Contacts of the helix formed by residues 430 - 443 (chain C) in PDB entry 1I43
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 ASP 430 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B SER* 2.7 41.2 + - - +
58B GLY* 4.5 7.9 + - - -
59B SER* 3.1 10.5 + - - +
311B HIS* 4.7 7.4 + - - +
315B GLN* 5.4 5.7 + - - -
316C GLN* 4.5 5.5 + - - +
429C GLU* 1.3 74.2 - - - +
431C PHE* 1.3 70.3 + - - +
432C ASP* 4.5 13.3 + - - +
433C ASP* 3.0 18.9 + - + +
434C LEU* 3.1 9.2 + - - +
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Residues in contact with PHE 431 (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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316C GLN* 4.5 5.9 - - - +
320C THR* 4.0 26.7 - - + +
323C ARG* 3.0 63.9 - - + +
324C MET* 3.4 32.5 - - + -
327C ILE* 3.9 20.2 - - + -
429C GLU 3.4 5.5 + - - -
430C ASP* 1.3 71.3 + - - +
432C ASP* 1.3 66.9 + - - +
434C LEU* 2.8 10.6 + - - +
435C LYS* 2.7 48.6 + - + -
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Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 6.5 0.4 - - - -
430C ASP* 3.4 13.0 + - + +
431C PHE* 1.3 91.3 - - - +
433C ASP* 1.3 58.4 + - - +
435C LYS* 3.9 18.5 + - - +
436C ALA* 2.9 33.7 + - - +
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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
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53B PHE 3.6 12.7 - - - +
54B LEU* 4.2 0.4 - - - -
55B ASN* 3.1 34.9 + - - +
56B SER* 2.9 29.0 + - - -
59B SER* 2.7 27.6 + - - +
382C ILE* 3.3 22.6 - - + +
430C ASP* 3.0 11.4 + - - +
432C ASP* 1.3 80.8 - - - +
434C LEU* 1.3 62.0 - - + +
436C ALA* 3.9 4.5 - - - +
437C ASP* 3.2 16.1 + - - +
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Residues in contact with LEU 434 (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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320C THR* 3.7 27.8 - - + -
324C MET* 5.5 0.7 - - + -
382C ILE* 4.0 25.6 - - + -
383C PRO* 5.3 0.2 - - + -
394C SER* 3.4 24.9 - - - +
424C PHE* 4.7 15.3 - - + -
426C PHE* 4.4 9.0 - - + -
427C GLY 4.9 3.8 - - - +
429C GLU* 3.6 38.8 - - + +
430C ASP 3.1 9.4 + - - +
431C PHE* 2.8 7.9 + - + +
433C ASP* 1.3 75.1 - - - +
435C LYS* 1.3 66.6 + - - +
437C ASP* 3.1 4.5 + - - +
438C ILE* 3.0 28.6 + - + +
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Residues in contact with LYS 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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324C MET* 3.6 28.4 - - - +
327C ILE* 3.7 25.3 - - + +
431C PHE* 2.7 35.0 + - + +
432C ASP* 3.9 16.0 + - - +
434C LEU* 1.3 71.7 - - - +
436C ALA* 1.3 66.6 + - - +
438C ILE* 3.2 3.1 + - - +
439C LEU* 2.9 45.5 + - + +
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Residues in contact with ALA 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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55B ASN* 6.2 1.6 - - - +
432C ASP 2.9 19.0 + - - +
433C ASP* 3.9 4.9 - - - +
435C LYS* 1.3 81.2 - - - +
437C ASP* 1.3 58.3 + - - +
439C LEU* 3.7 7.9 - - - +
440C GLN* 2.9 32.4 + - - +
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Residues in contact with ASP 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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53B PHE* 5.1 5.8 - - + +
380C LEU* 3.8 8.0 - - - +
381C LYS* 3.0 36.2 + - - +
382C ILE* 3.1 24.4 + - + +
383C PRO* 3.3 13.3 - - - +
433C ASP 3.2 12.1 + - - +
434C LEU* 3.1 10.3 + - + +
436C ALA* 1.3 79.5 - - - +
438C ILE* 1.3 58.0 + - + +
440C GLN* 2.8 32.7 - - - +
441C ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 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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324C MET* 3.5 20.9 - - + -
328C LEU* 3.9 28.7 - - + -
364C PHE* 5.3 1.1 - - + -
376C PHE* 3.7 12.1 - - + -
380C LEU* 4.0 10.5 - - + -
424C PHE* 3.9 25.1 - - + -
426C PHE* 3.4 36.1 - - + -
434C LEU* 3.0 18.7 + - + +
435C LYS 3.7 5.4 - - - +
437C ASP* 1.3 76.8 - - + +
439C LEU* 1.3 58.9 + - + +
441C ALA* 3.5 2.3 + - - +
442C LEU* 2.9 34.0 + - + +
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Residues in contact with LEU 439 (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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324C MET* 6.0 1.1 - - + -
327C ILE* 4.5 17.5 - - + -
328C LEU* 6.4 0.4 - - + -
331C HIS* 3.9 29.7 + - + +
435C LYS* 2.9 45.8 + - + +
436C ALA* 3.7 7.0 - - - +
438C ILE* 1.3 76.2 - - + +
440C GLN* 1.3 67.5 + - - +
442C LEU* 3.0 8.4 + - + +
443C ASP* 2.9 27.1 + - - +
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Residues in contact with GLN 440 (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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379C ALA* 3.2 26.9 + - - +
381C LYS* 4.2 21.7 + - - +
436C ALA 2.9 17.4 + - - +
437C ASP* 2.8 32.9 - - - +
439C LEU* 1.3 75.0 - - - +
441C ALA* 1.3 68.4 + - - +
443C ASP* 3.2 21.4 - - - +
444C SER* 3.6 8.3 + - - -
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Residues in contact with ALA 441 (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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376C PHE* 3.5 32.9 - - + +
379C ALA* 3.7 28.0 - - + +
380C LEU* 3.9 12.6 - - + +
437C ASP 2.9 18.0 + - - +
438C ILE 3.5 0.7 - - - +
440C GLN* 1.3 75.9 - - - +
442C LEU* 1.3 64.5 + - - +
443C ASP 3.0 1.6 - - - -
444C SER* 3.0 22.2 + - - -
445C ILE 4.1 1.6 + - - -
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LEU* 3.8 26.9 - - + -
331C HIS* 3.8 37.5 - - + +
333C LYS* 3.3 31.2 + - + +
334C VAL* 4.1 14.6 - - + -
364C PHE* 5.4 0.7 - - + -
366C VAL* 4.7 6.7 - - + -
376C PHE* 3.6 18.8 - - + -
438C ILE* 2.9 26.2 + - + +
439C LEU* 3.0 7.2 + - + +
441C ALA* 1.3 76.0 - - - +
443C ASP* 1.3 58.4 + - - +
444C SER 2.9 6.1 + - - -
445C ILE* 3.4 29.7 + - + +
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Residues in contact with ASP 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C HIS* 5.1 7.6 + - - -
333C LYS* 3.9 13.6 + - - +
439C LEU* 2.9 12.9 + - - +
440C GLN* 3.2 18.2 - - - +
441C ALA 3.0 0.8 - - - -
442C LEU* 1.3 75.5 - - - +
444C SER* 1.3 58.9 + - - +
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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