Contacts of the helix formed by residues 503 - 519 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424E GLU* 5.5 4.8 + - - -
499E THR* 5.0 0.9 - - - +
500E HIS* 3.3 9.9 + - + +
501E ARG 2.7 4.4 + - - -
502E ASP* 1.3 88.8 - - + +
504E SER* 1.3 57.0 + - - +
505E GLN* 3.3 3.6 - - - +
506E ASN* 3.1 33.1 + - - +
507E ARG* 3.0 49.7 + - - +
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Residues in contact with SER 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481E VAL* 3.7 22.3 - - - +
483E VAL* 4.3 4.3 - - - +
499E THR* 3.8 15.0 - - - -
500E HIS 3.0 12.6 + - - -
501E ARG* 2.6 31.6 + - - +
503E ASN* 1.3 69.4 - - - +
505E GLN* 1.3 65.6 + - - +
507E ARG* 3.3 2.1 + - - +
508E GLY* 3.0 19.2 + - - -
532E ILE* 4.1 15.5 - - - +
537E ILE* 3.7 9.5 - - - +
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Residues in contact with GLN 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E ARG 4.4 0.4 + - - -
502E ASP 6.1 0.2 - - - +
503E ASN* 3.3 1.3 - - - -
504E SER* 1.3 78.6 + - - +
506E ASN* 1.3 64.2 + - - +
508E GLY* 3.3 2.1 + - - -
509E ARG* 3.0 21.6 + - + +
532E ILE* 5.5 0.4 - - - +
537E ILE* 2.9 43.5 + - + +
538E ALA* 4.6 2.6 - - - +
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Residues in contact with ASN 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E ASN* 3.1 37.8 + - + +
505E GLN* 1.3 80.8 - - - +
507E ARG* 1.3 58.6 + - - +
509E ARG* 3.1 34.5 + - - +
510E GLU* 2.9 60.7 + - - +
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Residues in contact with ARG 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E GLU* 3.1 29.9 + - - -
452E LEU* 4.6 27.2 - - + +
497E LEU* 3.8 26.2 - - + -
499E THR* 3.6 33.4 + - + +
503E ASN* 3.0 44.5 + - - +
504E SER 3.3 6.9 + - - +
506E ASN* 1.3 77.2 - - - +
508E GLY* 1.3 57.4 + - - +
510E GLU* 3.3 25.1 + - - +
511E LEU* 2.9 30.9 + - - +
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Residues in contact with GLY 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483E VAL* 4.4 7.5 - - - +
504E SER 3.0 14.1 + - - -
505E GLN 3.7 3.6 - - - -
507E ARG* 1.3 73.9 - - - +
509E ARG* 1.3 64.6 + - - +
511E LEU* 3.1 6.3 + - - +
512E VAL* 3.1 26.7 + - - +
530E ALA* 3.7 17.1 - - - +
537E ILE* 4.0 8.5 - - - -
538E ALA* 4.0 6.5 - - - -
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Residues in contact with ARG 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505E GLN* 3.0 16.7 + - + +
506E ASN* 3.1 38.2 + - - +
508E GLY* 1.3 74.1 - - - +
510E GLU* 1.3 77.3 + - - +
512E VAL* 3.4 3.7 + - - +
513E GLU* 3.1 48.1 + - - +
538E ALA* 3.9 17.3 - - + +
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Residues in contact with GLU 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E LEU* 5.8 0.9 - - - +
506E ASN* 2.9 38.8 + - - +
507E ARG* 3.5 30.6 + - - +
509E ARG* 1.3 94.9 + - - +
511E LEU* 1.3 56.0 + - - +
513E GLU* 3.9 4.4 - - - +
514E LYS* 3.0 29.3 + - - +
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Residues in contact with LEU 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ALA* 5.9 5.8 - - + -
483E VAL* 4.6 11.2 - - + -
485E VAL* 3.8 33.4 - - + -
495E LEU* 3.8 31.2 - - + +
497E LEU* 3.8 32.8 - - + +
507E ARG 2.9 11.5 + - - +
508E GLY* 3.1 11.0 + - - +
510E GLU* 1.3 75.4 - - - +
512E VAL* 1.3 65.9 + - + +
514E LYS* 3.4 14.2 + - + +
515E MET* 3.2 27.7 + - + +
530E ALA* 5.0 1.6 - - + -
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Residues in contact with VAL 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E GLY 3.1 13.7 + - - +
509E ARG* 3.4 7.2 + - - +
511E LEU* 1.3 76.0 - - + +
513E GLU* 1.3 66.4 + - - +
515E MET* 3.3 5.0 + - - +
516E LYS* 3.1 20.7 + - + +
528E ILE* 4.0 24.2 - - + +
529E GLN 4.3 0.4 - - - -
530E ALA* 3.8 15.9 - - + +
538E ALA* 3.5 29.8 - - + +
539E ARG 4.3 1.3 - - - -
540E SER* 3.4 39.0 - - - +
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Residues in contact with GLU 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E ARG* 3.1 38.5 + - - +
510E GLU* 3.9 5.6 - - - +
512E VAL* 1.3 79.5 - - - +
514E LYS* 1.3 63.6 + - - +
516E LYS* 2.8 51.4 + - - +
517E ASP* 3.3 16.1 + - - -
540E SER* 4.7 2.9 - - - -
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Residues in contact with LYS 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E THR* 3.9 19.4 + - - +
366E THR* 4.4 1.5 - - - +
367E ALA* 3.9 30.7 - - + +
368E PRO* 5.7 0.4 - - - +
495E LEU* 6.2 2.5 - - + -
510E GLU 3.0 18.6 + - - +
511E LEU* 3.5 19.1 - - + +
512E VAL 3.3 0.2 - - - -
513E GLU* 1.3 76.7 - - - +
515E MET* 1.3 68.5 + - - +
517E ASP* 3.3 18.6 + - - +
518E LEU* 3.5 24.5 + - + +
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Residues in contact with MET 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E LEU* 3.9 21.8 - - + -
364E ILE* 6.1 0.2 - - - -
485E VAL* 5.4 0.7 - - + -
487E ILE* 4.7 6.7 - - + -
495E LEU* 3.6 41.5 - - + -
511E LEU* 3.2 20.0 + - + +
512E VAL 3.7 7.2 - - - +
513E GLU 3.2 0.4 - - - -
514E LYS* 1.3 81.4 - - - +
516E LYS* 1.3 59.1 + - - +
517E ASP 3.2 0.2 - - - -
518E LEU* 3.2 21.7 + - + +
519E ILE* 3.0 56.0 + - + +
528E ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E VAL 3.1 18.4 + - - +
513E GLU* 2.8 43.6 + - - +
515E MET* 1.3 76.4 - - - +
517E ASP* 1.3 61.8 + - - +
519E ILE 3.0 23.2 - - - +
520E PRO* 5.0 0.5 - - - +
528E ILE* 4.4 14.4 - - + -
540E SER* 3.2 29.6 - - - +
541E THR 5.3 1.3 - - - +
542E VAL* 4.6 14.1 - - + +
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Residues in contact with ASP 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ASP* 5.2 6.1 - - - +
553D CYS* 4.5 10.0 - - - +
513E GLU 3.3 10.0 + - - +
514E LYS* 3.3 13.1 + - - +
515E MET 3.2 0.4 - - - -
516E LYS* 1.3 80.6 - - - +
518E LEU* 1.3 64.8 + - + +
519E ILE 3.7 1.2 + - - -
520E PRO 5.2 0.2 - - - -
553E CYS* 5.1 3.6 - - - -
554E TYR* 5.9 2.8 - - - -
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Residues in contact with LEU 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552D LYS* 3.3 8.5 - - + +
553D CYS 2.8 48.5 + - - +
555D GLY* 4.5 15.0 - - - +
334E LEU* 6.4 0.2 - - + -
364E ILE* 3.7 39.7 - - + -
365E THR 5.5 1.6 - - - +
514E LYS* 3.5 23.3 + - + +
515E MET* 3.2 31.0 + - + +
517E ASP* 1.3 81.8 - - + +
519E ILE* 1.3 62.6 + - + +
520E PRO* 3.5 2.0 - - - +
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Residues in contact with ILE 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D LEU* 4.6 10.1 - - + -
551D ALA 4.0 4.5 - - - +
552D LYS* 5.2 6.1 - - + -
334E LEU* 6.1 0.7 - - + -
487E ILE* 3.9 21.1 - - + -
515E MET* 3.0 46.4 + - + +
516E LYS 3.0 17.3 - - - +
517E ASP 3.4 0.9 - - - -
518E LEU* 1.3 83.4 - - + +
520E PRO* 1.3 65.8 - - - +
522E GLN* 3.3 23.6 - - - +
526E ILE* 3.8 22.0 - - + -
528E ILE* 4.3 8.1 - - + -
542E VAL* 3.8 18.9 - - + +
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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