Contacts of the helix formed by residues 511 - 518 (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 ALA 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477B MET* 4.3 9.0 - - + -
482B LEU* 5.9 3.4 - - + -
505B LEU* 3.8 32.5 - - + +
508B ASP* 2.9 2.5 + - + +
510B ARG* 1.3 81.0 - - - +
512B THR* 1.3 56.4 + - - +
513B LEU 3.3 2.5 - - - -
514B LEU* 2.8 12.7 + - + -
515B LEU* 2.7 56.0 + - + -
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Residues in contact with THR 512 (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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506B ALA 4.5 1.0 + - - -
508B ASP 3.3 5.9 + - - -
509B GLU* 3.8 8.8 + - - -
510B ARG 3.5 1.4 - - - -
511B ALA* 1.3 76.2 - - - +
513B LEU* 1.3 58.7 + - - +
515B LEU* 3.7 9.5 - - - +
516B LEU* 2.9 32.9 + - + +
523B PHE* 4.3 5.1 - - + -
533B ILE* 3.2 40.3 - - + +
536B ILE* 3.5 30.1 - - + +
537B ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLU 5.2 2.6 + - - +
510B ARG 5.2 1.5 + - - +
511B ALA 3.3 0.8 - - - -
512B THR* 1.3 76.7 - - - +
514B LEU* 1.3 59.9 + - + +
516B LEU* 3.6 6.0 + - + -
517B GLY* 2.8 23.7 + - - -
536B ILE* 3.9 16.2 - - + -
540B THR* 3.0 40.4 - - + +
545B ALA* 3.5 13.6 - - + +
548B LEU* 3.5 19.7 - - + -
565B VAL* 4.6 8.7 - - + +
568B PHE* 3.3 34.1 - - + -
569B ILE* 4.1 22.0 - - + -
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Residues in contact with LEU 514 (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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477B MET* 4.3 17.5 - - + -
482B LEU* 4.1 28.0 - - + -
510B ARG 4.3 3.6 - - - +
511B ALA* 2.8 16.5 + - + +
513B LEU* 1.3 70.1 - - + +
515B LEU* 1.3 67.4 + - + +
517B GLY 3.0 0.2 + - - -
518B MET* 2.8 42.7 + - + +
548B LEU* 3.7 31.2 - - + -
549B ALA* 4.3 9.2 - - - -
552B ALA* 4.0 21.3 - - + -
561B LEU* 5.0 2.5 - - + -
565B VAL* 3.9 25.1 - - + -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 5.3 3.4 - - + -
485B ILE* 4.6 7.6 - - + -
489B ILE* 5.8 0.2 - - - -
501B MET* 3.3 33.0 - - + -
505B LEU* 3.4 30.3 - - + +
506B ALA* 3.8 9.0 - - - +
511B ALA* 2.7 34.5 + - + +
512B THR 3.7 1.3 - - - +
514B LEU* 1.3 72.3 - - - +
516B LEU* 1.3 64.1 + - - +
518B MET* 3.3 15.7 + - - +
519B GLY 3.3 2.9 + - - -
520B LEU* 3.2 30.8 + - + +
523B PHE* 3.5 31.6 - - + -
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Residues in contact with LEU 516 (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* 3.7 33.7 - - + -
267B HIS* 3.9 12.9 - - - +
269B VAL* 4.4 13.9 - - + -
512B THR* 2.9 21.9 + - + +
513B LEU* 3.6 4.7 - - + +
515B LEU* 1.3 78.0 - - - +
517B GLY* 1.3 57.5 + - - +
519B GLY* 2.9 19.4 + - - -
520B LEU 4.9 2.9 - - - +
523B PHE* 3.9 10.0 - - + -
537B ILE* 4.7 18.8 - - + -
540B THR* 3.9 28.0 - - + +
542B PHE* 3.3 35.7 - - + -
545B ALA* 4.3 5.8 - - + -
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Residues in contact with GLY 517 (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 2.8 15.0 + - - -
514B LEU 3.0 1.1 + - - -
516B LEU* 1.3 74.9 - - - +
518B MET* 1.3 58.5 + - - +
519B GLY* 3.1 2.2 + - - -
542B PHE* 4.5 1.5 - - - -
545B ALA* 3.5 33.7 - - - -
546B LYS* 3.4 25.6 - - - +
549B ALA* 3.6 8.7 - - - +
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Residues in contact with MET 518 (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* 3.3 42.6 - - - +
485B ILE* 3.6 15.9 - - + -
486B LYS* 3.5 31.3 + - + +
489B ILE* 3.5 26.7 - - + +
490B ASP* 4.7 5.2 - - - +
493B HIS* 5.3 0.3 - - - -
514B LEU* 2.8 37.6 + - - +
515B LEU* 3.7 11.0 - - - +
516B LEU 3.1 0.2 - - - -
517B GLY* 1.3 77.2 - - - +
519B GLY* 1.3 57.4 + - - +
520B LEU 3.5 0.2 - - - -
549B ALA* 3.6 16.4 - - + -
553B LEU* 4.1 17.0 - - + -
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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