Contacts of the helix formed by residues 504 - 516 (chain B) in PDB entry 4DBG
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 CYS 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B GLY 3.5 3.0 + - - -
503B ALA* 1.3 75.6 - - - +
505B PRO* 1.3 72.4 - - - +
506B GLU* 2.9 4.9 + - + +
507B GLU* 3.0 28.7 + - + +
508B ILE* 3.5 11.8 + - - +
528B LEU* 4.5 0.4 - - - -
532B LEU* 4.2 2.9 - - - -
551B CYS* 2.1 59.0 - - + -
552B GLN* 4.1 3.6 - - - +
555B ARG* 3.5 27.4 - - - +
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Residues in contact with PRO 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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503B ALA 4.1 1.8 - - - +
504B CYS* 1.3 84.8 - - + +
506B GLU* 1.3 67.2 + - - +
508B ILE* 3.5 3.4 + - + -
509B PHE* 3.0 24.6 + - - +
521B LEU* 3.7 20.1 - - + +
524B LEU* 3.7 19.8 - - + +
525B ARG* 4.1 24.5 - - + +
528B LEU* 3.7 25.4 - - + -
533B GLU* 4.8 8.7 - - - +
551B CYS* 4.4 8.7 - - + -
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B CYS* 2.9 4.7 + - + -
505B PRO* 1.3 81.9 - - - +
507B GLU* 1.3 62.8 + - + +
509B PHE* 3.2 11.5 + - + +
510B SER* 2.8 35.5 + - - +
521B LEU* 3.7 26.5 - - - +
551B CYS* 6.0 2.3 - - + +
552B GLN* 5.2 6.7 - - - +
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Residues in contact with GLU 507 (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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491B LEU* 3.7 35.1 - - + +
494B MET* 5.2 1.0 - - - +
504B CYS* 3.0 13.9 + - + +
506B GLU* 1.3 76.3 - - + +
508B ILE* 1.3 58.6 + - + +
510B SER* 3.2 6.9 + - - -
511B ALA* 2.8 28.9 + - - +
552B GLN* 2.9 29.6 + - - +
555B ARG* 2.8 43.7 + - - -
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Residues in contact with ILE 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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491B LEU* 3.5 31.9 - - + +
492B VAL* 4.2 12.3 - - + -
494B MET* 4.8 0.9 - - + -
495B ILE* 4.0 21.5 - - + -
503B ALA* 3.8 29.2 - - + -
504B CYS 3.5 10.9 + - - +
505B PRO* 3.5 7.9 + - + +
506B GLU 3.2 0.2 - - - -
507B GLU* 1.3 74.7 - - + +
509B PHE* 1.3 67.7 + - - +
511B ALA* 3.2 7.3 + - - +
512B LEU* 3.1 39.7 + - + +
524B LEU* 4.1 21.3 - - + -
528B LEU* 5.0 3.6 - - + -
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Residues in contact with PHE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PRO 3.0 19.5 + - - +
506B GLU* 3.4 9.4 - - + +
508B ILE* 1.3 76.4 - - - +
510B SER* 1.3 67.4 + - - +
512B LEU* 3.2 5.4 + - - +
513B GLN* 3.2 60.5 + - + +
518B GLU* 4.8 6.2 - - + -
519B VAL* 3.2 36.1 - - + +
520B PRO* 4.9 0.2 - - + -
521B LEU* 3.8 35.7 - - + -
524B LEU* 3.9 9.6 - - + +
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Residues in contact with SER 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 GLU* 2.8 20.9 + - - +
507B GLU* 3.6 6.7 - - - -
509B PHE* 1.3 77.8 - - - +
511B ALA* 1.3 67.1 + - - +
512B LEU 3.1 1.6 - - - -
513B GLN* 3.1 8.7 + - - +
514B TYR* 2.9 26.8 + - - +
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Residues in contact with ALA 511 (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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488B GLY* 4.0 29.2 - - - +
491B LEU* 4.0 14.6 - - + -
492B VAL* 5.1 5.4 - - + -
507B GLU 2.8 21.1 + - - +
508B ILE* 3.6 8.1 - - - +
510B SER* 1.3 72.7 - - - +
512B LEU* 1.3 58.5 + - - +
514B TYR* 3.7 8.2 + - - +
515B SER* 3.1 26.3 + - - -
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Residues in contact with LEU 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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492B VAL* 4.0 17.5 - - + -
508B ILE* 3.1 40.3 + - + +
509B PHE 3.8 5.8 - - - +
510B SER 3.1 1.2 - - - -
511B ALA* 1.3 76.4 - - - +
513B GLN* 1.3 59.7 + - - +
515B SER* 3.1 7.2 + - - -
516B GLY 2.9 24.6 + - - -
517B THR* 3.0 32.3 + - - +
518B GLU* 4.3 13.9 - - - +
519B VAL* 4.1 26.7 - - + -
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Residues in contact with GLN 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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509B PHE* 3.2 44.7 + - + +
510B SER* 3.1 8.2 + - - +
512B LEU* 1.3 74.3 - - - +
514B TYR* 1.3 64.3 + - - +
516B GLY* 3.1 14.6 + - - -
517B THR 3.5 10.3 + - - +
518B GLU* 3.5 37.1 - - - +
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Residues in contact with TYR 514 (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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482B ASP 4.9 6.9 + - - -
484B MET* 2.9 56.9 - - + +
485B ARG* 4.6 2.2 - - - -
510B SER 2.9 18.0 + - - +
511B ALA* 3.8 7.4 - - - +
513B GLN* 1.3 79.2 - - - +
515B SER* 1.3 63.8 + - - +
516B GLY* 4.6 0.2 - - - -
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Residues in contact with SER 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ARG* 4.6 13.7 + - - -
511B ALA 3.1 17.7 + - - -
512B LEU* 3.1 14.3 + - - -
514B TYR* 1.3 81.7 - - - +
516B GLY* 1.3 56.8 + - - +
517B THR* 4.7 4.5 + - - -
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Residues in contact with GLY 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 LEU 2.9 3.6 + - - -
513B GLN 3.1 10.0 + - - -
514B TYR 3.4 0.4 - - - -
515B SER* 1.3 78.4 - - - +
517B THR* 1.3 63.9 + - - +
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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
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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