Contacts of the helix formed by residues 503 - 519 (chain B) in PDB entry 3CB4
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 ASN 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B GLU 5.6 1.9 - - - +
499B THR* 5.1 0.7 - - - -
500B HIS* 3.6 6.1 + - + +
501B ARG 3.1 0.6 - - - -
502B ASP* 1.3 85.8 + - - +
504B SER* 1.3 60.2 + - - +
505B GLN* 3.2 4.0 - - - +
506B ASN* 3.1 23.7 + - + +
507B ARG* 2.9 54.3 + - - +
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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
----------------------------------------------------------
481B VAL* 3.7 21.9 - - - +
483B VAL* 4.3 4.8 - - - +
499B THR* 3.7 15.9 - - - -
500B HIS 3.2 15.7 + - - -
501B ARG* 2.7 21.8 + - - +
503B ASN* 1.3 74.7 - - - +
505B GLN* 1.3 66.5 + - - +
507B ARG* 3.8 1.1 - - - +
508B GLY* 3.0 20.8 + - - -
532B ILE* 4.0 15.0 - - - +
537B ILE* 3.8 8.0 - - - +
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Residues in contact with GLN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ARG 4.5 0.8 + - - -
502B ASP 5.5 0.9 - - - +
503B ASN* 3.2 1.7 - - - -
504B SER* 1.3 83.5 + - - +
506B ASN* 1.3 63.1 - - - +
508B GLY* 3.3 1.6 + - - -
509B ARG* 3.2 20.6 + - + +
532B ILE* 5.3 1.1 - - - +
537B ILE* 2.9 41.6 + - - +
538B ALA* 5.1 0.2 - - - +
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Residues in contact with ASN 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ASN* 3.1 29.5 + - + +
505B GLN* 1.3 81.2 - - - +
507B ARG* 1.3 59.7 + - - +
509B ARG* 2.8 37.4 + - - +
510B GLU* 2.7 55.3 + - - +
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Residues in contact with ARG 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LYS* 5.8 3.6 - - - +
449B GLU* 3.7 30.1 + - - +
452B LEU* 4.7 22.0 - - + +
483B VAL* 5.6 0.9 - - - -
497B LEU* 4.4 22.0 - - + +
499B THR* 4.1 32.7 + - + +
500B HIS* 6.2 1.0 - - - +
503B ASN* 2.9 44.8 + - - +
504B SER 3.8 4.5 - - - +
505B GLN 3.3 0.2 - - - -
506B ASN* 1.3 75.8 - - - +
508B GLY* 1.3 59.4 + - - +
510B GLU* 3.6 28.3 + - + +
511B LEU* 2.8 30.9 + - - +
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Residues in contact with GLY 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B VAL* 4.4 8.2 - - - +
504B SER 3.0 13.5 + - - -
505B GLN 3.3 4.0 + - - -
507B ARG* 1.3 75.1 - - - +
509B ARG* 1.3 59.4 + - - +
511B LEU* 3.3 4.2 + - - +
512B VAL* 3.1 28.1 + - - +
530B ALA* 3.7 21.9 - - - +
537B ILE* 3.9 8.1 - - - -
538B ALA* 3.8 7.4 - - - +
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Residues in contact with ARG 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B GLN* 3.2 12.9 + - + +
506B ASN* 2.8 45.0 + - - +
508B GLY* 1.3 74.8 - - - +
510B GLU* 1.3 65.1 + - - +
512B VAL* 3.5 4.3 + - + +
513B GLU* 3.1 42.4 + - + +
538B ALA* 3.8 15.7 - - + +
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Residues in contact with GLU 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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506B ASN* 2.7 41.7 + - - +
507B ARG* 3.6 28.3 + - - +
508B GLY 3.3 0.2 - - - -
509B ARG* 1.3 80.4 - - - +
511B LEU* 1.3 63.2 + - - +
513B GLU* 3.7 5.0 + - - +
514B LYS* 3.2 23.0 + - - +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B VAL* 4.8 8.5 - - + -
485B VAL* 3.6 29.6 - - + -
495B LEU* 3.4 39.9 - - + +
497B LEU* 3.6 30.5 - - + +
507B ARG 2.8 15.8 + - - +
508B GLY* 3.6 6.7 - - - +
509B ARG 3.3 0.4 - - - -
510B GLU* 1.3 74.5 - - - +
512B VAL* 1.3 64.4 + - - +
514B LYS* 3.3 11.2 + - + +
515B MET* 3.2 35.2 + - + +
530B ALA* 5.4 2.5 - - + -
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B VAL* 5.8 1.6 - - + -
508B GLY 3.1 17.7 + - - +
509B ARG* 3.9 6.3 - - + +
510B GLU 3.4 0.2 - - - -
511B LEU* 1.3 77.4 - - - +
513B GLU* 1.3 65.3 + - + +
515B MET* 3.1 6.8 + - - +
516B LYS* 3.0 26.5 + - + +
528B ILE* 4.0 28.0 - - + +
529B GLN 4.1 0.7 - - - -
530B ALA* 4.0 12.1 - - + +
538B ALA* 3.8 28.3 - - + +
539B ARG 4.7 1.3 - - - -
540B SER* 3.4 32.3 - - - +
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ARG* 3.1 35.8 + - + +
510B GLU* 4.0 6.1 - - - +
512B VAL* 1.3 81.1 - - + +
514B LYS* 1.3 64.6 + - - +
516B LYS* 3.3 49.0 + - - +
517B ASP* 3.4 15.4 + - - +
540B SER* 4.5 2.6 + - - -
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR 3.1 26.4 + - - -
366B THR* 4.1 2.0 - - - +
367B ALA* 3.8 22.6 - - + +
495B LEU* 6.2 0.6 - - - +
510B GLU 3.2 17.9 + - - +
511B LEU* 3.6 10.3 - - + +
512B VAL 3.3 0.4 - - - -
513B GLU* 1.3 75.6 - - - +
515B MET* 1.3 66.6 + - + +
517B ASP* 3.3 19.0 + - + +
518B LEU* 3.4 33.2 + - + +
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Residues in contact with MET 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.4 16.6 - - + -
485B VAL* 5.1 0.9 - - + -
487B ILE* 5.1 7.0 - - + -
495B LEU* 3.6 40.8 - - + -
511B LEU* 3.2 24.4 + - + +
512B VAL 3.1 7.7 + - - +
514B LYS* 1.3 78.7 - - - +
516B LYS* 1.3 63.2 + - - +
517B ASP 3.1 1.8 - - - -
518B LEU* 3.0 32.2 + - + +
519B ILE* 3.0 40.0 + - + +
528B ILE* 3.8 29.6 - - + -
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Residues in contact with LYS 516 (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 VAL 3.0 14.1 + - - +
513B GLU* 3.3 38.8 + - - +
515B MET* 1.3 76.8 - - - +
517B ASP* 1.3 59.7 + - - +
519B ILE 3.3 20.0 - - - +
520B PRO* 5.0 1.6 - - - +
528B ILE* 4.1 10.5 - - + +
540B SER* 3.3 29.4 - - - +
541B THR 4.9 6.1 - - - -
542B VAL* 4.0 21.8 - - + -
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Residues in contact with ASP 517 (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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362A ASP* 4.8 9.0 - - - +
553A CYS* 4.2 12.1 - - - +
554A TYR 5.6 1.0 - - - +
513B GLU 3.4 14.1 + - - +
514B LYS* 3.3 13.8 + - + +
515B MET 3.1 0.6 - - - -
516B LYS* 1.3 81.6 - - - +
518B LEU* 1.3 63.9 + - + +
519B ILE 3.6 0.9 + - - -
520B PRO* 5.1 0.3 - - - +
553B CYS* 4.8 5.0 - - - -
554B TYR* 5.7 3.3 - - - +
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Residues in contact with LEU 518 (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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552A LYS* 3.3 9.4 - - + +
553A CYS 2.9 47.4 + - - +
554A TYR 4.8 0.4 - - - -
555A GLY* 4.6 16.4 - - - +
334B LEU* 5.7 0.7 - - + -
364B ILE* 3.7 36.8 - - + -
365B THR 5.9 0.7 - - - +
514B LYS* 3.5 32.1 - - + +
515B MET* 3.0 28.5 + - + +
517B ASP* 1.3 80.3 - - + +
519B ILE* 1.3 65.5 + - + +
520B PRO* 4.0 1.3 - - - -
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Residues in contact with ILE 519 (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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550A LEU* 4.8 6.3 - - + -
551A ALA 4.0 3.4 - - - +
552A LYS* 5.2 7.9 - - + -
334B LEU* 5.9 2.5 - - + -
487B ILE* 3.7 28.3 - - + -
515B MET* 3.0 36.2 + - + +
516B LYS 3.3 14.3 - - - +
517B ASP 3.3 0.8 - - - -
518B LEU* 1.3 87.4 - - + +
520B PRO* 1.3 64.5 - - - +
522B GLN* 3.3 21.3 - - - +
526B ILE* 3.5 24.5 - - + -
528B ILE* 4.5 11.0 - - + -
542B VAL* 3.7 16.1 - - + +
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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
------------------------------------------------------------
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