Contacts of the helix formed by residues 428 - 441 (chain B) in PDB entry 5D3O
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 THR 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B THR 3.4 12.3 + - - -
284B LYS* 3.9 16.3 - - - +
285B VAL 3.6 17.9 - - - +
286B PRO* 3.9 2.0 - - + -
287B PHE* 4.0 6.3 - - - -
375B TYR* 3.6 27.2 - - + +
427B VAL* 1.3 81.1 - - - +
429B CYS* 1.3 69.2 + - - +
430B GLU* 3.2 14.4 + - - +
431B SER* 2.9 18.6 + - - -
432B ALA* 3.0 22.5 + - - +
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Residues in contact with CYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY* 3.4 33.9 - - - -
269B SER* 3.2 20.3 - - - +
282B ASP 4.3 2.9 - - - -
283B THR* 3.2 21.2 + - + -
285B VAL 4.4 0.6 + - - -
287B PHE* 3.8 4.9 - - - -
428B THR* 1.3 72.9 - - - +
430B GLU* 1.3 56.2 + - - +
433B SER* 2.9 32.6 + - - -
504B MET* 3.4 19.5 - - - +
506B TRP* 3.5 26.7 - - - -
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 3.7 19.5 + - - +
269B SER* 3.6 17.9 - - - +
277B ARG* 3.5 17.5 + - - +
279B SER* 3.2 19.0 + - - +
283B THR* 3.2 17.9 + - - +
284B LYS* 2.9 44.9 + - - +
374B GLU* 3.8 7.2 - - - +
428B THR* 3.0 6.8 + - - +
429B CYS* 1.3 74.2 - - - +
431B SER* 1.3 66.8 + - - +
433B SER* 2.8 21.3 + - - -
434B VAL 3.3 4.0 + - - -
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Residues in contact with SER 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ALA* 3.7 7.4 - - - +
374B GLU* 3.7 17.8 + - - -
375B TYR 2.8 46.6 + - - -
427B VAL* 3.8 0.7 - - - +
428B THR* 2.9 29.0 + - - -
430B GLU* 1.3 75.5 - - - +
432B ALA* 1.3 55.6 + - - +
434B VAL* 3.0 20.3 + - - +
435B MET* 3.1 17.7 + - - +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 5.3 0.9 - - + -
427B VAL* 4.0 12.7 - - + +
428B THR 3.0 17.7 + - - +
431B SER* 1.3 75.1 + - - +
433B SER* 1.3 66.7 + - - +
435B MET* 2.9 16.1 + - + +
436B ALA* 2.8 23.4 + - - +
494B LEU* 3.8 6.7 - - + +
504B MET* 3.5 37.5 - - + -
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 3.4 34.6 - - - -
270B VAL 3.9 3.6 + - - -
271B CYS* 3.6 17.4 - - - +
277B ARG* 4.3 3.1 + - - -
429B CYS 2.9 18.8 + - - -
430B GLU* 2.8 15.8 + - - -
432B ALA* 1.3 76.5 - - - +
434B VAL* 1.3 56.4 + - - +
436B ALA* 3.5 2.8 + - - +
437B ALA* 2.9 27.5 + - - +
502B GLY 3.8 2.4 - - - -
503B MET* 3.9 13.7 - - - -
504B MET* 3.7 3.9 - - - +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B CYS* 4.2 9.6 - - - -
277B ARG* 3.3 43.5 - - - +
370B MET 3.7 3.8 - - - +
371B ALA 3.5 26.5 - - - +
372B GLY 4.0 1.8 - - - +
374B GLU* 4.1 8.3 - - - +
430B GLU 3.5 4.3 - - - +
431B SER 3.0 9.2 + - - +
433B SER* 1.3 76.3 + - - +
435B MET* 1.3 64.9 + - - +
437B ALA* 3.0 6.8 + - - +
438B THR* 3.0 24.4 + - - -
445B CYS* 4.0 9.9 - - - -
446B PRO* 4.8 2.2 - - + -
447B ILE* 4.0 12.8 - - + -
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Residues in contact with MET 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 5.2 1.3 - - - -
296B LEU* 4.2 32.2 - - + +
367B LEU* 4.2 19.5 - - + +
370B MET* 3.5 21.6 + - + +
371B ALA* 3.8 25.4 - - + +
375B TYR 4.6 0.9 - - - +
376B VAL* 3.8 15.7 - - + -
427B VAL* 3.2 34.5 - - + -
431B SER 3.1 14.3 + - - +
432B ALA* 3.2 11.7 - - - +
434B VAL* 1.3 76.3 - - - +
436B ALA* 1.3 62.6 + - - +
438B THR* 3.0 15.9 + - - -
439B LEU* 3.3 15.9 + - - +
494B LEU* 5.1 5.6 - - + -
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ALA 2.8 8.6 + - - +
433B SER 3.6 4.5 - - - +
435B MET* 1.3 76.1 - - - +
437B ALA* 1.3 56.6 + - - +
439B LEU* 3.1 8.3 + - - +
440B ALA 2.9 22.9 + - - -
494B LEU* 4.0 18.1 - - + +
495B LEU 3.6 7.4 - - - +
496B VAL* 3.5 12.0 - - + +
502B GLY* 3.6 4.4 - - - -
503B MET 3.3 39.3 - - - +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B CYS* 3.2 31.6 - - - +
272B THR 4.1 1.3 - - - +
273B ALA* 5.0 0.7 - - - -
433B SER 2.9 13.4 + - - +
434B VAL 3.0 11.2 + - - +
436B ALA* 1.3 78.5 - - - +
438B THR* 1.3 53.8 - - - +
440B ALA* 3.1 4.3 + - - +
441B ASN* 3.0 30.1 + - - +
446B PRO* 3.5 21.7 - - + +
502B GLY* 3.5 10.5 - - - +
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Residues in contact with THR 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET* 2.9 30.1 + - - -
434B VAL 3.0 6.4 + - - -
435B MET* 3.0 7.6 + - - -
437B ALA* 1.3 75.5 - - - +
439B LEU* 1.3 61.3 + - - +
441B ASN 3.3 5.2 + - - -
443B GLY* 3.0 56.1 + - - +
444B PHE 3.7 15.3 - - - -
445B CYS* 3.7 12.6 - - + +
446B PRO* 3.9 2.0 - - - +
452B VAL* 4.3 13.2 - - + -
453B LEU* 4.8 9.6 - - + -
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 5.3 0.9 - - + -
296B LEU* 4.4 21.3 - - + -
299B ALA* 5.0 3.8 - - + -
370B MET* 6.2 0.7 - - - -
435B MET 3.3 10.1 + - - +
436B ALA* 3.3 8.1 - - - +
438B THR* 1.3 74.9 - - - +
440B ALA* 1.3 63.3 + - - +
441B ASN 3.1 1.7 + - - -
442B GLY 4.0 1.7 + - - -
453B LEU* 4.3 22.7 - - + -
458B VAL* 3.3 37.2 - - + +
461B THR* 4.3 28.5 - - + -
462B LEU* 3.6 15.6 - - + +
465B MET* 4.4 10.3 - - - -
494B LEU* 4.5 11.0 - - + -
496B VAL* 3.8 19.7 - - + -
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Residues in contact with ALA 440 (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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537A ASN* 3.0 19.6 + - - -
273B ALA* 5.1 2.7 - - + -
436B ALA 2.9 10.5 + - - +
437B ALA 3.4 8.5 - - - +
439B LEU* 1.3 77.2 - - - +
441B ASN* 1.3 58.2 + - + +
462B LEU* 5.7 0.2 - - - +
496B VAL* 3.7 11.3 - - + +
497B VAL 3.8 9.4 - - - +
498B PRO* 4.1 4.6 - - - +
499B ASN* 3.2 15.7 + - - +
500B VAL 4.6 1.3 - - - +
501B MET* 3.2 39.0 - - - +
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Residues in contact with ASN 441 (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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537A ASN* 3.9 7.0 + - - +
539A ARG* 3.5 30.9 + - - +
540A HIS* 3.4 11.2 + - - -
273B ALA* 3.8 30.7 + - + +
437B ALA 3.0 15.9 + - - +
438B THR 3.3 0.4 + - - -
439B LEU 3.1 1.2 - - - -
440B ALA* 1.3 76.9 - - - +
442B GLY* 1.3 58.4 + - - +
443B GLY 3.1 6.7 + - - -
444B PHE* 2.8 41.7 + - - +
446B PRO* 4.1 9.8 - - + +
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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