Contacts of the helix formed by residues 548 - 563 (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 LEU 548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B THR* 5.2 5.1 - - + +
545B ARG* 3.6 32.5 - - - +
547B HIS* 1.3 70.7 - - - +
549B PHE* 1.3 64.7 + - - +
550B PRO* 3.0 5.2 - - - -
551B GLY* 2.9 17.3 + - - -
552B LEU* 3.5 9.0 + - + +
572B GLU* 3.8 27.1 - - + +
574B GLY* 3.7 12.3 - - - +
576B VAL* 3.2 24.5 - - + -
584B HIS* 3.2 44.2 - - + +
585B LEU* 3.9 3.4 - - - +
586B ALA* 4.0 7.4 - - + +
672B GLU* 2.8 17.5 + - - +
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Residues in contact with PHE 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B PHE* 4.1 15.9 - + + -
526B LEU* 3.4 25.1 - - + -
547B HIS* 3.5 27.1 - + + -
548B LEU* 1.3 71.8 - - - +
550B PRO* 1.3 93.7 - - + +
552B LEU* 2.9 21.0 + - + +
553B VAL* 2.8 28.7 + - + +
586B ALA* 4.1 8.9 - - + +
633B PHE* 3.8 21.8 - + + -
634B LEU* 6.4 0.7 - - + -
651B PHE* 3.7 22.4 - + + -
655B LEU* 5.9 3.8 - - + -
670B LEU* 4.1 29.6 - - + -
671B PHE 5.4 0.4 - - - +
672B GLU* 2.7 28.0 + - - +
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Residues in contact with PRO 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B MET* 5.2 7.9 - - + -
520B ASP* 5.8 3.6 - - + -
524B PHE* 3.9 26.6 - - + -
526B LEU* 4.7 11.4 - - + -
547B HIS* 3.4 24.9 - - + +
548B LEU 3.0 7.6 - - - +
549B PHE* 1.3 121.5 - - + +
551B GLY* 1.3 55.6 + - - +
553B VAL* 3.4 3.3 + - - +
554B ARG* 2.9 33.9 + - - +
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Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B THR* 4.2 18.8 - - - -
547B HIS 5.0 0.6 + - - -
548B LEU 2.9 9.6 + - - -
550B PRO* 1.3 77.8 - - - +
552B LEU* 1.3 64.2 + - - +
554B ARG* 3.3 9.5 + - - +
555B VAL* 2.9 30.0 + - - +
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B VAL* 4.5 20.0 - - + -
512B THR* 4.7 1.7 + - - +
548B LEU 3.5 5.3 + - - +
549B PHE* 2.9 18.1 + - + +
551B GLY* 1.3 74.6 - - - +
553B VAL* 1.3 54.2 - - + +
555B VAL* 2.6 32.6 + - + +
556B LEU* 2.8 11.3 + - - +
570B LEU* 4.7 9.4 - - + +
571B PHE* 4.6 3.8 - - - -
572B GLU* 4.1 28.5 - - + +
586B ALA* 3.8 39.5 - - + +
587B GLY* 4.0 2.0 - - - +
588B LEU* 3.9 31.0 - - + +
670B LEU* 6.1 0.4 - - + -
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Residues in contact with VAL 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B PHE* 4.5 13.7 - - + -
549B PHE* 2.8 33.9 - - + +
550B PRO* 3.6 5.4 - - + +
552B LEU* 1.3 73.4 - - + +
554B ARG* 1.3 64.6 + - - +
556B LEU* 2.9 20.3 + - + +
557B LYS 3.0 5.0 + - - -
588B LEU* 3.6 17.2 - - + +
655B LEU* 4.2 23.3 - - + -
659B ILE* 6.2 0.4 - - + -
663B LEU* 6.2 4.5 - - + -
665B LEU* 4.0 20.9 - - + +
668B VAL* 5.0 4.7 - - + -
670B LEU* 4.2 15.3 - - + -
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Residues in contact with ARG 554 (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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517B ASP* 5.3 1.8 - - - +
520B ASP* 2.4 39.6 + - - -
523B ARG* 3.7 25.3 - - - +
524B PHE* 4.2 12.8 - - + -
550B PRO 2.9 16.8 + - - +
551B GLY* 3.4 13.5 - - - +
553B VAL* 1.3 77.2 - - - +
555B VAL* 1.3 60.3 + - + +
557B LYS* 3.3 18.9 - - - +
558B GLU* 2.8 30.9 + - + +
663B LEU* 4.7 15.9 - - + +
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Residues in contact with VAL 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY* 3.4 31.9 - - - +
340A LEU* 5.3 2.2 - - + -
510B VAL* 4.7 12.6 - - + -
512B THR* 3.9 16.8 - - - +
551B GLY 2.9 26.1 + - - +
552B LEU* 2.6 23.6 + - + +
554B ARG* 1.3 68.3 - - + +
556B LEU* 1.3 69.3 + - - +
557B LYS 3.2 0.2 + - - -
558B GLU* 2.8 35.7 + - - +
559B ASN* 2.9 15.2 + - - +
570B LEU* 5.9 4.5 - - + -
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Residues in contact with LEU 556 (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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552B LEU 2.8 8.0 + - - +
553B VAL* 2.9 17.0 - - - +
555B VAL* 1.3 78.0 - - - +
557B LYS* 1.3 67.8 + - - +
559B ASN* 2.8 14.9 + - + +
560B LEU* 3.0 34.0 + - + +
568B ALA* 5.2 5.2 - - + -
588B LEU* 3.8 29.4 - - + -
590B PHE* 4.0 24.7 - - + -
665B LEU* 3.9 11.4 - - + -
668B VAL* 3.6 31.4 - - + -
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Residues in contact with LYS 557 (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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553B VAL 3.0 6.2 + - - +
554B ARG* 3.3 22.2 - - - +
556B LEU* 1.3 77.6 - - - +
558B GLU* 1.3 56.8 + - + +
559B ASN 2.7 1.0 + - - -
560B LEU* 2.6 41.8 + - - +
561B ASP* 3.1 15.5 + - - +
663B LEU* 3.4 40.9 - - + +
664B GLU* 3.1 44.0 - - + +
665B LEU* 3.5 17.7 - - + +
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Residues in contact with GLU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY* 4.4 9.3 + - - +
554B ARG* 2.8 17.7 - - - +
555B VAL* 2.8 43.3 - - - +
557B LYS* 1.3 76.6 - - + +
559B ASN* 1.3 65.9 + - - +
561B ASP* 3.6 13.4 + - - +
562B LEU* 3.3 26.3 + - + +
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Residues in contact with ASN 559 (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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338A GLY 2.7 29.7 + - - -
339A ARG* 3.9 5.0 - - - +
340A LEU* 3.2 37.4 + - - +
341A LYS* 4.2 10.2 + - - -
555B VAL* 2.9 22.8 + - - +
556B LEU* 2.8 16.3 + - + +
557B LYS 2.7 4.9 + - - -
558B GLU* 1.3 73.2 + - - +
560B LEU* 1.3 54.5 + - + +
562B LEU* 3.0 4.6 + - - +
563B ASP* 2.3 43.8 + - - +
565B PRO* 4.1 9.3 - - + +
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Residues in contact with LEU 560 (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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556B LEU* 3.0 31.8 + - + +
557B LYS* 2.6 10.0 + - - +
559B ASN* 1.3 72.0 - - + +
561B ASP* 1.3 64.1 + - - +
563B ASP 3.0 18.6 - - - +
564B ARG* 3.6 16.7 + - + +
565B PRO* 4.2 14.6 - - + +
590B PHE* 3.5 33.0 - - + -
664B GLU 5.8 0.2 - - - +
665B LEU* 3.6 33.9 - - + -
666B PRO* 4.8 8.3 - - + -
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Residues in contact with ASP 561 (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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557B LYS* 3.1 21.3 + - - +
558B GLU* 3.7 14.6 - - - +
559B ASN 3.2 0.2 - - - -
560B LEU* 1.3 82.9 - - - +
562B LEU* 1.3 61.1 + - - +
564B ARG* 5.9 0.2 - - - -
664B GLU* 3.1 38.5 - - - +
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 3.2 43.7 - - + +
558B GLU* 3.3 15.8 + - + +
559B ASN* 3.0 5.1 + - - +
561B ASP* 1.3 80.4 - - - +
563B ASP* 1.3 67.2 + - - +
564B ARG* 5.6 1.1 - - - +
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Residues in contact with ASP 563 (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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339A ARG* 2.6 42.6 + - - -
341A LYS* 2.9 45.7 - - + +
559B ASN* 2.3 32.1 + - - +
560B LEU 3.0 4.9 - - - +
562B LEU* 1.3 79.2 - - - +
564B ARG* 1.3 62.5 + - - +
565B PRO* 2.7 10.0 - - + +
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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