Contacts of the strand formed by residues 542 - 550 (chain B) in PDB entry 3V9G
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 THR 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.5 0.2 - - + -
197B TYR* 3.3 37.0 - - + -
198B ARG 2.7 20.9 + - - -
200B LEU* 3.7 3.8 - - - -
226B MET* 4.4 19.3 - - + -
310B ARG* 2.9 20.1 + - - -
538B ILE 4.1 2.2 - - - +
539B LEU* 3.4 32.4 - - + +
541B TRP* 1.3 81.9 - - - +
543B SER* 1.3 60.7 + - - +
544B PRO* 3.7 8.6 - - + +
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Residues in contact with SER 543 (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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499A ASN* 5.7 1.1 - - - -
523A ALA* 3.7 15.7 - - - +
529A ASN* 2.8 25.9 + - - +
198B ARG* 2.6 56.5 + - - +
199B GLY 4.6 5.8 - - - -
200B LEU* 3.8 17.3 - - - +
201B GLU 5.9 0.2 - - - -
310B ARG* 3.9 6.0 + - - +
542B THR* 1.3 73.2 - - - +
544B PRO* 1.3 60.3 - - - +
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Residues in contact with PRO 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLY 4.3 0.5 - - - +
529A ASN* 3.1 36.3 + - - +
531A LYS* 3.4 29.3 + - + -
536A HIS* 5.6 4.5 - - - +
195B THR* 4.0 21.3 - - + -
196B VAL 3.5 7.9 - - - +
197B TYR* 4.2 20.0 - - + -
198B ARG* 3.5 4.7 + - - +
539B LEU* 6.3 0.9 - - + -
542B THR* 3.7 11.2 - - + +
543B SER* 1.3 86.0 - - - +
545B GLN* 1.3 58.6 + - - +
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Residues in contact with GLN 545 (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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494A THR* 5.1 4.8 + - - +
497A LEU 4.2 3.8 + - - -
498A ARG* 3.2 31.4 + - - +
501A ALA 3.2 26.4 + - - +
502A GLY 3.4 6.5 - - - +
504A PHE* 3.8 16.9 - - + +
195B THR* 3.4 4.5 - - - +
196B VAL* 2.8 49.5 + - + +
198B ARG* 3.8 20.5 - - - +
544B PRO* 1.3 74.4 - - - +
546B VAL* 1.3 70.5 + - - +
547B ILE* 3.6 23.3 + - + +
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLY 2.9 7.1 + - - +
503A ASN* 3.5 12.7 + - - +
504A PHE* 2.9 27.2 + - - +
517A GLN 4.0 7.0 - - - +
518A GLN* 3.8 31.2 - - + -
519A PRO* 3.4 33.4 - - + +
531A LYS* 3.8 10.8 - - + -
185B PRO* 4.6 4.7 - - + -
193B ASN* 5.0 0.4 - - + -
194B SER 3.4 9.4 - - - +
195B THR* 4.1 14.4 - - + +
544B PRO* 5.7 0.2 - - + -
545B GLN* 1.3 76.3 - - - +
547B ILE* 1.3 69.8 + - - +
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Residues in contact with ILE 547 (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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494A THR* 4.1 22.9 - - + -
504A PHE* 3.3 17.9 - - + +
506A ILE* 3.9 27.4 - - + -
192B THR 3.6 1.7 - - - +
193B ASN* 3.3 4.0 - - - -
194B SER* 2.8 46.3 + - - +
196B VAL* 3.8 20.4 - - + -
545B GLN* 3.6 28.7 - - + +
546B VAL* 1.3 80.8 - - - +
548B LYS* 1.3 64.0 + - - +
549B GLU* 4.7 2.5 - - + +
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Residues in contact with LYS 548 (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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504A PHE 3.0 7.1 + - - +
505A TYR* 3.4 32.4 - - + +
506A ILE* 2.8 26.6 + - - +
508A ASP* 3.3 29.3 + - + +
511A THR 5.5 2.2 + - - -
512A GLY 4.7 10.7 + - - -
514A ILE* 5.5 6.1 - - - +
518A GLN* 3.6 26.8 - - + +
191B SER* 3.3 26.7 - - - +
192B THR 3.5 0.2 - - - -
193B ASN* 3.1 19.7 - - - +
546B VAL* 4.2 0.6 - - - +
547B ILE* 1.3 73.6 - - - +
549B GLU* 1.3 62.6 + - - +
550B THR* 3.6 3.5 + - - +
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Residues in contact with GLU 549 (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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490A VAL* 5.2 4.5 - - - +
506A ILE* 3.7 40.1 - - + +
507A ASN* 5.3 2.5 + - - +
191B SER* 3.1 4.3 - - - -
192B THR* 2.9 48.1 + - - +
547B ILE* 4.0 3.0 - - + +
548B LYS* 1.3 75.0 - - - +
550B THR* 1.3 67.3 + - - +
551B HIS* 3.7 27.4 + - + +
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Residues in contact with THR 550 (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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506A ILE 3.1 8.3 + - - +
507A ASN* 3.4 38.7 + - - +
508A ASP* 2.7 29.4 + - - +
190B PRO* 3.5 13.0 - - + +
191B SER* 2.7 20.7 + - - +
548B LYS* 3.6 4.0 + - - -
549B GLU* 1.3 75.3 - - - +
551B HIS* 1.3 63.7 + - - +
552B LYS 3.4 22.7 - - - +
554B LEU* 4.3 7.0 - - + -
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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