Contacts of the helix formed by residues 425 - 430 (chain C) in PDB entry 3DLX
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 425 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLN* 3.9 7.3 - - - +
344C GLU* 4.0 11.9 + - - -
386C PHE* 3.9 26.6 - - - -
423C MET 3.3 0.2 + - - -
424C GLY* 1.3 71.3 - - - -
426C ALA* 1.3 57.4 + - - +
427C MET 3.4 2.5 - - - -
428C ASP* 3.2 9.7 + - - +
429C LEU* 3.0 36.8 + - - +
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Residues in contact with ALA 426 (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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399C LEU* 4.3 11.2 - - + +
412C ASN* 3.8 14.4 - - - +
413C TRP* 5.6 0.4 - - + -
423C MET* 3.0 18.0 + - - +
424C GLY 3.4 0.2 - - - -
425C GLY* 1.3 75.7 - - - +
427C MET* 1.3 62.1 + - - +
429C LEU* 3.3 19.8 + - - +
430C VAL* 3.4 21.7 + - - +
461C THR* 3.7 18.8 - - + -
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Residues in contact with MET 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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1C GOL 3.0 36.2 - - - +
137C PRO* 3.9 15.5 - - + +
159C THR* 3.8 12.8 - - + -
160C GLY* 4.0 6.3 - - - -
163C THR* 3.6 23.1 - - - +
165C VAL* 3.8 20.0 - - + -
413C TRP* 3.5 40.4 - - + +
423C MET* 3.9 25.1 + - + +
425C GLY 3.4 0.6 - - - -
426C ALA* 1.3 75.7 - - - +
428C ASP* 1.3 61.4 + - - +
430C VAL* 3.6 5.8 - - - +
431C SER* 3.6 1.9 + - - -
460C LEU 3.7 8.1 - - - +
461C THR* 3.4 17.5 - - + +
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Residues in contact with ASP 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C PRO* 3.9 6.4 - - - +
138C GLN 4.1 1.4 + - - -
139C GLY* 3.0 33.3 + - - -
159C THR* 2.7 34.7 + - - +
386C PHE* 3.6 27.1 - - + -
389C ILE* 3.4 14.4 - - + +
390C ARG* 3.9 17.9 + - + +
425C GLY* 3.2 9.8 + - - +
427C MET* 1.3 77.1 - - - +
429C LEU* 1.3 64.5 + - - +
431C SER* 2.7 21.9 + - - +
432C SER 4.6 0.7 + - - -
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Residues in contact with LEU 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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320C ASN* 3.5 46.7 - - + +
322C GLY* 5.6 2.2 - - - -
344C GLU* 4.2 12.6 - - - +
386C PHE* 5.4 0.2 - - + -
389C ILE* 3.7 29.9 - - + +
394C VAL* 5.8 1.1 - - + -
397C THR* 3.3 40.2 + - + +
399C LEU* 4.3 12.3 - - + -
425C GLY 3.0 26.5 + - - +
426C ALA* 3.3 8.9 + - - +
428C ASP* 1.3 76.4 - - - +
430C VAL* 1.3 61.1 + - + +
431C SER 3.4 0.7 + - - -
432C SER* 5.0 1.8 + - - +
435C THR* 4.3 8.5 - - - +
437C VAL* 4.3 4.5 - - - +
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Residues in contact with VAL 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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1C GOL 4.0 9.1 - - - -
397C THR* 5.7 0.2 - - + -
399C LEU* 3.8 21.5 - - + -
410C LEU* 3.9 14.6 - - + -
426C ALA 3.5 13.7 - - - +
427C MET 3.6 13.0 - - - +
429C LEU* 1.3 77.0 - - - +
431C SER* 1.3 60.9 + - - +
432C SER 3.5 5.8 + - - +
437C VAL* 4.1 22.7 - - + +
461C THR* 3.9 20.0 - - + +
462C GLY* 4.2 2.0 - - - -
465C CYS* 3.6 36.1 - - + +
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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