Contacts of the helix formed by residues 474 - 488 (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 SER 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B GLN* 1.3 78.6 - - - +
475B TYR* 1.3 65.9 + - - +
476B TRP* 3.1 50.4 + - - -
477B GLU* 3.1 19.6 + - - +
478B VAL* 3.2 12.5 + - - +
504B LEU* 4.2 0.2 - - - -
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Residues in contact with TYR 475 (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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473B GLN 3.5 3.6 + - - -
474B SER* 1.3 71.0 - - - +
476B TRP* 1.3 100.7 + + + +
478B VAL* 4.5 1.1 - - - -
479B GLY* 2.9 26.0 + - - -
501B LEU* 3.6 6.2 - - - +
504B LEU* 3.9 22.1 - - + +
505B LYS 5.6 0.2 - - - -
506B THR* 3.7 24.7 - - + +
507B PRO* 3.4 37.5 - - + +
509B TRP* 3.6 16.5 + + - -
510B TYR* 3.6 36.4 - + + -
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Residues in contact with TRP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B SER* 3.3 29.6 - - - -
475B TYR* 1.3 110.4 - + + +
477B GLU* 1.3 97.8 + - + +
480B PHE* 3.0 26.4 + + + -
510B TYR* 2.9 39.4 + - + -
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 5.4 1.7 - - - +
466B LYS* 2.9 48.3 + - - +
472B LEU* 4.2 27.8 - - + +
473B GLN 5.8 0.2 - - - +
474B SER* 3.1 18.5 + - - +
476B TRP* 1.3 98.3 + - + +
478B VAL* 1.3 60.2 + - - +
480B PHE* 3.5 3.9 + - - +
481B PHE* 3.0 29.7 + - - +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU* 4.2 11.0 - - + -
472B LEU* 3.5 31.4 - - + +
474B SER 3.2 10.8 + - - +
475B TYR 3.4 6.5 + - - +
477B GLU* 1.3 74.1 - - - +
479B GLY* 1.3 59.5 + - - +
481B PHE* 3.3 7.4 + - - +
482B LEU* 2.8 28.6 + - + +
497B ALA* 3.6 24.6 - - + +
500B LYS* 4.0 19.5 - - + -
501B LEU* 3.9 14.8 - - + +
504B LEU* 3.8 14.6 - - + -
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Residues in contact with GLY 479 (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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475B TYR 2.9 13.3 + - - -
477B GLU 3.4 0.2 - - - -
478B VAL* 1.3 77.3 - - - +
480B PHE* 1.3 56.9 + - - +
482B LEU* 3.3 8.1 + - - +
483B GLY* 3.1 21.5 + - - -
501B LEU* 3.7 14.5 - - - +
510B TYR* 3.2 20.4 - - - -
514B ILE* 3.9 16.7 - - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 3.9 26.7 - - + +
430B GLN* 3.5 59.2 - - + -
433B ILE* 4.1 11.4 - - + +
434B ASN* 5.3 2.9 - - - -
476B TRP* 3.0 29.3 + + + +
477B GLU* 4.3 4.0 - - - +
478B VAL 3.3 0.6 - - - -
479B GLY* 1.3 72.3 - - - +
481B PHE* 1.3 65.4 + - - +
483B GLY* 3.2 1.8 + - - +
484B ALA* 3.1 23.7 + - - +
510B TYR* 3.6 24.5 - + - -
513B SER* 5.7 2.5 - - - -
514B ILE* 3.6 23.6 - - + -
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Residues in contact with PHE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 4.1 10.6 - - + +
463B LEU* 3.5 27.4 - - + +
466B LYS* 5.5 1.6 - - + -
467B GLY 4.2 16.2 - - - -
469B LEU* 3.7 38.4 - - + -
472B LEU* 3.8 21.1 - - + -
477B GLU 3.0 18.8 + - - +
478B VAL* 3.5 5.2 - - - +
480B PHE* 1.3 77.4 - - - +
482B LEU* 1.3 58.2 + - - +
484B ALA* 3.4 1.4 + - - +
485B SER* 2.7 46.4 + - - -
493B ARG* 3.5 32.1 - - + -
497B ALA* 3.8 10.5 - - + -
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Residues in contact with LEU 482 (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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478B VAL 2.8 14.4 + - - +
479B GLY* 3.3 8.7 - - - +
480B PHE 3.2 0.2 - - - -
481B PHE* 1.3 75.7 - - - +
483B GLY* 1.3 60.5 + - - +
485B SER* 3.1 4.8 + - - -
486B VAL* 2.8 40.6 + - + +
494B VAL* 3.7 28.7 - - + +
497B ALA* 4.0 12.1 - - + -
498B SER* 3.4 24.7 - - - +
501B LEU* 3.7 28.3 - - + -
514B ILE* 4.2 13.7 - - + -
518B ILE* 4.4 6.3 - - + -
543B MET* 4.5 1.6 - - + -
546B LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 483 (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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433B ILE* 3.8 22.2 - - - -
479B GLY 3.1 9.3 + - - -
480B PHE 3.2 3.5 + - - -
482B LEU* 1.3 81.7 - - - +
484B ALA* 1.3 56.3 + - - +
486B VAL* 3.4 7.5 + - - +
487B LEU* 3.0 34.2 + - - +
514B ILE* 5.4 5.6 - - - -
517B THR* 6.0 1.3 - - - -
518B ILE* 5.5 4.5 - - - -
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Residues in contact with ALA 484 (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 20.2 - - + -
433B ILE* 3.6 19.8 - - + +
459B LEU* 4.8 9.3 - - + +
463B LEU* 4.2 19.0 - - + +
480B PHE 3.1 16.5 + - - +
481B PHE 4.1 2.5 - - - +
483B GLY* 1.3 75.9 - - - +
485B SER* 1.3 57.2 + - - +
487B LEU* 3.3 5.1 + - - +
488B ALA* 2.9 30.9 + - - +
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 4.9 7.0 - - - +
481B PHE* 2.7 42.7 + - - -
482B LEU* 3.4 6.3 - - - -
484B ALA* 1.3 74.1 - - - +
486B VAL* 1.3 63.6 + - - +
488B ALA* 3.3 6.2 + - - -
489B ASN 3.2 3.5 + - - -
490B ASP* 2.9 32.0 + - - -
493B ARG* 3.8 18.5 - - - +
494B VAL* 3.7 16.1 - - - +
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Residues in contact with VAL 486 (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 LEU* 2.8 32.9 + - + +
483B GLY* 3.5 10.1 - - - +
485B SER* 1.3 72.1 - - - +
487B LEU* 1.3 61.3 + - + +
489B ASN* 2.8 21.5 + - - +
494B VAL* 3.7 23.1 - - + -
518B ILE* 4.4 28.3 - - + -
521B TYR* 3.5 43.7 + - + -
522B LYS* 5.9 2.5 - - - +
543B MET* 4.5 7.2 - - - -
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Residues in contact with LEU 487 (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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433B ILE* 3.9 24.9 - - + +
436B ALA* 3.3 35.0 - - + -
437B VAL* 3.8 24.2 - - + -
440B LEU* 5.1 4.0 - - + -
459B LEU* 4.3 12.6 - - + -
483B GLY* 3.0 27.4 + - - +
484B ALA* 3.3 9.4 + - - +
486B VAL* 1.3 79.7 - - + +
488B ALA* 1.3 59.8 + - - +
489B ASN* 3.3 1.9 + - - +
517B THR* 5.1 3.1 - - + -
521B TYR* 4.2 26.5 + - + -
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 5.6 6.7 - - + -
484B ALA 2.9 17.3 + - - +
485B SER* 3.7 8.5 - - - +
486B VAL 3.1 0.6 - - - -
487B LEU* 1.3 75.4 - - - +
489B ASN* 1.3 68.6 + - - +
490B ASP* 3.4 10.2 + - + +
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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
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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