Contacts of the helix formed by residues 415 - 425 (chain C) in PDB entry 1RQQ
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 SER 415 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C THR 3.2 5.8 + - - -
414C LEU* 1.3 78.8 - - - +
416C ARG* 1.3 54.4 + - - +
417C VAL* 3.2 19.2 + - - +
418C LYS* 3.2 14.2 + - - +
419C ALA* 2.7 32.9 + - - +
440C GLU* 2.9 19.9 + - - -
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Residues in contact with ARG 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127B LYS* 3.5 19.3 - - - +
1158B PTR 2.7 75.6 + - - +
1160B THR 5.4 0.2 - - - -
1161B ASP* 3.1 32.8 + - - +
414C LEU 3.7 1.4 + - - -
415C SER* 1.3 70.2 - - - +
417C VAL* 1.3 78.8 + - + +
419C ALA* 3.3 1.7 + - - +
420C ALA* 2.9 24.9 + - - +
437C ARG* 3.0 34.7 - - - +
440C GLU* 2.8 28.3 + - - +
458C HIS* 3.7 25.9 + - - +
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Residues in contact with VAL 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C SER* 3.1 11.6 + - - +
416C ARG* 1.3 92.8 - - + +
418C LYS* 1.3 61.4 + - - +
420C ALA* 3.4 6.6 + - - +
421C GLN* 3.3 25.1 + - + +
440C GLU* 5.2 0.7 - - - +
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Residues in contact with LYS 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C LEU* 3.3 26.6 - - + +
415C SER* 3.2 16.0 + - - +
417C VAL* 1.3 79.9 - - - +
419C ALA* 1.3 62.6 + - - +
421C GLN* 3.2 19.1 + - - +
422C LEU* 3.0 22.9 + - - +
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Residues in contact with ALA 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C LEU* 3.6 21.9 - - + +
415C SER 2.7 20.9 + - - +
416C ARG 3.5 4.9 - - - +
418C LYS* 1.3 71.5 - - - +
420C ALA* 1.3 66.4 + - - +
422C LEU* 3.2 4.9 + - - +
423C VAL* 3.1 26.3 + - - +
435C VAL* 4.2 5.3 - - + +
437C ARG* 3.8 22.2 - - - +
449C THR* 4.0 14.4 - - + +
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Residues in contact with ALA 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ARG 2.9 16.3 + - - +
417C VAL* 3.7 6.5 - - - +
419C ALA* 1.3 76.2 - - - +
421C GLN* 1.3 64.3 + - - +
423C VAL* 3.2 12.6 - - - +
424C LEU* 2.9 30.4 + - + +
449C THR* 4.1 4.0 - - - +
456C ALA* 3.9 20.2 - - + -
458C HIS* 4.2 10.3 - - + +
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Residues in contact with GLN 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C VAL* 3.3 13.8 + - + +
418C LYS* 3.3 21.2 + - - +
419C ALA 3.2 0.2 - - - -
420C ALA* 1.3 80.1 - - - +
422C LEU* 1.3 56.6 + - - +
424C LEU* 3.2 4.3 + - - +
425C ALA* 2.9 34.4 + - - +
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Residues in contact with LEU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C HIS* 4.3 18.8 - - + +
414C LEU* 4.0 23.8 - - + -
418C LYS 3.0 9.6 + - - +
419C ALA* 3.5 9.2 - - - +
421C GLN* 1.3 82.4 - - - +
423C VAL* 1.3 62.2 + - + +
424C LEU 3.5 0.2 + - - -
425C ALA* 3.7 16.3 + - - +
433C LEU* 4.2 25.0 - - + +
435C VAL* 4.3 12.3 - - + -
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ALA 3.1 12.4 + - - +
420C ALA* 3.2 19.5 - - - +
422C LEU* 1.3 76.2 - - - +
424C LEU* 1.3 64.5 + - + +
430C SER* 3.3 12.0 + - - +
433C LEU* 3.5 40.0 - - + +
434C PHE* 3.9 4.5 - - - -
435C VAL* 4.3 8.7 - - + -
449C THR* 3.8 27.1 - - + +
450C PHE 4.0 17.7 - - - +
451C ASN* 2.9 24.3 + - + +
456C ALA* 4.5 1.6 - - + -
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Residues in contact with LEU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C ALA* 2.9 21.9 + - + +
421C GLN* 4.1 4.0 - - - +
423C VAL* 1.3 77.3 - - + +
425C ALA* 1.3 57.9 + - - +
426C GLY 2.8 0.2 + - - -
427C GLY* 2.7 30.4 + - - -
451C ASN* 3.6 15.5 - - + +
454C GLY* 2.9 39.5 - - - +
455C LYS* 3.7 11.0 - - - -
456C ALA* 3.6 27.1 - - + +
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C GLN 2.9 16.4 + - - +
422C LEU* 4.0 12.1 - - - +
423C VAL 3.5 0.4 - - - -
424C LEU* 1.3 74.5 - - - +
426C GLY* 1.3 56.8 + - - +
430C SER* 3.6 10.4 + - - -
433C LEU* 5.2 1.9 - - - +
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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