Contacts of the helix formed by residues 412 - 433 (chain C) in PDB entry 1IR1
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 GLY 412 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C THR 4.4 3.8 - - - -
407C LEU* 5.5 1.6 - - - -
409C HIS* 3.1 15.4 + - - +
410C PRO 3.5 0.8 - - - -
411C TRP* 1.3 80.0 - - - +
413C ASN* 1.3 62.9 + - - -
414C ALA 3.6 2.5 - - - -
415C PRO* 3.4 2.5 - - - +
416C GLY* 3.0 25.3 + - - -
71T LYS 5.5 0.2 - - - -
72T LEU* 3.7 23.6 - - - +
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Residues in contact with ASN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ALA* 3.1 39.4 + - - +
191C GLU* 3.6 21.0 - - + +
192C CYS* 3.5 20.1 - - - +
406C THR* 3.7 9.4 - - - +
407C LEU* 3.4 30.1 - - - +
412C GLY* 1.3 70.6 - - - -
414C ALA* 1.3 61.7 + - - +
416C GLY* 3.1 1.7 + - - -
417C ALA* 2.8 31.0 + - - +
72T LEU* 5.1 1.4 - - - +
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Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU* 3.2 26.5 + - - +
194C ARG* 3.9 33.4 - - + +
195C GLY* 3.7 3.9 - - - -
413C ASN* 1.3 74.9 - - - +
415C PRO* 1.3 67.9 - - + +
417C ALA* 3.2 3.6 + - - +
418C VAL* 2.9 33.3 + - - +
4U TRP* 4.0 12.6 - - + +
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Residues in contact with PRO 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C HIS* 3.9 11.3 - - + +
411C TRP* 3.7 37.5 - - + +
412C GLY 3.4 12.6 - - - +
414C ALA* 1.3 96.1 - - + +
416C GLY* 1.3 56.1 + - - +
418C VAL* 3.3 4.7 + - + +
419C ALA* 2.9 29.6 + - - +
454C GLU* 3.8 24.0 - - + +
2U LYS 3.9 14.8 - - - +
3U VAL* 5.4 0.4 - - - -
4U TRP* 4.9 9.9 - - + +
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Residues in contact with GLY 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLY 4.5 1.7 - - - +
406C THR* 3.8 13.9 - - - -
409C HIS* 3.5 28.7 - - - -
412C GLY 3.0 12.0 + - - -
413C ASN 3.1 4.2 + - - -
415C PRO* 1.3 77.6 - - - +
417C ALA* 1.3 60.0 + - - +
419C ALA* 3.5 3.8 + - - +
420C ASN* 3.2 27.2 + - - -
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C CYS 3.2 27.6 - - - +
195C GLY* 3.4 13.5 - - - -
196C GLY* 4.8 0.2 - - - -
197C LEU* 3.6 25.3 - - + +
406C THR* 3.8 3.7 - - - +
413C ASN 2.8 11.0 + - - +
414C ALA 3.5 7.9 - - - +
416C GLY* 1.3 74.4 - - - +
418C VAL* 1.3 65.0 + - - +
420C ASN* 3.2 4.5 + - - +
421C ARG* 2.9 24.8 + - - +
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Residues in contact with VAL 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C GLY* 3.3 17.0 - - - +
414C ALA 2.9 19.7 + - - +
415C PRO* 3.3 7.6 + - + +
417C ALA* 1.3 76.8 - - - +
419C ALA* 1.3 56.6 + - - +
421C ARG* 3.8 2.4 - - - +
422C VAL* 2.8 51.1 + - + +
454C GLU* 3.9 22.7 - - + +
4U TRP* 3.5 55.4 - - + +
17U TYR* 4.8 2.9 - - + -
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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
----------------------------------------------------------
384C VAL* 4.2 4.3 - - + -
409C HIS* 4.1 2.7 - - + -
415C PRO 2.9 17.7 + - - +
416C GLY 3.6 6.1 - - - +
417C ALA 3.2 0.2 - - - -
418C VAL* 1.3 77.6 - - - +
420C ASN* 1.3 57.4 + - - +
422C VAL* 3.9 1.0 - - - +
423C ALA* 3.0 30.7 + - - +
454C GLU* 3.6 19.9 - - - +
455C LEU* 3.6 25.0 - - + +
458C ALA* 4.0 16.4 - - + -
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Residues in contact with ASN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 4.0 4.2 - - + +
197C LEU* 4.6 9.5 - - + +
383C HIS* 5.1 0.2 - - - -
384C VAL* 3.5 20.1 + - - +
387C MET* 3.4 17.3 - - + +
402C PHE* 3.6 33.5 - - + +
405C GLY 3.4 13.4 + - - +
406C THR* 3.1 27.1 + - - -
416C GLY 3.2 13.5 + - - -
417C ALA* 3.2 7.8 + - - +
419C ALA* 1.3 75.5 - - - +
421C ARG* 1.3 65.1 + - - +
423C ALA* 4.4 0.4 - - - -
424C LEU* 3.0 24.9 + - - +
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Residues in contact with ARG 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ARG* 3.6 24.0 - - - +
170C LEU* 3.6 20.3 - - + +
195C GLY 4.5 1.8 - - - +
196C GLY* 2.9 34.6 + - - +
198C ASP* 4.7 0.6 + - - -
234C GLU* 3.0 38.8 + - - -
417C ALA 2.9 16.7 + - - +
418C VAL 3.9 3.1 - - - +
420C ASN* 1.3 75.7 - - - +
422C VAL* 1.3 58.2 + - - +
424C LEU* 3.4 1.9 + - - +
425C GLU* 3.0 63.3 + - - +
13U GLU* 3.2 18.6 + - - +
17U TYR* 3.3 39.5 - - + -
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Residues in contact with VAL 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C VAL* 2.8 36.7 + - + +
419C ALA* 3.9 3.4 - - - +
421C ARG* 1.3 73.9 - - - +
423C ALA* 1.3 65.6 + - - +
425C GLU* 3.3 3.3 + - - +
426C ALA* 3.0 22.9 + - - +
448C ALA* 4.5 1.6 - - + -
451C TRP* 3.5 32.5 - - + -
452C SER* 4.0 20.9 - - - +
455C LEU* 4.2 12.6 - - + -
17U TYR* 4.1 29.2 - - + +
18U LEU* 4.3 1.3 - - - +
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Residues in contact with ALA 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 4.2 7.0 - - + -
387C MET* 3.8 20.0 - - + -
419C ALA 3.0 19.9 + - - +
420C ASN 3.8 3.8 - - - +
422C VAL* 1.3 78.5 - - - +
424C LEU* 1.3 63.7 + - - +
426C ALA* 3.4 5.3 + - - +
427C CYS* 3.2 27.0 + - - -
445C ILE* 4.1 16.6 - - + +
455C LEU* 4.0 17.5 - - + -
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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
----------------------------------------------------------
167C ARG* 4.2 12.6 - - - +
168C PRO* 3.4 52.0 - - + +
170C LEU* 3.6 28.7 - - + -
387C MET* 3.7 12.7 - - - +
391C THR* 3.9 18.8 - - - +
400C LEU* 4.2 12.1 - - + -
420C ASN 3.0 17.9 + - - +
421C ARG* 3.7 4.3 - - - +
423C ALA* 1.3 77.6 - - - +
425C GLU* 1.3 58.6 + - - +
427C CYS* 3.1 3.8 + - - +
428C VAL* 3.0 30.2 + - + +
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ARG* 4.1 9.6 + - - -
421C ARG* 3.0 54.8 + - - +
422C VAL* 4.1 1.3 - - - +
424C LEU* 1.3 76.0 - - + +
426C ALA* 1.3 58.1 + - - +
428C VAL* 3.7 8.9 - - - +
429C GLN* 2.9 30.8 + - - +
13U GLU 3.6 0.7 - - - +
14U THR* 3.6 4.3 - - + -
15U LEU* 2.8 34.2 + - + +
17U TYR* 2.8 33.8 + - - +
18U LEU* 3.5 20.8 + - + +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C VAL 3.0 18.4 + - - +
423C ALA* 3.5 6.3 - - - +
424C LEU 3.1 0.2 - - - -
425C GLU* 1.3 76.7 - - - +
427C CYS* 1.3 58.9 + - - +
429C GLN* 3.9 6.3 - - - +
430C ALA* 3.1 28.6 + - - +
444C ILE* 3.7 15.3 - - + +
445C ILE* 5.6 1.3 - - + -
448C ALA* 4.2 24.0 - - + -
451C TRP* 5.3 0.4 - - + -
18U LEU* 3.9 13.6 - - + +
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Residues in contact with CYS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C MET* 4.0 7.0 - - - -
388C PRO* 3.7 43.3 - - - -
391C THR* 4.0 16.8 - - - +
423C ALA 3.2 14.3 + - - +
424C LEU* 3.1 8.6 + - - +
426C ALA* 1.3 79.7 - - - +
428C VAL* 1.3 60.0 + - - +
430C ALA* 3.5 0.4 + - - -
431C ARG* 3.0 30.7 + - - +
437C LEU* 3.8 19.8 - - + +
444C ILE* 4.4 7.6 - - - -
445C ILE* 4.2 7.0 - - - -
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLY 3.7 18.4 - - - +
167C ARG* 4.0 20.9 - - + -
168C PRO* 4.1 14.8 - - + -
391C THR* 4.8 6.7 - - + -
424C LEU* 3.0 23.5 + - + +
425C GLU* 3.7 8.5 - - - +
426C ALA 3.3 0.4 - - - -
427C CYS* 1.3 78.5 - - - +
429C GLN* 1.3 63.0 + - - +
431C ARG* 3.4 16.8 + - - +
432C ASN* 3.0 44.8 + - - +
14U THR* 4.8 5.6 - - + -
15U LEU* 4.6 11.2 - - + -
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Residues in contact with GLN 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLU 2.9 18.1 + - - +
426C ALA* 3.9 5.6 - - - +
428C VAL* 1.3 79.1 - - - +
430C ALA* 1.3 61.7 + - - +
432C ASN* 3.2 3.4 + - - +
433C GLU* 3.0 41.2 + - - +
15U LEU* 4.3 5.6 - - + -
18U LEU* 3.6 26.8 - - + +
19U PRO* 5.5 1.9 + - - +
21U LEU* 3.4 29.7 - - - +
25U GLN* 3.8 26.2 + - - +
29U GLN* 4.0 17.4 + - - +
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Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA 3.1 16.7 + - - +
427C CYS 3.9 3.1 - - - +
428C VAL 3.4 0.2 - - - -
429C GLN* 1.3 78.5 - - - +
431C ARG* 1.3 63.9 + - - +
433C GLU* 3.2 12.3 + - - +
434C GLY 3.3 0.2 + - - -
435C ARG* 3.0 44.8 + - + +
444C ILE* 3.5 35.4 - - + -
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Residues in contact with ARG 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLY 4.2 2.6 + - - -
391C THR* 4.3 16.4 + - - +
395C GLY* 4.6 3.8 - - - -
396C ASP* 2.8 48.2 + - - +
427C CYS 3.0 18.9 + - - +
428C VAL* 3.7 21.7 + - - +
430C ALA* 1.3 75.9 - - - +
432C ASN* 1.3 79.5 + - - +
434C GLY* 2.9 21.1 + - - -
435C ARG 4.0 12.5 + - - +
437C LEU* 4.0 23.2 - - + +
32U TYR* 3.5 19.5 + - + -
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Residues in contact with ASN 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLY 5.3 1.6 + - - -
428C VAL* 3.0 28.7 + - - +
429C GLN* 3.2 4.4 + - - +
431C ARG* 1.3 104.1 + - - +
433C GLU* 1.3 60.3 + - - +
434C GLY* 3.3 1.0 + - - -
15U LEU* 5.6 1.2 - - - +
28U ARG 4.1 4.3 - - - +
29U GLN* 3.0 34.6 - - - +
32U TYR* 3.2 56.3 - - + +
113U VAL* 6.0 0.6 - - - +
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Residues in contact with GLU 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C GLN* 3.0 31.2 + - - +
430C ALA* 3.7 10.5 - - - +
431C ARG 3.2 0.4 - - - -
432C ASN* 1.3 77.0 - - - +
434C GLY* 1.3 58.6 + - - +
435C ARG* 3.6 16.3 + - + +
25U GLN* 4.0 32.8 + - - +
28U ARG* 2.9 61.5 + - + +
29U GLN* 4.3 7.0 - - - +
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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) + - + + + + + -
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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