Contacts of the strand formed by residues 502 - 513 (chain B) in PDB entry 3QGT
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 LYS 502 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B SER* 6.4 2.0 - - - -
497B TYR* 3.6 1.9 - - - +
498B VAL* 3.3 8.6 - - - +
499B PHE* 2.9 43.1 + - - +
500B ASP* 3.4 29.9 + - - +
501B GLY* 1.3 84.8 - - - +
503B LEU* 1.3 60.9 + - - +
504B SER* 4.1 0.5 + - - -
538B LEU* 4.3 1.5 - - - +
539B GLN* 3.3 19.7 - - + +
540B PRO 5.5 1.3 - - - +
541B ALA* 4.1 17.9 - - + -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ILE* 4.0 11.2 - - + -
496B PHE* 3.8 29.2 - - + -
497B TYR 3.5 13.2 - - - +
498B VAL* 3.9 18.2 - - + +
502B LYS* 1.3 73.6 - - - +
504B SER* 1.3 64.7 + - - +
529B THR* 3.8 17.0 - - + +
532B ILE* 3.6 17.9 - - + -
533B ALA* 3.6 35.7 - - + +
538B LEU* 4.2 11.8 - - + +
539B GLN 2.9 13.9 + - - +
540B PRO* 3.6 2.6 - - - +
541B ALA 2.7 28.6 + - - -
542B GLN 3.9 0.5 + - - -
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE* 4.0 21.8 - - - -
496B PHE* 3.3 7.6 - - - -
497B TYR* 2.9 43.1 + - - -
502B LYS 4.1 0.5 + - - -
503B LEU* 1.3 73.2 - - - +
505B CYS* 1.3 62.4 + - - +
529B THR* 5.0 0.7 - - - -
541B ALA* 3.2 9.4 - - - +
542B GLN* 3.1 36.6 + - - +
544B ILE* 5.1 0.7 - - - -
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Residues in contact with CYS 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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354A PHE* 4.0 1.1 - - - -
494B CYS* 3.9 19.3 - - - -
495B GLN 3.3 6.3 - - - -
496B PHE* 3.4 31.6 - - + -
504B SER* 1.3 75.9 - - - +
506B ILE* 1.3 70.7 + - - +
507B MET 4.6 0.4 - - - -
525B TYR* 5.1 2.0 - - - -
528B PHE* 5.4 1.6 - - - -
529B THR* 3.5 23.8 - - + +
542B GLN 2.8 9.5 + - - +
543B PHE* 3.4 12.2 - - - -
544B ILE* 2.6 33.8 + - - +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE* 3.3 39.2 - - + -
355A GLY* 3.9 19.5 - - - -
508A TYR* 3.6 37.9 - - + +
546A VAL* 6.0 0.4 - - + -
547A LEU 4.3 0.7 - - - +
548A GLY* 3.7 12.8 - - - -
493B LEU* 3.8 1.0 - - + +
494B CYS* 3.1 4.9 - - - -
495B GLN* 2.8 31.3 + - + +
505B CYS* 1.3 75.9 - - - +
507B MET* 1.3 66.5 + - - +
508B TYR 4.5 0.4 - - - +
544B ILE* 3.1 23.8 - - + +
546B VAL* 3.9 17.9 - - + -
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Residues in contact with MET 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B HIS* 3.4 37.0 - - + +
493B LEU 3.2 11.2 - - - +
494B CYS* 4.1 2.7 - - - -
505B CYS* 4.1 0.4 - - - -
506B ILE* 1.3 78.0 - - - +
508B TYR* 1.3 77.5 + - - +
509B GLN* 3.5 4.0 - - - +
521B ASN* 4.7 2.2 - - + +
525B TYR* 3.7 42.6 - - + -
543B PHE* 3.9 20.4 - - + -
544B ILE 2.9 7.2 + - - +
545B HIS* 3.4 32.4 - - + +
546B VAL 3.0 23.9 + - - +
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Residues in contact with TYR 508 (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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473A LEU* 5.1 0.7 - - + -
493A LEU* 4.4 17.9 - - + -
495A GLN* 2.6 40.5 + - - +
506A ILE* 3.7 36.6 - - + +
508A TYR* 4.1 26.2 - + + -
546A VAL* 4.9 0.2 - - + -
492B ILE* 3.0 40.8 + - + +
493B LEU* 3.1 27.7 + - + +
506B ILE* 4.2 1.2 - - - +
507B MET* 1.3 76.2 - - - +
509B GLN* 1.3 61.2 + - - +
510B ARG* 3.8 14.4 - - + -
546B VAL* 3.6 30.5 - - + -
548B GLY* 4.0 4.8 - - - -
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Residues in contact with GLN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B CYS* 3.4 12.7 - - - +
491B HIS* 3.5 17.7 + - + -
507B MET* 3.5 5.6 - - - +
508B TYR* 1.3 76.7 - - - +
510B ARG* 1.3 61.2 + - - +
511B SER 2.9 29.4 + - - +
512B CYS* 3.5 21.0 - - - +
518B VAL* 4.5 1.2 - - - +
521B ASN* 2.6 30.0 + - - +
545B HIS* 2.8 38.4 + - - +
546B VAL 2.9 10.3 + - - +
548B GLY* 2.8 27.7 + - - -
611B UMP 3.3 15.2 + - - -
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Residues in contact with ARG 510 (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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470A ARG 2.9 27.4 + - - +
471A ARG* 3.6 8.1 - - - +
473A LEU* 3.9 8.7 - - + -
495A GLN* 2.9 43.9 + - - +
477B TRP* 3.6 15.6 - - - -
487B LEU* 5.5 0.8 - - - +
488B PRO* 2.9 31.9 + - - +
489B PRO 2.6 20.0 + - - -
490B CYS* 3.0 27.1 + - - +
492B ILE* 3.7 20.2 - - + -
508B TYR* 3.8 5.4 - - + -
509B GLN* 1.3 73.2 - - - +
511B SER* 1.3 66.0 + - - +
549B ASN* 3.0 17.4 + - - +
611B UMP 3.0 40.4 + - - -
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Residues in contact with SER 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ARG* 3.2 17.8 + - - -
490B CYS* 3.9 7.7 - - - +
509B GLN* 2.9 19.8 + - - +
510B ARG* 1.3 97.9 - - - +
512B CYS* 1.3 62.3 + - - +
549B ASN* 3.6 3.8 - - - -
551B HIS* 3.3 4.0 - - - -
611B UMP 2.7 49.9 + - - +
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Residues in contact with CYS 512 (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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509B GLN* 3.5 31.0 - - - +
511B SER* 1.3 81.2 + - - +
513B ASP* 1.3 60.9 + - - +
514B LEU* 3.1 11.9 + - + +
518B VAL* 3.7 20.0 - - + -
547B LEU* 3.5 34.1 - - + -
548B GLY 4.0 0.4 - - - -
549B ASN 2.8 17.6 + - - +
550B ALA* 4.1 0.9 - - - -
551B HIS* 2.9 34.8 + - - -
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Residues in contact with ASP 513 (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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512B CYS* 1.3 68.2 - - - +
514B LEU* 1.3 59.5 + - - +
515B GLY* 3.2 6.1 + - - -
516B LEU* 3.1 36.3 + - - +
517B GLY* 2.9 22.6 + - - +
518B VAL* 2.9 11.2 + - - -
551B HIS* 3.7 11.4 + - - +
553B TYR* 3.5 30.1 + - + -
556B HIS* 3.9 4.3 + - - -
611B UMP 2.9 37.5 + - - +
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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