Contacts of the helix formed by residues 516 - 523 (chain B) in PDB entry 2XWU
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 LEU 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B PHE* 3.9 29.2 - - + -
477B ALA* 4.1 20.2 - - + +
480B ILE* 5.4 1.6 - - + -
488B VAL* 4.2 19.3 - - + -
492B ILE* 4.4 15.3 - - + -
495B ILE* 4.8 4.7 - - + -
512B THR* 3.0 38.2 + - + +
513B ILE* 3.4 11.0 + - + +
514B GLY 3.1 0.4 - - - -
515B ALA* 1.3 74.4 - - - +
517B SER* 1.3 63.8 + - - +
518B GLU 3.3 1.8 - - - -
519B TRP* 3.1 16.7 + - + +
520B LEU* 2.9 34.4 + - + +
530B VAL* 5.9 2.9 - - + -
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Residues in contact with SER 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 ILE 3.4 4.0 + - - -
514B GLY* 2.6 28.8 + - - -
515B ALA 3.1 0.6 - - - -
516B LEU* 1.3 79.7 - - - +
518B GLU* 1.3 65.0 + - - +
520B LEU* 3.3 16.3 + - - +
521B ALA 3.3 9.0 + - - -
553B LYS* 3.1 27.2 - - - +
554B ILE* 3.6 10.8 + - - +
557B GLU* 3.6 28.7 - - - +
558B CYS* 3.9 1.2 - - - -
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Residues in contact with GLU 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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478B GLU* 5.4 10.0 - - - +
515B ALA 4.4 5.9 + - - +
516B LEU 3.3 0.6 - - - -
517B SER* 1.3 78.7 - - - +
519B TRP* 1.3 62.9 + - - +
521B ALA* 3.2 17.6 + - - +
522B ASP* 3.8 9.4 + - - +
557B GLU* 3.8 32.0 - - + +
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Residues in contact with TRP 519 (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 ALA 6.1 0.7 - - - +
480B ILE* 5.5 4.0 - - + -
481B ASP 4.9 3.6 - - - -
482B VAL* 4.2 19.1 - - + -
485B SER* 3.0 40.9 - - - -
488B VAL* 3.5 26.0 - - + +
489B PRO* 3.5 22.2 - - + -
492B ILE* 3.4 25.8 - - + -
515B ALA 5.3 0.4 + - - -
516B LEU* 3.1 21.8 + - + +
518B GLU* 1.3 77.7 - - - +
520B LEU* 1.3 78.6 + - + +
522B ASP* 3.2 7.0 + - - +
523B HIS* 2.8 73.5 + + + -
526B MET* 4.0 7.2 - - + -
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Residues in contact with LEU 520 (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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492B ILE* 4.1 8.5 - - + -
513B ILE* 4.3 11.0 - - + +
516B LEU* 2.9 29.6 + - + +
517B SER* 3.6 8.7 - - - +
518B GLU 3.2 0.2 - - - -
519B TRP* 1.3 92.8 - - + +
521B ALA* 1.3 65.3 + - - +
523B HIS 3.0 22.7 + - - +
524B PRO* 3.4 6.1 - - - +
526B MET* 3.8 32.8 - - + -
527B ILE* 4.4 10.4 - - + +
530B VAL* 3.6 28.5 - - + -
554B ILE* 4.6 10.8 - - + -
558B CYS* 4.2 10.1 - - - -
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Residues in contact with ALA 521 (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 SER 3.3 6.4 + - - +
518B GLU* 3.2 13.5 + - - +
520B LEU* 1.3 78.6 - - - +
522B ASP* 1.3 64.0 + - - +
524B PRO* 4.2 0.7 - - - +
557B GLU* 3.2 34.8 - - + +
558B CYS* 3.9 10.7 - - - +
561B ASP* 3.4 20.2 - - - +
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Residues in contact with ASP 522 (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 VAL* 4.3 20.4 - - + +
518B GLU 3.8 8.3 + - - +
519B TRP* 3.2 4.1 + - - +
520B LEU 3.1 0.4 - - - -
521B ALA* 1.3 81.5 - - - +
523B HIS* 1.3 84.3 + - + +
524B PRO* 3.5 9.6 - - - +
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Residues in contact with HIS 523 (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 VAL* 3.4 31.2 - - + +
485B SER* 5.1 3.1 - - - -
489B PRO* 5.8 0.8 - - - +
519B TRP* 2.8 71.1 + + + +
520B LEU* 3.0 12.1 + - - +
522B ASP* 1.3 90.9 + - + +
524B PRO* 1.3 67.4 - - - +
525B VAL* 3.1 4.9 + - + -
526B MET* 3.4 17.1 + - + +
527B ILE 4.4 1.4 + - - -
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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