Contacts of the helix formed by residues 514 - 522 (chain B) in PDB entry 5XA0
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 514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B MET 3.0 2.9 + - - -
511B ARG 3.4 11.9 + - - -
512B GLU 3.0 8.9 + - - -
513B GLN* 1.3 84.4 + - - +
515B ILE* 1.3 51.8 + - - +
516B LEU 3.3 2.7 - - - -
517B LYS* 2.5 38.2 + - - +
518B GLN* 2.1 60.7 + - - +
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Residues in contact with ILE 515 (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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446B ALA* 4.0 2.7 - - + +
449B ALA* 2.8 21.3 - - + -
450B SER* 2.8 37.0 - - - +
453B LEU* 2.9 27.8 - - + +
476B LEU* 5.5 2.2 - - + -
480B LEU* 6.0 2.7 - - + -
510B MET* 2.8 29.6 - - + +
513B GLN* 2.7 34.3 + - - +
514B ASN* 1.3 69.4 - - - +
516B LEU* 1.3 58.9 + - - +
518B GLN* 2.7 30.6 + - - +
519B ILE* 2.8 15.6 + - + +
559B VAL* 5.3 6.3 - - + -
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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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507B GLN 4.0 5.4 - - - +
510B MET* 2.8 58.1 - - + +
511B ARG* 3.0 16.6 - - + -
515B ILE* 1.3 70.9 - - + +
517B LYS* 1.3 63.0 + - + +
519B ILE* 2.6 47.4 + - + +
520B PHE* 3.0 7.1 + - - +
559B VAL* 5.2 4.3 - - + -
560B LEU* 4.6 16.7 - - + +
563B SER* 3.2 26.9 - - - +
564B GLN* 4.7 11.9 - - - +
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Residues in contact with LYS 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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511B ARG* 4.9 6.1 - - + +
514B ASN* 2.5 42.2 + - - +
516B LEU* 1.3 78.3 - - + +
518B GLN* 1.3 61.6 + - - -
520B PHE* 3.2 7.8 + - - +
521B LYS* 2.9 25.1 + - - +
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Residues in contact with GLN 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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450B SER* 3.5 25.8 - - - +
453B LEU* 2.9 17.9 - - + +
454B GLY* 4.6 12.0 - - - +
513B GLN 4.7 0.7 - - - -
514B ASN* 2.1 60.8 + - + +
515B ILE* 2.7 19.2 + - - +
517B LYS* 1.3 69.6 + - - +
519B ILE* 1.3 54.3 + - - -
521B LYS* 3.3 6.8 + - - +
522B LEU* 2.7 33.4 + - - +
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Residues in contact with ILE 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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453B LEU* 4.6 11.7 - - + -
476B LEU* 6.4 1.1 - - + -
477B LEU* 6.1 5.6 - - + -
515B ILE* 2.8 15.7 + - + +
516B LEU* 2.6 55.5 + - + +
518B GLN* 1.3 68.2 - - - +
520B PHE* 1.3 54.9 + - - +
522B LEU* 2.7 26.7 - - + +
523B LEU* 2.7 22.7 - - + +
556B CYS* 5.2 20.8 - - + +
559B VAL* 3.8 34.8 - - + -
560B LEU* 5.6 9.0 - - + +
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Residues in contact with PHE 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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516B LEU 3.0 9.8 + - - +
517B LYS* 3.2 8.5 + - - +
519B ILE* 1.3 78.3 - - - +
521B LYS* 1.3 61.0 + - - +
523B LEU* 2.9 25.7 + - + +
560B LEU* 6.4 2.2 - - + -
573B TYR* 2.9 35.2 - - + -
574B ILE* 4.3 7.0 - - + -
575B ALA 4.7 0.9 - - - -
576B LYS* 4.6 11.0 - - + -
577B GLN* 3.3 42.6 - - + -
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Residues in contact with LYS 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 LYS 2.9 16.6 + - - +
518B GLN* 3.3 8.7 + - - +
520B PHE* 1.3 77.1 - - - +
522B LEU* 1.3 53.2 + - - +
523B LEU 2.7 24.7 + - - +
524B GLN* 4.7 6.1 - - - +
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Residues in contact with LEU 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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453B LEU* 4.0 25.8 - - + +
456B ILE* 5.7 2.9 - - + -
457B ALA* 3.4 32.8 - - + +
460B LEU* 3.5 26.9 - - + +
473B VAL* 6.4 2.2 - - + -
518B GLN 2.7 18.7 + - - +
519B ILE* 2.7 41.7 - - + +
521B LYS* 1.3 68.9 - - - +
523B LEU* 1.3 69.8 + - + +
524B GLN* 4.2 3.4 + - - +
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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