Contacts of the helix formed by residues 451 - 467 (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 GLU 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B LYS* 5.1 3.6 - - - +
435B TYR* 3.7 23.8 - - + +
439B LEU* 3.8 12.1 - - + -
444B HIS* 5.1 6.5 + - + +
450B PHE* 1.3 65.3 + - - +
452B LEU* 1.3 54.1 + - - +
453B ARG 3.4 0.2 - - - -
454B LYS* 2.9 20.9 + - + +
455B VAL* 2.6 43.8 + - + +
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Residues in contact with LEU 452 (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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436B ALA* 3.7 43.0 - - + +
439B LEU* 4.1 12.8 - - + +
440B LEU* 3.6 24.0 - - + -
444B HIS* 3.7 16.0 + - + -
445B GLN* 3.4 10.3 - - - +
446B PHE* 3.4 36.5 - - + +
449B SER* 3.4 15.5 - - - +
450B PHE* 3.2 3.4 - - - +
451B GLU* 1.3 76.3 - - - +
453B ARG* 1.3 57.0 + - - +
455B VAL* 3.6 2.7 + - + +
456B GLY* 3.1 21.1 + - - -
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Residues in contact with ARG 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A VAL 5.8 0.6 + - - -
647A PHE* 3.5 35.7 - - - -
651A ASN* 4.2 13.9 + - - +
655A GLU* 4.2 17.7 - - - +
446B PHE* 3.7 25.7 + - - +
447B GLU* 4.2 16.6 + - - +
449B SER 3.1 12.1 + - - +
450B PHE* 3.4 37.7 - - + -
452B LEU* 1.3 72.1 - - - +
454B LYS* 1.3 55.6 + - - +
456B GLY* 3.2 3.6 + - - +
457B VAL* 2.9 34.0 + - + +
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Residues in contact with LYS 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLU* 5.2 9.1 + - - +
450B PHE* 4.3 10.5 - - + +
451B GLU* 2.9 28.0 + - + +
453B ARG* 1.3 74.8 - - - +
455B VAL* 1.3 62.6 + - + +
456B GLY 3.1 0.2 - - - -
457B VAL* 3.3 16.6 + - - +
458B LYS* 3.3 27.2 + - + +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.0 24.2 - - + -
432B GLY* 3.6 24.5 - - - +
435B TYR* 3.4 35.7 - - + -
436B ALA* 4.2 9.9 - - + -
439B LEU* 4.5 4.9 - - + -
451B GLU* 2.6 28.1 + - + +
452B LEU* 3.9 5.4 - - - +
454B LYS* 1.3 73.4 - - + +
456B GLY* 1.3 56.7 - - - +
458B LYS* 3.3 3.1 + - - +
459B LEU* 2.9 39.1 + - + +
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Residues in contact with GLY 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU 3.1 14.6 + - - -
453B ARG* 3.3 7.2 - - - -
454B LYS 3.1 0.4 - - - -
455B VAL* 1.3 77.7 - - - +
457B VAL* 1.3 60.2 + - - +
459B LEU* 3.7 10.6 - - - +
460B SER* 3.1 26.8 + - - -
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A GLU* 3.2 51.6 - - + +
453B ARG* 2.9 20.7 + - + +
454B LYS* 3.3 11.4 + - - +
456B GLY* 1.3 71.4 - - - +
458B LYS* 1.3 64.6 + - + +
460B SER* 3.1 18.2 + - - -
461B SER* 3.2 13.9 + - - +
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Residues in contact with LYS 458 (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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423B PHE* 3.5 43.6 + - + -
424B GLU* 4.5 13.1 + - - +
427B PRO* 3.4 35.3 - - + +
454B LYS* 3.3 20.7 + - + +
455B VAL 3.3 4.4 + - - +
457B VAL* 1.3 77.7 - - + +
459B LEU* 1.3 59.4 + - - +
461B SER* 3.0 11.7 + - - +
462B LEU* 3.0 36.9 + - + +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.5 4.7 - - + -
428B THR 4.5 2.0 - - - +
429B LEU* 3.6 33.1 - - + +
432B GLY* 4.0 28.7 - - - +
433B ILE* 4.1 15.5 - - + +
436B ALA* 4.9 0.7 - - + -
455B VAL* 2.9 37.6 + - + +
456B GLY* 3.7 9.0 - - - +
458B LYS* 1.3 76.2 - - - +
460B SER* 1.3 55.3 + - - +
462B LEU* 3.5 2.5 + - + +
463B LEU* 2.9 34.5 + - + +
484B ALA* 4.8 7.0 - - + -
487B LEU* 4.3 16.8 - - + -
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Residues in contact with SER 460 (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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456B GLY 3.1 14.1 + - - -
457B VAL* 3.1 13.7 + - - -
459B LEU* 1.3 74.7 - - - +
461B SER* 1.3 58.0 + - - +
463B LEU* 3.6 11.7 + - - +
464B GLY* 3.0 20.4 + - - -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B VAL* 3.2 10.5 + - - +
458B LYS* 3.0 20.8 + - - +
460B SER* 1.3 73.1 - - - +
462B LEU* 1.3 62.8 + - - +
464B GLY* 3.3 2.4 + - - +
465B LYS* 2.9 27.2 + - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.0 13.2 - - + -
427B PRO* 3.7 26.0 - - + +
428B THR* 3.5 38.8 - - - +
429B LEU* 3.8 20.4 - - + +
458B LYS* 3.0 23.8 + - + +
459B LEU* 4.5 0.9 - - + -
461B SER* 1.3 74.6 + - - +
463B LEU* 1.3 64.2 + - - +
465B LYS* 3.0 30.7 + - + +
466B LYS* 3.0 29.0 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 4.0 19.9 - - + +
459B LEU* 2.9 21.0 + - + +
460B SER* 3.7 11.2 - - - +
461B SER 3.3 0.2 - - - -
462B LEU* 1.3 75.0 - - - +
464B GLY* 1.3 62.4 + - - +
466B LYS* 3.3 7.1 + - + +
467B GLY* 3.1 23.2 + - - +
481B PHE* 3.5 40.2 - - + +
484B ALA* 4.2 30.1 - - + +
485B SER* 4.9 5.8 - - - +
488B ALA* 5.6 5.4 - - + -
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Residues in contact with GLY 464 (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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460B SER 3.0 16.6 + - - -
461B SER* 3.3 5.1 + - - -
462B LEU 3.2 0.4 - - - -
463B LEU* 1.3 75.5 - - - +
465B LYS* 1.3 60.7 + - - +
467B GLY* 3.4 12.6 + - - -
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Residues in contact with LYS 465 (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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427B PRO 4.9 4.8 + - - -
461B SER 2.9 13.7 + - - +
462B LEU* 3.0 34.0 + - + +
464B GLY* 1.3 76.0 - - - +
466B LYS* 1.3 79.3 + - + +
467B GLY* 3.5 0.9 + - - -
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Residues in contact with LYS 466 (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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429B LEU* 4.5 22.9 - - + +
462B LEU* 3.0 20.6 + - - +
463B LEU* 3.3 11.2 + - + +
465B LYS* 1.3 92.8 - - + +
467B GLY* 1.3 65.0 + - - +
468B ASN 4.7 0.5 - - - +
471B LYS* 5.7 2.6 - - - +
472B LEU* 3.6 32.6 - - + +
477B GLU* 2.9 41.4 + - - +
481B PHE* 5.5 0.4 - - + -
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Residues in contact with GLY 467 (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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463B LEU 3.1 13.5 + - - +
464B GLY* 3.4 10.0 + - - -
465B LYS 3.3 3.5 - - - -
466B LYS* 1.3 81.3 - - - +
468B ASN* 1.3 66.3 + - - -
469B LEU 3.7 1.2 + - - -
471B LYS* 6.3 0.9 - - - -
472B LEU* 4.5 1.9 - - - +
481B PHE* 4.2 12.8 - - - -
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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
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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