Contacts of the helix formed by residues 431 - 441 (chain C) in PDB entry 1JPW
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 ASN 431 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C THR 2.7 29.8 + - - +
394C LYS* 4.3 6.9 - - - +
395C GLN 4.7 5.5 + - - +
427C LEU 4.3 3.8 - - - +
428C THR 4.9 0.2 - - - -
429C CYS 3.1 5.4 + - - +
430C ASN* 1.3 78.7 - - - +
432C TYR* 1.3 65.5 + - - +
433C LYS* 2.9 22.5 + - - +
434C ASN* 2.8 47.8 + - + +
435C LYS* 3.0 30.8 + - - +
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Residues in contact with TYR 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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430C ASN 3.9 3.8 + - - -
431C ASN* 1.3 73.4 + - - +
433C LYS* 1.3 95.5 + - + +
435C LYS* 4.0 11.3 - - - +
436C MET* 3.2 42.1 + - + +
474C ARG 4.3 6.3 - - - +
475C HIS* 4.1 21.4 - - + +
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Residues in contact with LYS 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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645B HIS* 4.2 17.4 + - + -
396C GLU* 2.9 33.5 + - - +
399C GLU* 4.7 14.8 - - - +
431C ASN* 2.9 13.6 + - - +
432C TYR* 1.3 112.9 - - + +
434C ASN* 1.3 65.2 + - - +
436C MET* 3.3 10.6 + - + +
437C MET* 3.1 23.0 + - - +
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Residues in contact with ASN 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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392C ALA 5.5 1.4 + - - -
393C THR 5.4 0.8 + - - -
395C GLN 4.8 2.3 - - - +
398C MET* 4.0 20.4 - - - +
399C GLU* 5.2 3.2 - - - +
402C LEU* 3.5 27.0 - - + +
427C LEU* 2.5 47.6 + - - +
428C THR* 4.4 3.1 - - + -
431C ASN* 2.8 33.9 + - + +
433C LYS* 1.3 74.8 - - - +
435C LYS* 1.3 63.7 + - - +
437C MET* 3.2 3.1 + - - +
438C VAL* 3.0 28.7 + - - +
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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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428C THR* 3.1 29.4 - - - +
430C ASN* 4.2 4.0 - - - +
431C ASN 3.0 25.1 + - - +
432C TYR* 4.0 7.6 - - - +
434C ASN* 1.3 74.4 - - - +
436C MET* 1.3 63.8 + - - +
438C VAL 3.2 2.1 + - - -
439C CYS* 3.1 27.4 + - - -
470C HIS 3.1 21.5 + - - +
471C LEU* 3.5 23.9 - - + +
473C SER 3.0 19.6 + - - +
474C ARG* 4.1 11.1 + - - +
475C HIS* 3.9 24.0 - - + -
16F ASP* 2.9 24.5 + - - -
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Residues in contact with MET 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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432C TYR* 3.2 40.4 + - + +
433C LYS* 3.7 8.3 - - + +
434C ASN 3.3 0.2 - - - -
435C LYS* 1.3 78.3 - - - +
437C MET* 1.3 57.0 + - - +
439C CYS* 3.2 9.5 + - + +
440C GLN* 2.8 42.1 + - - +
475C HIS* 4.2 20.6 - - + +
476C GLN* 5.0 21.8 - - - -
477C GLU* 4.9 11.4 - - + -
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Residues in contact with MET 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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647B ARG* 3.1 40.8 - - - +
399C GLU* 4.0 38.1 - - - +
402C LEU* 3.9 23.3 - - + -
403C GLY* 4.9 1.1 - - - +
433C LYS 3.1 12.7 + - - +
434C ASN 3.6 7.9 - - - +
436C MET* 1.3 76.7 - - - +
438C VAL* 1.3 63.4 + - - +
440C GLN* 3.0 25.2 + - + +
441C VAL* 3.1 42.9 + - + +
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Residues in contact with VAL 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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402C LEU* 4.3 12.8 - - + -
406C VAL* 4.5 7.9 - - + -
424C LEU* 4.1 21.8 - - + -
428C THR* 3.7 21.1 - - + -
434C ASN 3.0 15.2 + - - +
435C LYS 3.2 6.3 + - - +
437C MET* 1.3 77.7 - - - +
439C CYS* 1.3 54.9 + - - +
441C VAL* 3.5 8.7 - - - +
442C GLY 3.4 3.3 + - - -
443C GLY* 2.6 49.3 + - - -
447C LEU* 4.6 7.4 - - + -
471C LEU* 3.7 21.1 - - + -
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Residues in contact with CYS 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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435C LYS 3.1 20.4 + - - -
436C MET* 3.5 8.7 - - + +
438C VAL* 1.3 77.4 - - - +
440C GLN* 1.3 64.8 + - - +
442C GLY* 3.3 11.4 + - - -
443C GLY* 4.4 3.6 - - - +
444C ILE* 4.5 10.8 - - + +
471C LEU* 4.1 21.5 - - - -
475C HIS* 4.4 12.6 - - + -
477C GLU* 5.4 3.4 - - + -
481C ALA* 4.2 24.0 - - - -
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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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436C MET* 2.8 31.0 + - - +
437C MET* 3.1 27.3 - - + +
439C CYS* 1.3 80.5 - - - +
441C VAL* 1.3 62.2 + - + +
442C GLY 3.3 0.6 + - - -
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Residues in contact with VAL 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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647B ARG* 3.5 20.0 - - - +
402C LEU 4.7 1.1 - - - +
403C GLY* 4.4 10.1 - - - +
406C VAL* 3.6 35.1 - - + +
437C MET* 3.3 43.1 - - + +
438C VAL* 3.5 10.8 - - - +
440C GLN* 1.3 76.8 - - + +
442C GLY* 1.3 59.1 + - - +
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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