
582B GLU 3.2 11.9 - - - +
583B THR* 3.3 22.7 + - - +
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Residues in contact with VAL 576 (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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545B ARG* 3.4 7.6 - - - +
546B THR 3.3 30.3 - - - +
547B HIS 4.0 0.7 - - - -
548B LEU* 3.2 37.7 - - + +
575B ARG* 1.3 73.1 - - - +
577B PHE* 1.3 66.9 + - - +
578B ARG* 4.2 6.7 - - + +
580B ARG 4.0 0.5 - - - +
581B GLU* 3.7 1.4 - - - +
582B GLU* 2.7 41.1 + - + +
584B HIS* 3.5 41.1 - - + +
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Residues in contact with PHE 577 (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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126A GLU* 3.8 22.9 - - + -
127A VAL* 3.5 30.7 - - + -
159A PHE* 4.3 11.9 - + + -
175A LEU* 5.4 2.7 - - + -
203A PHE* 5.6 0.2 - + - -
514B SER* 4.2 20.0 - - - -
530B ARG* 4.8 5.7 + - - +
531B LEU* 4.4 6.1 + - + -
544B LEU* 3.6 34.8 - - + +
545B ARG* 2.9 19.6 + - + +
546B THR* 3.5 22.9 - - - +
575B ARG* 3.3 23.1 - - + -
576B VAL* 1.3 73.3 - - - +
578B ARG* 1.3 63.3 + - - +
580B ARG 4.2 2.7 - - - -
581B GLU* 3.5 34.5 - - + -
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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