Contacts of the helix formed by residues 325 - 332 (chain C) in PDB entry 1D7W
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 ALA 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.4 0.4 - - - -
30A VAL* 3.3 13.5 - - - +
32A TRP* 3.3 53.6 - - + +
1601A BR 4.7 0.7 - - + -
323C ARG 3.4 2.0 + - - -
324C ILE* 1.3 78.9 - - - +
326C ASN* 1.3 66.6 + - - +
327C VAL* 4.3 7.0 - - + -
328C PHE* 3.0 19.3 + - - +
329C THR* 3.7 0.7 + - - +
502C GLN* 2.8 12.8 + - - +
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Residues in contact with ASN 326 (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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29A PHE* 3.8 22.2 - - + +
30A VAL 3.0 11.5 + - - +
31A ARG* 3.6 19.7 - - - +
1601A BR 3.5 14.3 - - + +
162C ASN* 2.9 19.8 + - - -
163C GLN* 2.9 28.3 + - - +
325C ALA* 1.3 71.9 - - - +
327C VAL* 1.3 61.1 + - - +
329C THR* 2.7 27.8 + - - -
330C ASN 4.0 0.5 + - - -
428C HIS* 2.7 31.5 + - - +
430C LEU* 3.9 4.1 - - + +
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Residues in contact with VAL 327 (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* 4.0 14.1 - - + -
1601A BR 3.3 5.6 - - + +
325C ALA* 4.3 2.0 - - + -
326C ASN* 1.3 78.3 - - - +
328C PHE* 1.4 54.8 + - - +
330C ASN* 3.0 5.5 + - - +
331C ALA* 2.8 32.1 + - + +
430C LEU* 3.7 12.9 - - + +
436C TRP* 3.4 57.2 - - + +
476C ILE* 3.9 27.8 - - + -
498C ILE* 4.0 21.5 - - + -
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Residues in contact with PHE 328 (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* 5.6 0.4 - - + -
97A LEU* 3.7 28.7 - - + -
98A ASP* 3.6 23.8 - - - -
324C ILE* 3.8 13.0 - - + -
325C ALA* 3.0 16.2 + - + +
327C VAL* 1.4 81.0 - - - +
329C THR* 1.4 56.8 + - - +
331C ALA* 4.3 5.2 - - - +
332C PHE* 2.8 73.5 + + + +
498C ILE* 4.4 10.8 - - + -
499C ILE* 4.3 11.4 - - + -
502C GLN* 3.4 45.1 - - + +
503C PHE* 3.8 13.0 - + - -
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Residues in contact with THR 329 (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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29A PHE* 3.4 42.8 - - + -
98A ASP* 3.4 26.2 - - - +
100A THR* 4.4 2.7 - - - -
605A HEM 3.3 19.4 - - - +
324C ILE* 4.1 3.6 - - + -
326C ASN* 2.7 26.8 + - - +
328C PHE* 1.4 73.6 - - - +
330C ASN* 1.3 59.6 + - - +
333C ARG* 2.8 28.4 + - - +
424C ARG* 5.9 0.5 - - - +
428C HIS* 4.1 11.4 + - - -
430C LEU* 5.5 0.3 - - - +
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Residues in contact with ASN 330 (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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327C VAL 3.0 7.8 + - - +
329C THR* 1.3 83.3 + - - +
331C ALA* 1.4 58.9 + - - +
332C PHE 3.4 0.4 - - - -
333C ARG* 3.1 38.9 - - - +
421C ASN 2.9 28.4 + - - +
424C ARG* 4.0 10.5 - - - +
425C SER* 3.6 19.8 - - - +
430C LEU* 4.0 16.4 - - + +
476C ILE* 3.4 19.9 - - + +
477C TRP* 3.4 28.7 + - - +
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Residues in contact with ALA 331 (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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327C VAL* 2.8 22.7 + - + +
328C PHE* 4.1 1.8 - - + +
330C ASN* 1.4 68.7 - - - +
332C PHE* 1.4 59.2 + - - +
333C ARG 3.1 4.9 - - - -
334C TYR* 3.1 22.0 + - - +
476C ILE* 4.8 5.8 - - + +
477C TRP* 5.1 3.8 - - - +
495C LEU* 3.7 27.1 - - + +
498C ILE* 3.7 33.7 - - + -
499C ILE* 4.2 6.3 - - + +
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Residues in contact with PHE 332 (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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90A GLY 3.4 22.4 - - - -
93A LEU* 4.2 4.5 - - + -
94A ASP* 3.4 28.9 - - + -
97A LEU* 5.2 0.2 - - + -
605A HEM 3.2 31.6 - - + +
296C TYR* 3.5 30.7 - + - -
297C LEU* 5.3 0.2 - - + -
300C VAL* 5.4 0.7 - - + -
328C PHE* 2.8 51.4 + + + +
331C ALA* 1.4 67.4 - - - +
333C ARG* 1.3 56.3 + - - +
334C TYR* 2.9 28.9 + + - -
335C GLY 3.4 2.1 + - - -
499C ILE* 4.0 19.2 - - + +
503C PHE* 3.7 24.9 - + - -
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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