Contacts of the helix formed by residues 418 - 432 (chain C) in PDB entry 1OHV
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 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416C THR* 3.2 5.9 + - - -
417C PRO* 1.3 84.4 - - - +
419C GLU* 1.3 63.3 + - - +
420C SER* 3.1 12.9 + - - +
421C ILE* 2.8 36.3 + - - +
422C ARG 3.1 17.2 + - - -
442C LYS* 3.7 13.7 - - - -
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Residues in contact with GLU 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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203C LYS* 5.3 6.2 + - - +
418C ASP* 1.3 75.2 - - - +
420C SER* 1.3 63.7 + - - +
422C ARG* 3.2 16.7 + - - +
423C ASN* 3.0 40.1 + - - +
441C ASP* 3.4 31.5 - - + +
442C LYS* 3.9 4.0 - - - +
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Residues in contact with SER 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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418C ASP* 3.1 11.4 + - - -
419C GLU* 1.3 78.6 - - - +
421C ILE* 1.3 59.7 + - - +
423C ASN* 3.5 7.4 + - - +
424C LYS* 3.1 28.2 + - - +
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Residues in contact with ILE 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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401C PHE* 4.8 9.6 - - + -
416C THR* 4.2 0.9 - - - -
417C PRO* 4.0 29.2 - - + -
418C ASP* 2.8 38.8 + - - +
420C SER* 1.3 72.7 - - - +
422C ARG* 1.3 61.2 + - - +
424C LYS* 3.2 6.3 + - - +
425C LEU* 2.9 43.3 + - + +
471C PHE* 3.8 33.4 - - + -
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Residues in contact with ARG 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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203C LYS* 5.3 2.8 - - - +
416C THR* 3.3 19.6 + - - +
418C ASP 3.1 7.7 + - - +
419C GLU* 3.3 23.0 + - - +
421C ILE* 1.3 78.3 - - - +
423C ASN* 1.3 84.2 + - - +
425C LEU* 3.3 2.8 + - - +
426C ILE* 3.1 47.9 + - - +
438C GLY* 4.2 4.9 - - - -
439C CYS* 3.1 21.2 + - - +
440C GLY 3.4 13.5 + - - -
441C ASP* 3.3 17.9 + - - +
442C LYS* 3.7 13.9 - - - +
443C SER 3.0 36.2 + - - +
444C ILE* 3.8 9.7 - - + +
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Residues in contact with ASN 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 GLU* 3.0 36.0 + - - +
420C SER* 3.9 6.7 - - - +
422C ARG* 1.3 102.2 + - - +
424C LYS* 1.3 58.5 + - - +
426C ILE* 3.5 8.4 + - - +
427C SER* 2.9 30.4 + - - -
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Residues in contact with LYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C SER* 3.1 18.4 + - - +
421C ILE* 3.6 7.4 - - - +
423C ASN* 1.3 77.6 - - - +
425C LEU* 1.3 57.3 + - - +
427C SER* 3.2 7.1 + - - -
428C ILE* 2.8 45.7 + - + +
471C PHE* 4.1 22.7 - - + -
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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
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401C PHE* 4.9 7.0 - - + -
402C ILE* 5.0 2.0 - - + -
416C THR* 4.0 19.1 - - + -
421C ILE* 2.9 35.8 + - + +
422C ARG 3.8 3.6 - - - +
424C LYS* 1.3 72.5 - - - +
426C ILE* 1.3 60.9 + - - +
428C ILE* 3.8 3.1 - - + +
429C ALA* 2.9 31.5 + - - +
436C LEU* 5.4 0.7 - - - -
444C ILE* 3.9 10.3 - - + -
464C PHE* 4.2 22.3 - - + -
467C ILE* 4.0 20.1 - - + +
468C LEU* 4.3 14.8 - - + -
471C PHE* 4.0 33.2 - - + -
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Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 3.1 42.8 + - - +
423C ASN* 3.7 8.5 - - - +
425C LEU* 1.3 75.6 - - - +
427C SER* 1.3 65.9 + - - +
429C ALA* 3.4 6.9 + - - +
430C ARG* 3.0 39.1 + - + +
434C VAL 4.6 0.5 - - - +
435C MET* 6.0 1.6 - - + -
436C LEU* 3.9 29.9 + - + +
437C GLY 3.7 5.6 - - - +
438C GLY* 3.6 25.6 - - - +
444C ILE* 4.1 13.0 - - + -
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Residues in contact with SER 427 (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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22C VAL 5.6 1.6 + - - -
423C ASN 2.9 18.6 + - - -
424C LYS* 3.5 8.5 - - - -
426C ILE* 1.3 80.7 - - - +
428C ILE* 1.3 64.9 + - - +
430C ARG* 3.4 17.0 + - - +
431C ASN* 3.2 32.3 + - - -
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Residues in contact with ILE 428 (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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424C LYS* 2.8 43.6 + - + +
425C LEU* 3.8 5.2 - - - +
427C SER* 1.3 73.4 - - - +
429C ALA* 1.3 68.7 + - - +
431C ASN* 3.1 12.2 + - + +
432C LYS* 3.0 29.9 + - + +
467C ILE* 3.7 37.7 - - + -
471C PHE* 5.1 9.0 - - + -
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Residues in contact with ALA 429 (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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425C LEU 2.9 18.8 + - - +
426C ILE 3.7 3.6 - - - +
428C ILE* 1.3 75.0 - - - +
430C ARG* 1.3 61.3 + - - +
432C LYS* 3.0 12.0 + - - +
433C GLY 3.1 1.0 + - - -
434C VAL* 2.9 37.9 + - + +
436C LEU* 3.8 23.3 - - + -
460C PHE* 5.7 0.4 - - + -
463C ILE* 5.5 0.7 - - + -
464C PHE* 4.7 4.3 - - + -
467C ILE* 3.6 19.9 - - + +
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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
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18C MET* 3.4 14.0 - - - +
22C VAL* 3.3 49.6 + - + +
23C PRO* 4.0 9.1 - - - +
44C HIS* 4.1 34.3 + - - +
45C PHE* 4.0 5.7 - - - -
65C MET* 4.0 17.3 - - - +
426C ILE* 3.0 29.5 + - + +
427C SER* 3.6 17.7 + - - +
428C ILE 3.2 0.2 - - - -
429C ALA* 1.3 77.6 - - - +
431C ASN* 1.3 61.8 + - - +
433C GLY* 3.1 12.6 + - - -
434C VAL 3.2 12.4 + - - +
435C MET* 3.8 23.4 - - + +
436C LEU 5.8 0.4 - - - +
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Residues in contact with ASN 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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18C MET* 3.5 25.2 - - - +
20C THR 5.0 1.8 - - - +
21C GLU* 3.7 13.3 - - - +
22C VAL* 2.9 39.0 + - - +
427C SER* 3.2 20.1 + - - -
428C ILE* 3.1 15.3 + - + +
430C ARG* 1.3 76.7 - - - +
432C LYS* 1.3 59.8 + - + +
433C GLY 3.3 0.2 - - - -
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Residues in contact with LYS 432 (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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16C PRO* 4.7 2.6 - - - +
18C MET* 4.0 6.3 - - - +
428C ILE* 3.0 21.4 + - + +
429C ALA* 3.0 12.6 + - - +
431C ASN* 1.3 81.4 - - + +
433C GLY* 1.3 55.9 + - - +
434C VAL 3.7 0.2 - - - -
463C ILE* 3.8 36.7 - - + +
466C ASP* 6.3 2.9 - - - -
467C ILE* 4.1 21.3 - - + +
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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
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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