Contacts of the helix formed by residues 541 - 555 (chain B) in PDB entry 2N5T
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 ASN 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B LEU* 4.6 9.5 - - + +
265B ASP* 2.3 43.7 - - - +
539B ASN 4.2 0.2 + - - -
540B THR* 1.3 91.2 - - - +
542B PHE* 1.3 63.8 + - - +
543B GLU* 3.0 12.7 + - - +
544B ASP* 3.2 29.5 + - + +
545B ALA 3.2 11.8 + - - -
568B PHE* 5.6 0.6 - - - -
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Residues in contact with PHE 542 (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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263B THR* 3.6 10.2 - - + +
265B ASP* 2.9 22.4 + - - +
267B HIS* 3.2 56.8 - + + -
516B LEU* 3.3 37.0 - - + -
517B GLY 4.8 1.1 - - - -
519B GLY* 4.9 6.1 - - - -
540B THR* 4.7 0.2 - - - -
541B ASN* 1.3 76.2 + - - +
543B GLU* 1.3 77.4 + - - +
545B ALA* 3.3 7.0 + - - +
546B LYS* 3.0 52.9 + - + +
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Residues in contact with GLU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 3.0 13.7 + - + +
541B ASN* 3.0 10.1 + - - +
542B PHE* 1.3 98.7 - - - +
544B ASP* 1.3 66.1 + - - +
546B LYS* 3.3 25.8 + - - +
547B VAL* 3.2 25.1 + - - +
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Residues in contact with ASP 544 (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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541B ASN* 3.2 32.6 + - + +
542B PHE 3.2 0.4 - - - -
543B GLU* 1.3 81.2 - - - +
545B ALA* 1.3 51.0 + - - +
547B VAL* 3.2 12.8 + - - +
548B LEU 2.8 28.4 + - - -
568B PHE* 3.5 27.0 - - + -
572B LYS* 4.1 24.3 - - - +
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Residues in contact with ALA 545 (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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513B LEU* 3.5 22.4 - - + +
516B LEU* 4.3 7.6 - - + -
517B GLY* 3.5 10.6 - - - +
540B THR* 4.1 13.2 - - + -
541B ASN 3.2 9.4 + - - +
542B PHE 3.4 9.6 - - - +
544B ASP* 1.3 74.3 - - - +
546B LYS* 1.3 54.8 + - - +
548B LEU* 2.9 11.1 + - - +
549B ALA* 2.6 36.7 + - - +
568B PHE* 3.7 4.9 - - - -
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Residues in contact with LYS 546 (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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517B GLY* 3.4 24.2 - - - +
542B PHE* 3.0 45.5 + - + +
543B GLU* 3.3 28.7 + - - +
545B ALA* 1.3 73.0 - - - +
547B VAL* 1.3 67.7 + - + +
549B ALA* 2.8 3.5 + - - +
550B GLU* 2.8 26.2 + - - +
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Residues in contact with VAL 547 (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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543B GLU 3.2 12.1 + - - +
544B ASP* 3.2 12.4 + - - +
546B LYS* 1.3 79.8 - - + +
548B LEU* 1.3 63.7 + - - +
550B GLU* 3.5 10.1 + - - +
551B GLN* 3.0 42.7 + - + +
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Residues in contact with LEU 548 (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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513B LEU* 3.5 38.8 - - + -
514B LEU* 3.7 18.6 - - + -
544B ASP 2.8 12.9 + - - +
545B ALA* 3.1 8.3 - - - +
547B VAL* 1.3 75.3 - - - +
549B ALA* 1.3 64.2 + - - +
551B GLN* 3.1 13.6 + - - +
552B ALA* 2.9 20.8 + - - +
564B LEU* 3.7 45.3 - - + +
565B VAL* 3.8 6.7 - - + +
568B PHE* 3.7 29.8 - - + -
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Residues in contact with ALA 549 (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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514B LEU* 4.0 15.7 - - - +
517B GLY* 3.6 26.0 - - - +
518B MET* 3.6 20.9 - - + +
545B ALA 2.6 16.1 + - - +
546B LYS 2.8 7.2 + - - +
548B LEU* 1.3 68.8 - - - +
550B GLU* 1.3 72.1 + - - +
552B ALA* 3.0 3.7 + - - +
553B LEU* 2.9 26.1 + - + +
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Residues in contact with GLU 550 (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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546B LYS 2.8 14.8 + - - +
547B VAL* 3.8 9.1 - - - +
549B ALA* 1.3 79.9 - - - +
551B GLN* 1.3 68.8 + - + +
553B LEU* 3.0 17.5 + - - +
554B ALA* 3.4 9.0 + - - +
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Residues in contact with GLN 551 (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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547B VAL* 3.0 31.2 + - + +
548B LEU* 3.4 12.6 - - - +
550B GLU* 1.3 76.6 - - + +
552B ALA* 1.3 65.7 + - - +
554B ALA* 2.8 23.4 + - - +
555B GLN* 3.5 14.0 + - - +
564B LEU* 3.0 36.1 - - + +
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Residues in contact with ALA 552 (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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479B PRO* 5.4 0.7 - - - +
482B LEU* 5.2 2.5 - - + -
514B LEU* 4.0 24.9 - - + -
548B LEU 2.9 12.9 + - - +
549B ALA 3.0 7.6 + - - +
551B GLN* 1.3 75.9 - - - +
553B LEU* 1.3 62.0 + - + +
554B ALA 3.1 1.6 + - - -
555B GLN* 3.1 27.2 + - - +
561B LEU* 3.5 35.9 - - + +
564B LEU* 4.7 5.8 - - + -
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Residues in contact with LEU 553 (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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441A HIS* 4.6 4.0 + - - -
479B PRO* 6.2 0.7 - - - -
482B LEU* 3.4 20.9 - - + +
483B ASN* 3.3 65.3 + - - +
486B LYS* 3.5 43.3 - - + -
518B MET* 4.1 15.7 - - + -
549B ALA* 2.9 16.6 + - + +
550B GLU* 3.0 12.9 + - + +
552B ALA* 1.3 77.8 - - + +
554B ALA* 1.3 57.3 + - - +
555B GLN 4.6 2.3 - - - +
561B LEU* 5.6 0.4 - - - -
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Residues in contact with ALA 554 (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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441A HIS* 3.1 21.3 - - - -
550B GLU* 3.4 6.1 + - + +
551B GLN* 2.8 13.1 + - - +
553B LEU* 1.3 78.7 - - - +
555B GLN* 1.3 68.8 + - - +
556B PRO* 3.5 3.3 - - - +
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Residues in contact with GLN 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A HIS* 3.7 3.7 + - - -
479B PRO* 3.2 22.3 - - - +
551B GLN* 3.6 16.3 - - - +
552B ALA* 3.1 15.3 + - - +
553B LEU 4.6 1.0 - - - +
554B ALA* 1.3 80.6 - - - +
556B PRO* 1.3 64.0 - - + +
557B THR 3.2 18.8 - - - +
560B GLU* 3.3 31.8 + - + +
561B LEU* 3.9 22.2 - - + +
564B LEU* 3.8 19.5 - - + +
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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