Contacts of the helix formed by residues 432 - 440 (chain C) in PDB entry 1D2V
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 432 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 4.2 2.6 + - - -
53A ARG* 3.7 11.8 - - - +
18B ARG* 6.3 0.4 - - - +
430C LEU 4.7 0.2 - - - -
431C PRO* 1.3 77.4 - - - +
433C TYR* 1.3 65.5 + - - -
434C ASN 3.5 2.2 - - - -
435C ALA* 3.2 15.5 + - - +
436C TRP* 3.2 12.4 + - - -
472C ASN 3.2 19.7 + - - -
473C ASN 4.6 2.2 - - - -
474C ILE 3.4 11.2 - - - -
475C ASP* 5.2 0.9 - - - -
476C ILE 5.2 1.6 - - - -
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Residues in contact with TYR 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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432C GLY* 1.3 68.9 - - - -
434C ASN* 1.3 75.4 + - - +
436C TRP* 3.1 9.3 + - - +
437C ARG* 2.9 41.6 + - + +
445C PRO* 3.8 24.2 - - + -
451C LEU* 4.1 11.2 - - + -
454C VAL* 3.5 20.3 - - - +
455C LEU* 4.4 4.3 - - + +
471C PRO* 3.3 17.3 - - + +
472C ASN 3.9 2.8 + - - -
474C ILE* 2.8 33.7 + - + +
475C ASP 5.1 0.2 - - - +
476C ILE* 5.3 4.7 - - + +
479C GLY* 3.7 29.8 - - - -
483C GLU* 2.7 33.4 + - + +
494C LEU* 3.6 23.6 - - + -
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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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432C GLY 3.5 0.6 - - - -
433C TYR* 1.3 85.2 - - - +
435C ALA* 1.3 59.9 + - - +
437C ARG* 3.2 5.3 + - - +
438C ARG* 2.8 37.6 + - - +
444C GLN* 3.5 16.8 - - + +
445C PRO* 2.8 48.0 + - - +
446C GLU* 3.5 13.9 + - - -
471C PRO* 3.6 15.5 + - - +
472C ASN* 3.0 32.5 + - - +
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Residues in contact with ALA 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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33A LEU* 3.8 10.0 - - + +
18B ARG* 3.7 23.1 - - - +
431C PRO* 3.6 22.7 - - + -
432C GLY* 3.2 12.7 + - - +
434C ASN* 1.3 77.2 - - - +
436C TRP* 1.3 57.9 + - - +
438C ARG* 3.3 18.2 + - - +
439C PHE* 2.9 28.4 + - - +
472C ASN 5.4 0.8 + - - -
319D SER* 5.7 0.2 - - - +
2F NAG 4.6 1.2 - - - +
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Residues in contact with TRP 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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32A TRP* 3.9 10.3 - + + -
33A LEU* 3.6 30.5 - - + -
601A BR 3.6 17.7 - - + -
327C VAL* 3.4 46.7 - - + +
430C LEU* 4.5 3.9 - - + +
431C PRO* 3.1 52.4 + - + +
432C GLY 3.2 9.5 + - - -
433C TYR 3.1 8.5 + - - +
435C ALA* 1.3 75.8 - - - +
437C ARG* 1.4 62.9 + - - +
439C PHE* 3.4 32.1 + + - +
440C CYS* 3.0 29.8 + - - +
476C ILE* 3.9 33.7 - - + -
494C LEU* 3.6 9.0 - - + -
498C ILE* 4.6 7.0 - - + -
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Residues in contact with ARG 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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433C TYR* 2.9 43.5 + - + +
434C ASN* 3.4 11.9 - - - +
436C TRP* 1.4 74.3 - - - +
438C ARG* 1.3 58.5 + - - +
440C CYS* 3.2 3.8 + - - -
441C GLY 3.1 3.6 + - - -
442C LEU* 2.8 71.7 + - - +
443C PRO* 2.8 35.9 + - - +
444C GLN* 4.1 2.9 - - + -
445C PRO* 4.5 0.6 - - - +
454C VAL* 3.6 31.1 - - - +
483C GLU* 2.8 41.8 + - - -
493C PRO* 4.4 8.9 - - - +
494C LEU* 4.1 8.5 - - + -
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Residues in contact with ARG 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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18B ARG* 3.8 12.1 - - - +
434C ASN* 2.8 22.8 + - - +
435C ALA* 3.4 29.7 - - - +
437C ARG* 1.3 71.5 - - - +
439C PHE* 1.3 67.0 + - - +
441C GLY* 2.9 14.1 + - - +
442C LEU 4.8 0.2 - - - +
444C GLN* 3.0 47.0 + - - +
446C GLU* 4.7 6.5 + - - -
472C ASN* 4.8 3.4 + - - -
317D ASN* 5.0 0.9 + - - -
318D ASP* 4.6 4.6 + - - -
319D SER* 3.0 36.3 + - - -
1F NAG 3.8 29.4 + - - +
2F NAG 3.5 19.5 + - - +
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Residues in contact with PHE 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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32A TRP* 3.7 49.1 - + + -
33A LEU* 4.0 12.1 - - + -
435C ALA 2.9 17.2 + - - +
436C TRP* 3.4 26.9 + + + +
438C ARG* 1.3 76.9 - - - +
440C CYS* 1.3 72.8 + - - +
441C GLY 3.5 1.2 + - - -
497C CYS* 4.6 2.9 - - - -
498C ILE* 5.3 1.1 - - + -
501C THR* 5.3 1.3 - - + -
2F NAG 2.7 44.8 + - + +
3F BMA 3.1 24.2 - - - +
5F MAN 3.2 49.1 - - - -
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Residues in contact with CYS 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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308C LYS* 6.0 1.6 - - - -
309C TYR* 4.9 4.7 + - - -
436C TRP 3.0 19.0 + - - +
437C ARG 3.6 5.4 - - - +
438C ARG 3.1 0.2 - - - -
439C PHE* 1.3 85.7 - - - +
441C GLY* 1.3 60.9 + - - +
442C LEU* 3.4 20.0 + - + +
494C LEU* 3.7 13.2 - - + -
497C CYS* 2.1 54.9 - - + -
498C ILE* 4.1 7.4 - - - -
3F BMA 4.3 13.1 + - - +
4F MAN 5.7 0.2 - - - +
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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