Contacts of the helix formed by residues 503 - 519 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A GLU* 5.5 3.6 - - - +
499A THR* 4.2 0.6 + - - -
500A HIS* 3.5 8.6 + - + -
501A ARG 3.1 0.6 - - - -
502A ASP* 1.3 87.4 + - - +
504A SER* 1.3 60.4 + - - +
505A GLN 3.3 3.4 - - - +
506A ASN* 3.5 26.6 + - - +
507A ARG* 2.8 60.4 + - - +
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Residues in contact with SER 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A VAL* 3.9 19.0 - - - +
483A VAL* 4.2 4.4 - - - +
499A THR* 3.8 12.3 - - - -
500A HIS 3.2 10.8 + - - -
501A ARG* 2.9 21.0 + - - -
503A ASN* 1.3 77.0 - - - +
505A GLN* 1.3 60.5 + - - +
506A ASN 3.2 0.7 - - - -
508A GLY 3.1 21.8 + - - -
532A ILE* 3.6 21.3 - - - +
537A ILE* 3.5 13.6 - - - +
165C THR* 4.0 10.9 - - - +
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Residues in contact with GLN 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ARG 4.4 0.8 + - - +
502A ASP 5.6 2.5 - - - +
503A ASN* 5.6 0.9 - - - -
504A SER* 1.3 83.2 + - - +
506A ASN* 1.3 60.0 + - - +
508A GLY* 4.2 0.7 - - - -
509A ARG* 3.3 21.7 + - - +
537A ILE* 3.0 37.1 + - - +
23C ARG* 3.8 24.2 - - - +
26C GLN* 3.2 26.9 + - - +
27C ILE* 5.5 2.8 - - - +
164C LYS 4.0 12.4 + - - +
165C THR* 2.8 35.4 + - - +
166C GLY* 4.1 3.2 - - - -
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Residues in contact with ASN 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASN* 3.5 29.4 + - + +
504A SER 3.2 0.2 - - - -
505A GLN* 1.3 80.0 - - - +
507A ARG* 1.3 62.6 + - - +
508A GLY 3.2 0.2 - - - -
509A ARG* 3.1 34.9 + - - +
510A GLU* 2.8 60.7 + - - +
26C GLN* 5.8 0.2 - - - -
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Residues in contact with ARG 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A LYS* 5.3 6.4 - - - +
426A ARG* 5.8 0.6 - - - +
449A GLU* 2.8 40.6 + - - -
452A LEU* 5.6 14.5 - - + +
497A LEU* 4.4 24.6 - - + +
499A THR* 3.5 33.1 + - + +
500A HIS* 5.1 4.8 + - - +
503A ASN* 2.8 59.0 + - - +
504A SER 4.4 0.2 - - - +
506A ASN* 1.3 73.9 - - - +
508A GLY* 1.3 64.2 + - - +
510A GLU* 3.5 23.0 + - - +
511A LEU* 3.2 23.9 + - - +
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Residues in contact with GLY 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 4.2 9.1 - - - +
504A SER 3.1 18.4 + - - -
507A ARG* 1.3 76.7 - - - +
509A ARG* 1.3 61.2 + - - +
511A LEU* 3.4 5.3 + - - +
512A VAL* 3.3 26.9 + - - +
530A ALA* 3.8 11.4 - - - +
537A ILE* 3.9 17.9 - - - -
538A ALA* 4.4 3.4 - - - -
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Residues in contact with ARG 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A GLN* 3.3 19.4 + - - +
506A ASN* 3.1 40.1 + - - +
508A GLY* 1.3 74.1 - - - +
510A GLU* 1.3 74.3 + - - +
512A VAL* 3.5 4.4 + - + +
513A GLU* 3.2 31.3 + - - +
538A ALA* 4.0 19.9 - - + +
26C GLN* 4.1 30.5 + - + +
30C GLY* 5.8 9.6 - - - -
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Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ASN* 2.8 37.1 + - - +
507A ARG* 3.5 28.5 - - - +
509A ARG* 1.3 87.2 + - - +
511A LEU* 1.3 54.3 + - - +
513A GLU* 3.3 7.7 + - - +
514A LYS* 2.8 34.4 + - - +
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A VAL* 4.4 13.0 - - + +
485A VAL* 3.4 36.8 - - + -
495A LEU* 4.0 20.6 - - + +
497A LEU* 3.8 30.5 - - + -
507A ARG 3.2 11.1 + - - +
508A GLY 3.4 9.2 - - - +
510A GLU* 1.3 74.6 - - - +
512A VAL* 1.3 61.6 + - + +
514A LYS* 3.1 16.3 + - + +
515A MET* 3.0 49.9 + - + +
530A ALA* 5.2 1.3 - - + -
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 6.0 1.6 - - + -
508A GLY 3.3 14.4 + - - +
509A ARG* 3.5 6.9 + - + +
510A GLU 3.4 0.2 - - - -
511A LEU* 1.3 75.9 - - + +
513A GLU* 1.3 63.7 + - + +
515A MET* 3.7 3.1 + - - +
516A LYS* 3.3 22.6 + - + +
528A ILE* 4.1 21.9 - - + +
529A GLN* 4.3 4.5 - - - -
530A ALA* 3.9 22.2 - - + +
538A ALA* 3.8 22.0 - - + +
539A ARG 4.7 1.1 - - - -
540A SER* 3.5 38.1 - - - +
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Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.2 28.2 + - - +
510A GLU* 3.5 10.1 - - - +
511A LEU 3.1 0.4 - - - -
512A VAL* 1.3 79.5 - - - +
514A LYS* 1.3 65.8 + - - +
516A LYS* 3.1 48.4 + - - +
517A ASP* 3.4 15.0 + - - +
540A SER* 5.0 1.6 + - - -
30C GLY* 5.2 7.4 - - - +
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Residues in contact with LYS 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A THR 3.9 14.7 + - - -
366A THR* 4.3 1.4 - - - +
367A ALA* 3.4 38.2 - - - +
495A LEU* 5.9 4.9 - - + +
510A GLU 2.8 17.7 + - - +
511A LEU* 3.4 22.0 - - + +
513A GLU* 1.3 71.5 - - - +
515A MET* 1.3 66.9 + - - +
517A ASP* 3.1 24.6 + - - +
518A LEU* 3.3 23.8 + - + +
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Residues in contact with MET 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ALA* 5.9 0.7 - - + -
334A LEU* 4.7 12.6 - - + -
485A VAL* 5.0 2.0 - - + -
487A ILE* 5.1 7.0 - - + -
495A LEU* 3.6 39.7 - - + -
511A LEU* 3.0 31.1 + - + +
512A VAL 3.8 5.4 - - - +
514A LYS* 1.3 74.9 - - - +
516A LYS* 1.3 54.8 + - - +
517A ASP 3.0 5.2 - - - -
518A LEU* 2.9 27.3 + - + +
519A ILE* 2.8 60.1 + - + +
528A ILE* 4.2 28.5 - - + -
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Residues in contact with LYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A VAL 3.3 13.6 + - - +
513A GLU* 3.1 44.5 + - - +
515A MET* 1.3 76.6 - - - +
517A ASP* 1.3 61.5 + - - +
519A ILE 3.2 20.1 - - - +
520A PRO* 5.1 0.9 - - - +
528A ILE* 4.3 5.4 - - + -
540A SER* 3.1 27.6 - - - +
541A THR 4.9 4.0 - - - +
542A VAL* 4.0 25.9 - - + +
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Residues in contact with ASP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A GLU 3.4 11.4 + - - +
514A LYS* 3.1 14.2 + - - +
515A MET 3.0 0.6 - - - -
516A LYS* 1.3 83.0 - - - +
518A LEU* 1.3 64.4 + - + +
519A ILE 3.3 2.3 + - - -
520A PRO* 4.8 1.2 - - - +
553A CYS* 5.3 1.9 - - - -
554A TYR* 6.1 1.0 - - - -
362B ASP* 5.1 6.2 - - - +
553B CYS* 4.3 11.4 - - - +
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 5.0 4.5 - - + -
364A ILE* 3.6 37.0 - - + -
365A THR 5.6 0.7 - - - +
495A LEU* 6.2 0.9 - - + -
514A LYS* 3.3 26.6 + - + +
515A MET* 2.9 33.4 + - + +
517A ASP* 1.3 80.2 - - + +
519A ILE* 1.3 62.9 - - + +
520A PRO* 3.5 1.7 - - - +
552B LYS* 3.3 10.7 - - + +
553B CYS 2.9 44.7 + - - +
555B GLY* 4.7 12.3 - - - +
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Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ILE* 3.7 29.8 - - + -
515A MET* 2.8 32.6 + - + +
516A LYS 3.2 17.5 - - - +
517A ASP 4.6 0.7 - - - -
518A LEU* 1.3 84.6 - - + +
520A PRO* 1.3 65.6 - - - +
522A GLN* 3.3 22.9 - - - +
526A ILE* 3.5 22.7 - - + -
528A ILE* 4.3 14.8 - - + -
542A VAL* 3.8 19.7 - - + +
550B LEU* 4.9 5.6 - - + -
551B ALA 4.2 4.0 - - - +
552B LYS* 5.5 5.4 - - + -
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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