Contacts of the strand formed by residues 522 - 533 (chain B) in PDB entry 3H3T
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 522 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506B SER* 3.3 20.1 - - - +
507B VAL 5.5 2.6 + - - -
508B ASP* 4.5 13.9 + - - -
514B LEU* 5.7 1.8 - - - -
520B ARG* 3.9 27.1 - - + +
521B ALA* 1.3 86.4 - - - +
523B ILE* 1.3 62.2 + - - +
556B ASN 4.0 0.9 - - - +
557B VAL* 3.4 4.3 - - - +
558B ASN* 2.7 50.6 + - + +
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Residues in contact with ILE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 3.6 22.4 - - + -
482B TYR* 4.0 16.4 - - + -
504B ASN* 3.8 23.6 - - + +
505B PHE* 3.4 1.6 - - - +
506B SER* 2.9 39.7 + - - +
521B ALA* 4.7 2.7 - - + -
522B LYS* 1.3 80.8 - - - +
524B ASN* 1.3 63.2 + - - +
525B VAL* 3.9 8.7 - - + -
556B ASN 3.6 6.1 - - - -
557B VAL* 4.1 19.5 - - + +
600B 16H 3.6 43.5 - - + +
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Residues in contact with ASN 524 (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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374B MET* 2.8 36.7 - - + +
378B HIS* 2.9 20.9 + - - -
504B ASN 3.5 4.7 - - - +
505B PHE* 4.3 2.0 - - + -
523B ILE* 1.3 77.9 - - - +
525B VAL* 1.3 61.0 + - - +
554B VAL 4.1 0.3 - - - +
555B ALA* 3.9 0.5 - - - -
556B ASN* 2.9 48.9 + - + +
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Residues in contact with VAL 525 (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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378B HIS* 4.4 3.9 + - - -
436B PHE* 4.7 4.7 - - + -
503B CYS* 3.4 5.0 - - - +
504B ASN* 2.6 38.2 + - + +
523B ILE* 3.9 14.6 - - + -
524B ASN* 1.3 79.8 + - - +
526B ALA* 1.3 68.7 + - - +
553B TYR* 3.5 29.6 - - + +
554B VAL 3.2 11.9 - - - +
555B ALA* 4.1 12.6 - - + -
557B VAL* 4.8 1.6 - - + -
600B 16H 3.5 43.7 - - + +
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Residues in contact with ALA 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 3.6 33.9 - - + +
501B ILE* 4.2 5.8 - - + -
502B VAL 3.1 11.4 - - - +
503B CYS* 4.4 2.0 - - - -
525B VAL* 1.3 81.0 - - - +
527B MET* 1.3 59.7 + - - +
528B ILE* 4.1 13.7 - - + -
552B THR 3.9 0.5 - - - +
553B TYR* 3.5 4.2 - - - -
554B VAL* 2.9 38.6 + - + +
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Residues in contact with MET 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.8 28.3 - - - +
433B CYS* 4.0 5.4 - - - -
436B PHE* 3.5 53.4 - - + -
500B TRP 3.9 0.5 - - - +
501B ILE* 3.3 2.9 - - - -
502B VAL* 2.8 32.5 + - + +
526B ALA* 1.3 75.2 - - - +
528B ILE* 1.3 61.9 + - - +
529B CYS* 4.1 5.2 - - - -
551B ILE* 4.0 20.0 - - + -
552B THR 3.6 2.9 - - - +
553B TYR* 4.0 12.1 - - + -
579B PHE* 3.8 15.9 - - + -
580B LEU* 4.6 8.1 - - + -
583B PHE* 3.7 17.3 - - + -
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Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 4.4 8.7 - - + +
379B MET* 4.3 11.7 - - - -
382B SER* 3.8 28.7 - - - -
383B LEU* 4.3 18.5 - - + +
499B THR* 3.4 30.1 - - + -
500B TRP 3.4 4.7 - - - +
501B ILE* 3.7 24.5 - - + -
526B ALA* 4.2 11.7 - - + -
527B MET* 1.3 76.7 - - - +
529B CYS* 1.3 60.4 + - - +
530B GLN* 5.4 1.3 - - + +
550B LYS 3.6 1.6 - - - +
551B ILE* 3.5 4.0 - - - -
552B THR* 2.7 54.9 + - + +
554B VAL* 4.8 1.8 - - + -
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Residues in contact with CYS 529 (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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429B GLY* 3.5 27.3 - - - +
432B VAL* 3.4 31.9 - - - -
433B CYS* 3.8 13.9 - - - -
498B GLU 3.9 0.3 - - - +
499B THR* 3.5 1.6 - - - +
500B TRP* 2.7 38.8 + - - +
527B MET* 4.1 11.0 - - - -
528B ILE* 1.3 80.3 - - - +
530B GLN* 1.3 67.2 + - - +
549B CYS* 3.6 6.3 - - - -
550B LYS 3.4 3.1 - - - -
551B ILE* 3.8 12.3 - - - -
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Residues in contact with GLN 530 (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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451A ASN* 5.4 4.4 + - - -
379B MET* 5.4 0.2 - - - +
383B LEU* 4.3 23.0 - - - +
429B GLY* 5.0 0.2 - - - -
497B PRO* 4.0 23.5 + - + +
498B GLU 3.7 11.7 - - - +
499B THR* 3.4 28.5 + - + +
528B ILE* 5.4 1.6 - - + -
529B CYS* 1.3 80.7 - - - +
531B THR* 1.3 63.8 + - - +
532B LEU* 3.9 3.4 + - + +
548B LEU 3.7 0.2 - - - +
549B CYS* 3.4 5.5 - - - -
550B LYS* 2.8 56.4 + - + +
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Residues in contact with THR 531 (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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428B THR* 3.4 26.4 - - + -
429B GLY* 2.7 29.4 + - - +
430B HIS 4.6 0.5 + - - -
497B PRO* 3.5 19.8 - - - +
498B GLU 4.1 6.9 + - - -
500B TRP* 5.9 0.9 - - - -
530B GLN* 1.3 72.8 - - - +
532B LEU* 1.3 66.8 + - - +
533B VAL* 3.9 23.4 + - + +
547B ILE* 4.4 11.2 - - + -
548B LEU 3.5 8.1 - - - +
598B PHE* 4.8 8.0 + - + -
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO* 3.4 31.4 - - + -
530B GLN* 3.9 4.7 + - + +
531B THR* 1.3 73.1 - - - +
533B VAL* 1.3 60.7 + - - +
534B SER* 5.0 1.2 + - - -
546B ASN 3.6 1.4 - - - +
547B ILE* 3.5 4.5 - - - -
548B LEU* 2.8 59.2 + - + +
550B LYS* 3.9 31.9 - - + -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B THR* 3.9 17.0 + - + +
532B LEU* 1.3 77.7 - - - +
534B SER* 1.3 64.7 + - - +
535B PRO* 3.8 9.6 - - + +
542B ILE* 4.3 22.9 - - + -
546B ASN 3.4 7.0 - - - +
547B ILE* 4.1 11.7 - - + -
598B PHE* 4.0 27.1 - - + -
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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