Contacts of the helix formed by residues 519 - 528 (chain B) in PDB entry 5IXC
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 ARG 519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B GLU* 2.7 33.9 + - - -
430B LEU* 3.4 19.4 - - - +
433B GLU* 2.8 35.3 + - - +
440B VAL* 3.3 24.7 - - - +
441B MET 2.9 29.8 - - - +
442B ASP* 4.2 15.0 - - - +
443B GLN 3.8 6.7 - - - +
444B LYS* 4.3 3.8 - - - +
518B PRO* 1.3 75.1 - - - +
520B ILE* 1.3 67.8 + - - +
521B CYS* 3.2 3.9 - - - +
522B PHE* 2.9 38.6 + - + +
523B LEU 4.0 1.4 + - - -
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Residues in contact with ILE 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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368B ALA* 4.1 22.0 - - + +
437B HIS* 6.4 0.4 - - - +
441B MET* 5.3 7.4 - - + +
443B GLN* 2.9 35.8 + - + +
444B LYS* 4.6 4.0 - - - +
445B LEU* 4.4 15.7 - - + +
448B GLN* 3.2 31.0 - - - +
518B PRO 3.7 2.6 + - - -
519B ARG* 1.3 71.1 - - - +
521B CYS* 1.3 64.8 + - - +
522B PHE 3.1 0.2 - - - -
523B LEU* 3.1 13.5 + - + +
524B GLU* 2.9 35.2 + - + +
527B TRP* 4.3 21.5 - - + -
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Residues in contact with CYS 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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429B ALA* 3.4 25.5 - - - +
432B LEU* 5.2 1.7 - - + +
433B GLU* 3.5 52.7 - - + +
437B HIS* 6.2 0.4 - - + -
441B MET* 5.6 0.4 + - + -
519B ARG* 3.0 8.1 + - - +
520B ILE* 1.3 80.7 - - - +
522B PHE* 1.3 83.6 + - - +
524B GLU* 3.3 18.1 + - - +
525B ALA 3.1 20.6 + - - -
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Residues in contact with PHE 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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411B GLU* 4.1 5.2 - - - -
412B LEU* 5.3 0.2 - - + -
415B ARG* 3.9 44.4 - - - +
425B VAL* 5.8 0.5 - - - +
426B ASP* 3.7 31.0 - - + -
429B ALA* 3.4 14.3 - - + +
430B LEU* 3.9 22.0 - - + -
518B PRO* 4.2 15.7 - - + -
519B ARG* 2.9 53.9 + - + +
521B CYS* 1.3 82.9 - - - +
523B LEU* 1.3 64.0 + - - +
525B ALA* 3.7 4.0 + - - +
526B ILE* 3.4 23.4 + - - +
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Residues in contact with LEU 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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445B LEU* 3.7 41.3 - - + +
483B PHE* 4.1 9.0 - - + -
488B VAL* 5.8 0.2 - - + -
499B PRO* 5.8 2.0 - - + +
502B PHE* 3.7 37.0 - - + -
517B GLU* 5.9 1.6 - - + +
518B PRO* 4.5 19.3 - - + +
520B ILE* 3.1 17.0 + - + +
522B PHE* 1.3 76.9 - - - +
524B GLU* 1.3 64.6 + - - +
525B ALA 3.2 0.2 - - - -
526B ILE* 3.0 10.1 + - + +
527B TRP* 3.0 49.4 + - + -
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Residues in contact with GLU 524 (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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364B THR* 5.0 0.2 - - - +
365B TRP* 4.0 14.3 - - + +
368B ALA* 3.7 22.6 - - + +
432B LEU* 4.3 12.1 - - + -
436B LEU* 3.6 27.2 - - - +
437B HIS* 5.1 7.0 + - - -
520B ILE* 2.9 19.8 + - + +
521B CYS* 3.3 31.5 + - - +
523B LEU* 1.3 74.5 - - - +
525B ALA* 1.3 55.3 + - - +
527B TRP* 3.3 26.7 + - + +
528B SER* 2.4 39.8 + - - +
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Residues in contact with ALA 525 (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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425B VAL* 3.3 32.1 - - + +
428B TRP* 3.6 16.0 - - + +
429B ALA* 3.6 27.4 - - + +
432B LEU* 4.6 2.2 - - - +
521B CYS 3.1 6.4 + - - +
522B PHE 3.8 4.9 - - - +
523B LEU 3.2 0.2 - - - -
524B GLU* 1.3 73.8 - - - +
526B ILE* 1.3 61.3 + - - +
529B ASN* 2.8 34.3 + - - +
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Residues in contact with ILE 526 (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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425B VAL* 4.2 26.7 - - + -
464B SER* 3.6 19.9 + - - +
465B LEU 5.6 1.0 - - - +
466B ASN* 4.0 17.3 - - - +
483B PHE* 4.9 7.9 - - + -
502B PHE* 5.1 12.6 - - + -
522B PHE 3.4 17.5 - - - +
523B LEU* 3.0 18.6 + - + +
525B ALA* 1.3 81.2 - - - +
527B TRP* 1.3 66.4 + - + +
529B ASN* 3.3 13.5 + - - +
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Residues in contact with TRP 527 (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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360B ILE* 5.1 1.7 - - - +
361B SER* 3.5 18.5 + - - -
364B THR* 3.5 35.2 - - + +
368B ALA* 4.7 0.4 - - + -
445B LEU* 4.9 1.8 - - + -
462B TYR* 3.3 54.3 - + + -
463B LEU 4.8 7.6 - - - +
464B SER* 3.7 29.2 + - - -
483B PHE* 3.4 34.5 - + + -
520B ILE* 4.3 14.1 - - + -
523B LEU* 3.0 39.4 + - + -
524B GLU* 3.3 29.8 + - + +
526B ILE* 1.3 78.1 - - + +
528B SER* 1.3 57.5 + - - +
529B ASN 3.5 0.2 - - - -
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Residues in contact with SER 528 (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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361B SER* 3.5 22.2 - - - -
365B TRP* 2.9 35.0 + - - -
428B TRP* 3.4 12.2 + - - -
432B LEU* 3.9 2.8 - - - +
524B GLU 2.4 28.4 + - - -
525B ALA 3.6 2.0 - - - -
527B TRP* 1.3 77.5 - - - +
529B ASN* 1.3 67.4 + - - +
530B ILE* 3.3 5.2 + - - +
901B 7FA 3.7 19.7 - - - +
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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