Contacts of the helix formed by residues 428 - 442 (chain B) in PDB entry 5ULM
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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387B SER* 3.8 16.2 + - - +
423B PHE* 3.5 8.1 - - - -
426B GLU* 3.2 27.4 + - + +
427B PRO* 1.3 80.1 - - - +
429B LEU* 1.3 65.1 - - - +
430B GLN* 3.8 9.6 + - - +
431B SER* 3.3 22.8 + - - -
432B GLY 3.1 17.8 + - - -
462B LEU* 3.5 9.9 - - - -
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B THR* 1.3 72.2 - - - +
430B GLN* 1.3 56.5 + - - +
432B GLY 3.2 0.2 + - - -
433B ILE* 2.7 40.1 + - + +
459B LEU* 3.6 33.0 - - + +
462B LEU* 3.8 24.7 - - + +
463B LEU* 4.0 20.6 - - + +
466B LYS* 4.5 24.4 - - + +
477B GLU* 5.4 1.6 - - - +
480B PHE* 3.9 38.6 - - + +
481B PHE* 4.1 3.6 - - + +
484B ALA* 4.0 11.4 - - + -
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Residues in contact with GLN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B SER* 5.0 2.1 + - - -
388B ASP* 4.2 15.9 + - - +
391B CYS* 3.6 32.1 - - - +
419B PHE* 5.5 0.4 - - - -
428B THR* 3.2 8.2 + - - +
429B LEU* 1.3 78.3 - - - +
431B SER* 1.3 60.2 + - - +
433B ILE* 3.5 1.8 - - - +
434B ASN* 2.8 40.8 + - - +
480B PHE* 3.5 53.8 - - + -
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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
----------------------------------------------------------
387B SER* 4.7 0.2 - - - -
391B CYS* 3.8 11.2 - - - -
419B PHE* 3.7 21.9 - - - +
422B ALA* 3.6 28.5 - - - -
423B PHE* 3.3 24.0 + - - -
426B GLU 4.2 1.0 + - - -
428B THR* 3.3 17.1 + - - -
429B LEU 3.4 0.2 - - - -
430B GLN* 1.3 75.1 - - - +
432B GLY* 1.3 60.5 + - - +
434B ASN 3.5 0.3 + - - -
435B TYR* 2.9 31.9 + - - +
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 3.4 30.7 - - - -
428B THR 3.1 10.0 + - - -
429B LEU 3.6 2.5 - - - -
431B SER* 1.3 78.5 + - - +
433B ILE* 1.3 56.7 + - - +
435B TYR* 3.4 1.5 + - - +
436B ALA* 3.0 29.6 + - - +
455B VAL* 3.6 7.9 - - - +
459B LEU* 4.0 10.8 - - - -
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 2.7 26.4 + - - +
430B GLN 3.5 7.2 - - - +
432B GLY* 1.3 71.2 - - - -
434B ASN* 1.3 66.2 + - - +
436B ALA* 3.4 1.2 + - - +
437B VAL* 2.9 36.7 + - - +
459B LEU* 4.1 11.4 - - + +
479B GLY 5.1 0.4 - - - +
480B PHE* 4.1 26.9 - - + +
483B GLY* 3.8 25.1 - - - +
484B ALA* 3.6 34.5 - - + +
487B LEU* 4.0 18.6 - - + -
514B ILE* 5.3 4.3 - - + -
517B THR* 4.5 13.0 - - + -
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Residues in contact with ASN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 3.5 19.8 + - - +
419B PHE* 3.5 39.4 - - + -
430B GLN* 2.8 37.7 + - - +
433B ILE* 1.3 84.6 - - - +
435B TYR* 1.3 60.5 + - - +
437B VAL* 3.6 5.6 + - - +
438B LEU* 3.2 29.6 + - - +
480B PHE* 5.3 2.4 - - - -
517B THR* 2.8 28.8 + - - +
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Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ALA* 3.5 26.0 - - + -
419B PHE* 3.9 13.6 - - + +
420B LYS* 2.9 58.9 + - + +
423B PHE* 4.6 11.0 - + + -
424B GLU* 5.8 0.2 - - - -
431B SER 2.9 18.2 + - - +
432B GLY* 3.6 4.0 - - - +
434B ASN* 1.3 72.5 - - - +
436B ALA* 1.3 63.7 + - - +
438B LEU* 3.2 5.5 + - - +
439B LEU* 3.0 50.0 + - + +
451B GLU* 3.7 13.3 - - + +
455B VAL* 3.4 36.6 - - + -
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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 GLY 3.0 14.8 + - - +
435B TYR* 1.3 75.3 - - - +
437B VAL* 1.3 57.9 + - - +
439B LEU* 3.2 7.7 + - - +
440B LEU* 2.8 33.5 + - + +
452B LEU* 3.7 24.0 - - + +
455B VAL* 4.2 12.8 - - + -
459B LEU* 4.9 0.9 - - + -
487B LEU* 3.3 28.0 - - + -
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Residues in contact with VAL 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 6.2 0.9 - - + -
433B ILE 2.9 21.4 + - - +
434B ASN* 3.9 5.2 - - - +
436B ALA* 1.3 75.5 - - - +
438B LEU* 1.3 61.1 + - + +
440B LEU* 3.3 12.2 + - + +
441B ALA* 2.9 25.6 + - - +
487B LEU* 3.8 24.7 - - + -
517B THR* 3.8 28.3 - - + +
520B ILE* 3.5 39.6 - - + +
521B TYR* 4.0 13.4 - - + +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 4.6 20.9 - - + -
401B PHE* 4.0 28.9 - - + -
412B ARG* 3.9 20.9 - - + +
415B GLY* 3.6 11.0 - - - -
416B ALA* 3.5 38.5 - - + +
419B PHE* 3.9 15.0 - - + -
434B ASN 3.2 17.2 + - - +
435B TYR 3.2 5.1 + - - +
437B VAL* 1.3 77.0 - - + +
439B LEU* 1.3 60.3 + - - +
441B ALA* 3.3 3.8 + - - +
442B ALA* 2.9 27.9 + - - +
520B ILE* 4.6 7.4 - - + -
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ALA* 4.9 7.0 - - + -
435B TYR* 3.0 60.8 + - + +
436B ALA* 3.5 5.8 - - - +
438B LEU* 1.3 72.8 - - - +
440B LEU* 1.3 65.8 - - - +
442B ALA* 3.0 13.2 + - + -
443B GLY 3.2 0.7 + - - -
444B HIS* 3.1 56.9 + - + +
451B GLU* 3.8 18.8 - - + -
452B LEU* 4.1 22.4 - - + +
455B VAL* 4.5 1.8 - - + -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA 2.8 22.0 + - - +
437B VAL* 3.3 17.2 + - + +
439B LEU* 1.3 71.2 - - - +
441B ALA* 1.3 62.6 + - - +
443B GLY* 3.2 13.5 + - - -
444B HIS* 3.6 14.8 - - - +
445B GLN* 3.8 21.1 - - - +
446B PHE* 4.7 4.0 - - + +
452B LEU* 3.6 27.3 - - + +
487B LEU* 5.1 5.8 - - + -
521B TYR* 3.6 39.5 - - + +
524B PHE* 4.0 20.2 - - + +
525B VAL* 5.1 9.4 - - + -
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PHE* 3.8 22.0 - - + -
412B ARG* 3.6 14.5 + - - -
437B VAL 2.9 16.3 + - - +
438B LEU* 3.6 9.4 - - - +
439B LEU 3.3 0.4 - - - -
440B LEU* 1.3 73.3 - - - +
442B ALA* 1.3 58.3 + - - +
443B GLY* 3.3 1.3 + - - -
520B ILE* 4.1 2.9 - - + -
524B PHE* 3.4 49.5 - - + +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.6 32.2 + - - +
413B ASP* 4.2 5.4 - - - +
438B LEU 2.9 16.2 + - - +
439B LEU* 3.0 8.6 + - + +
441B ALA* 1.3 74.6 - - - +
443B GLY* 1.3 58.1 + - - +
444B HIS* 3.6 13.2 - - + +
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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
------------------------------------------------------------
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