Contacts of the strand formed by residues 498 - 506 (chain B) in PDB entry 6TXA
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 PHE 498 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B PRO* 3.7 25.2 - - + +
480B VAL* 3.6 35.0 - - + -
481B ALA* 4.1 21.5 - - + -
493B LEU* 3.8 28.3 - - + -
494B LYS 3.8 11.7 - - - -
495B ALA 3.2 15.7 + - - +
496B GLU* 4.1 4.5 - - - +
497B ASP* 1.3 82.4 - - + +
499B ILE* 1.3 66.0 + - - +
500B VAL* 5.0 1.8 - - + -
552B VAL* 3.9 11.7 - - + -
553B TYR 3.6 13.0 - - - +
554B CYS* 4.8 2.5 - - + -
555B LYS* 5.0 0.7 - - - -
565B ALA* 3.9 24.9 - - + -
568B TYR* 3.8 22.4 - + + -
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Residues in contact with ILE 499 (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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381B ILE* 4.2 10.8 - - + -
384B THR* 4.7 15.0 - - + +
388B ASP* 6.1 0.2 - - - +
454B PHE* 3.2 44.0 - - + -
477B PRO* 4.8 1.6 - - - -
498B PHE* 1.3 77.5 - - - +
500B VAL* 1.3 73.7 + - - +
501B ASP* 4.6 5.2 - - + +
551B ARG 3.8 0.7 - - - +
552B VAL* 3.4 3.5 - - - +
553B TYR* 2.9 50.7 + - + +
555B LYS* 3.8 21.5 - - + +
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Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TYR* 5.0 9.0 - - - +
476B LEU* 3.8 30.9 - - + +
477B PRO* 4.1 27.7 - - + +
480B VAL* 4.2 15.7 - - + -
498B PHE* 4.3 1.5 - - + -
499B ILE* 1.3 84.5 - - - +
501B ASP* 1.3 59.4 + - - +
502B VAL* 4.0 5.2 + - + +
550B ILE* 3.5 31.2 - - + -
551B ARG 3.4 3.8 - - - +
552B VAL* 4.1 16.8 - - + -
572B TRP* 4.5 2.5 - - + -
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Residues in contact with ASP 501 (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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220B ARG* 3.1 42.6 + - - -
380B ASN* 3.6 20.1 - - - +
384B THR* 4.6 4.8 - - + +
499B ILE* 4.1 6.0 - - + -
500B VAL* 1.3 72.0 - - - +
502B VAL* 1.3 66.4 + - - +
503B ILE* 3.6 10.9 - - - +
549B LEU 3.6 1.6 - - - +
550B ILE* 3.5 2.8 - - - +
551B ARG* 2.9 39.4 + - + +
553B TYR* 4.0 18.9 + - + -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 4.8 4.5 - - + -
473B TYR* 3.6 51.7 + - + +
476B LEU* 3.8 28.9 - - + -
500B VAL* 4.0 7.0 + - + +
501B ASP* 1.3 81.2 + - - +
503B ILE* 1.3 66.9 + - - +
504B ASN* 4.3 0.8 + - - +
548B GLN* 3.6 25.8 - - + +
549B LEU 3.4 7.2 - - - +
550B ILE* 4.4 17.0 - - + -
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 5.3 1.6 - - - +
375B GLN* 3.7 22.7 - - + +
380B ASN* 3.3 14.6 - - - +
501B ASP* 3.6 16.8 - - - +
502B VAL* 1.3 79.7 - - - +
504B ASN* 1.3 66.4 + - - +
505B MET* 3.6 29.3 + - + -
548B GLN* 3.3 4.4 - - - -
549B LEU* 2.8 45.6 + - + +
551B ARG* 3.1 43.7 - - - +
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Residues in contact with ASN 504 (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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470B ARG* 4.1 16.4 - - - +
473B TYR* 3.7 16.9 + - - -
502B VAL 5.7 0.2 + - - -
503B ILE* 1.3 74.6 - - - +
505B MET* 1.3 64.6 + - - +
506B ASP* 3.8 12.1 + - + +
547B GLU 3.6 5.4 - - - +
548B GLN* 3.1 35.4 + - - +
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Residues in contact with MET 505 (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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367B ASN* 3.5 22.9 - - - +
370B HIS* 3.7 24.2 - - + +
371B ARG* 3.4 36.1 - - + +
375B GLN* 4.1 12.1 - - + -
503B ILE* 3.7 21.5 - - + -
504B ASN* 1.3 74.1 - - - +
506B ASP* 1.3 59.5 + - - +
546B ALA* 3.2 2.3 - - - +
547B GLU* 2.8 51.0 + - + +
549B LEU* 3.8 29.2 - - + -
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Residues in contact with ASP 506 (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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363B PHE 5.6 0.2 - - - +
366B ARG* 3.3 21.5 + - - -
367B ASN* 4.4 9.7 + - - +
504B ASN* 3.8 13.2 + - + +
505B MET* 1.3 74.9 - - - +
507B TYR* 1.3 68.2 + - - +
508B GLY* 2.9 28.0 + - - -
509B MET 4.5 0.2 + - - -
510B GLN* 3.4 37.2 + - - +
545B PHE 3.3 8.7 - - - +
546B ALA* 3.8 5.8 - - + +
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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