Contacts of the helix formed by residues 422 - 440 (chain C) in PDB entry 1R4N
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 GLU 422 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C ASP 3.8 7.4 + - - +
421C ASN* 1.3 87.1 + - - +
423C ILE* 1.3 60.8 + - - +
424C VAL 3.1 0.2 - - - -
425C LEU* 3.0 37.0 + - + +
426C TYR 3.5 2.1 + - - -
521C ILE* 3.6 26.7 - - + +
523C SER* 5.0 2.5 - - - -
528C THR* 3.1 31.2 + - - +
529C SER 3.8 10.7 + - - +
530C ALA* 3.2 35.0 - - + +
532C PHE* 4.3 1.6 - - + -
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C GLU* 6.3 0.7 - - + -
412C ILE* 4.6 29.8 - - + +
415C SER* 3.8 11.4 - - - -
416C MET* 3.3 24.9 - - + -
421C ASN* 2.5 32.5 + - + +
422C GLU* 1.3 70.2 - - - +
424C VAL* 1.3 69.8 + - - +
426C TYR* 2.9 36.7 + - + +
427C LEU* 3.1 12.7 + - + +
532C PHE* 3.4 37.9 - - + -
533C GLN* 6.2 0.4 - - - +
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Residues in contact with VAL 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C MET* 4.0 23.8 - - + -
419C PRO 3.2 26.9 - - - +
420C ASP 4.4 0.7 - - - -
421C ASN 2.6 35.7 + - - +
423C ILE* 1.3 70.4 - - - +
425C LEU* 1.3 55.3 + - + +
427C LEU* 2.9 11.2 + - - +
428C MET* 2.8 32.6 + - + +
474C VAL* 4.1 19.5 - - + -
478C TYR* 3.7 42.4 - - + -
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 3.9 29.8 - - + -
421C ASN 5.5 0.2 - - - -
422C GLU* 3.0 24.5 - - - +
424C VAL* 1.3 78.4 - - + +
426C TYR* 1.3 59.5 + - - +
428C MET* 3.3 8.0 + - - +
429C LEU* 2.9 29.0 + - - +
478C TYR* 4.0 24.7 - - + -
482C PHE* 3.9 22.2 - - + -
521C ILE* 4.0 15.9 - - + -
523C SER* 3.8 30.5 - - - +
525C MET* 5.5 6.5 - - - -
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Residues in contact with TYR 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C TYR* 4.1 32.8 - + - -
401C GLU* 2.7 36.8 + - + +
402C TYR* 3.8 5.9 - - - -
412C ILE* 4.8 16.2 - - + -
422C GLU 3.5 1.2 + - - -
423C ILE* 2.9 30.8 + - + +
425C LEU* 1.3 77.2 - - - +
427C LEU* 1.3 75.0 + - + +
429C LEU* 2.9 21.2 + - + +
430C ARG* 3.0 52.7 + - + +
464C PHE* 5.2 2.2 - + - -
519C THR* 4.6 5.8 - - + -
521C ILE* 3.6 23.2 - - + +
533C GLN* 5.4 3.4 - - - -
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Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ILE* 4.1 22.9 - - + -
416C MET* 3.8 39.3 - - + -
423C ILE* 3.1 13.2 + - + +
424C VAL* 2.9 7.1 + - - +
426C TYR* 1.3 85.7 - - + +
428C MET* 1.3 52.2 + - + +
430C ARG* 2.8 12.0 + - - +
431C ALA* 2.6 35.3 + - - +
461C LEU* 4.6 11.0 - - + -
464C PHE* 3.4 30.4 - - + -
465C LEU* 3.9 10.3 - - + -
470C LEU* 4.2 3.8 - - + -
472C VAL* 4.5 9.4 - - + -
474C VAL* 4.6 7.6 - - + -
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Residues in contact with MET 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C VAL* 2.8 23.5 + - + +
425C LEU 3.4 8.7 - - - +
426C TYR 3.2 0.2 - - - -
427C LEU* 1.3 73.3 - - - +
429C LEU* 1.3 52.1 + - - +
431C ALA* 2.9 12.1 - - + +
432C VAL* 2.6 40.5 + - + +
457C LEU* 4.0 24.9 - - + -
461C LEU* 4.2 15.0 - - + -
474C VAL* 4.1 21.5 - - - -
478C TYR* 3.6 33.4 - - + +
479C VAL* 4.3 4.5 - - + -
482C PHE* 3.5 32.8 - - + -
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ARG* 4.3 21.7 + - - +
156C TYR* 4.0 26.9 - - + -
159C VAL* 4.7 10.5 - - + -
161C TYR* 3.5 45.8 - - + -
425C LEU 2.9 17.9 + - - +
426C TYR* 2.9 12.8 + - + +
428C MET* 1.3 74.3 - - - +
430C ARG* 1.3 57.4 + - + +
432C VAL* 2.9 6.9 + - + +
433C ASP* 2.6 39.6 + - - +
482C PHE* 3.5 22.7 - - + -
521C ILE* 6.0 0.7 - - + -
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Residues in contact with ARG 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 2.7 26.5 + - - +
401C GLU 5.3 0.8 + - - -
402C TYR* 3.5 35.0 + - - +
426C TYR* 3.0 60.2 + - + +
427C LEU 2.8 6.7 + - - +
429C LEU* 1.3 74.8 - - - +
431C ALA* 1.3 58.1 + - - +
433C ASP* 3.3 7.5 + - - +
434C ARG* 2.8 29.5 + - - +
464C PHE* 3.6 39.6 - - + -
468C TYR* 3.3 29.5 + - - -
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU 2.6 15.0 + - - +
428C MET* 2.9 27.1 - - + +
430C ARG* 1.3 72.3 - - - +
432C VAL* 1.3 61.4 + - - +
434C ARG* 2.7 20.4 + - - +
435C PHE* 2.7 14.4 + - - +
457C LEU* 4.5 5.6 - - + -
460C CYS* 4.3 3.2 - - - +
461C LEU* 3.8 37.2 - - + +
464C PHE* 4.8 4.0 - - - -
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ARG* 4.7 2.7 - - - +
156C TYR* 3.3 29.8 - - + +
428C MET* 2.6 21.6 + - + +
429C LEU* 3.4 9.2 - - + +
431C ALA* 1.3 70.2 - - - +
433C ASP* 1.3 53.6 + - - +
435C PHE* 2.9 11.8 + - - +
436C HIS* 2.7 33.1 + - - +
442C TYR* 3.4 15.9 - - + -
443C PRO* 3.4 23.1 - - + -
457C LEU* 4.1 8.5 - - + +
482C PHE* 3.7 30.5 - - + -
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Residues in contact with ASP 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU 5.0 1.0 - - - +
132C PRO* 4.5 1.6 - - - +
133C GLU* 3.6 47.1 + - + +
154C ARG* 2.7 42.8 + - - -
402C TYR* 4.8 5.0 + - - -
429C LEU* 2.6 20.1 + - - +
430C ARG* 3.5 7.4 - - - +
432C VAL* 1.3 73.2 - - - +
434C ARG* 1.3 62.3 + - - +
436C HIS* 3.2 7.4 + - - +
437C LYS* 3.0 22.3 + - - +
442C TYR* 4.2 7.8 + - - -
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Residues in contact with ARG 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 4.8 4.0 + - - +
430C ARG* 2.8 12.8 + - - +
431C ALA* 2.7 15.7 + - - +
433C ASP* 1.3 68.2 - - - +
435C PHE* 1.3 67.2 + - - +
436C HIS 2.9 0.7 + - - -
437C LYS* 3.0 7.6 + - - +
438C GLN* 2.8 36.6 + - + +
460C CYS* 3.2 33.9 + - + +
463C GLY* 3.4 27.3 + - - -
464C PHE* 3.4 27.1 - - + +
467C GLU* 3.5 30.3 + - - +
468C TYR* 5.9 0.4 - - - -
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Residues in contact with PHE 435 (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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431C ALA 2.7 13.6 + - - +
432C VAL* 3.1 10.1 - - - +
434C ARG* 1.3 73.3 - - - +
436C HIS* 1.3 51.9 + - - +
438C GLN* 4.3 1.1 - - - -
439C GLN* 2.7 52.8 + - + +
441C ARG* 3.2 26.7 - - + -
442C TYR 3.6 2.5 - - - -
443C PRO* 3.5 26.0 - - + -
453C ASP* 3.0 31.4 - - + -
456C LYS* 3.8 17.9 - - + -
457C LEU* 3.5 49.1 - - + -
460C CYS* 3.9 17.6 - - - +
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Residues in contact with HIS 436 (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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132C PRO* 4.5 18.5 - - + +
432C VAL 2.7 14.7 + - - +
433C ASP* 3.4 9.8 + - - +
434C ARG 2.9 1.4 + - - -
435C PHE* 1.3 70.0 - - - +
437C LYS* 1.3 75.3 + - + +
438C GLN 3.0 1.5 + - - -
440C GLY* 2.7 36.1 + - - -
441C ARG* 3.6 21.5 - - - +
442C TYR* 3.2 54.9 + + + +
270H GLN 5.8 2.0 + - - -
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Residues in contact with LYS 437 (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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133C GLU* 5.8 7.6 - - + +
134C SER* 5.9 9.0 - - - -
433C ASP 3.0 8.2 + - - +
434C ARG* 3.0 9.2 + - - +
436C HIS* 1.3 89.5 + - + +
438C GLN* 1.3 62.7 + - - +
439C GLN 4.7 0.2 - - - -
440C GLY* 4.4 2.6 + - - -
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Residues in contact with GLN 438 (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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434C ARG* 2.8 28.1 + - + +
435C PHE 3.7 3.6 - - - +
437C LYS* 1.3 82.2 - - - +
439C GLN* 1.3 77.2 + - + +
456C LYS* 5.2 1.8 + - - +
459C SER* 6.0 1.4 - - - -
460C CYS* 3.4 30.1 - - - -
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Residues in contact with GLN 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C PHE* 2.7 58.0 + - + +
437C LYS 4.7 0.2 - - - -
438C GLN* 1.3 93.7 + - + +
440C GLY* 1.3 57.7 + - - +
441C ARG* 3.4 27.6 + - - +
456C LYS* 3.8 29.5 + - - +
271H TYR* 5.3 4.2 + - - -
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C HIS* 2.7 34.2 + - - -
437C LYS 4.4 2.2 + - - -
438C GLN 3.8 0.2 - - - -
439C GLN* 1.3 73.9 - - - +
441C ARG* 1.3 59.6 + - - +
270H GLN* 3.3 34.2 - - - +
271H TYR* 5.4 5.3 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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