Contacts of the helix formed by residues 425 - 433 (chain C) in PDB entry 3WTU
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 THR 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361C TRP* 3.8 2.0 - - - -
419C GLN* 3.7 28.9 - - - +
424C TYR* 1.3 77.0 - - - +
426C PRO* 1.3 75.5 - - - +
427C GLU* 3.5 8.8 + - - +
428C GLU* 3.0 40.3 + - - +
429C LEU* 2.8 20.4 + - - +
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Residues in contact with PRO 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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360C GLY* 3.7 40.8 - - - +
361C TRP* 3.4 36.6 - - + +
419C GLN* 4.7 6.7 - - - +
425C THR* 1.3 85.8 - - - +
427C GLU* 1.3 65.3 + - + +
429C LEU 3.2 0.3 + - - -
430C HIS* 2.8 37.3 + - + +
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Residues in contact with GLU 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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425C THR* 3.2 7.7 + - - +
426C PRO* 1.3 83.7 - - + +
428C GLU* 1.3 66.7 + - + +
430C HIS* 3.3 8.5 + - - +
431C ALA* 3.1 22.6 + - - +
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Residues in contact with GLU 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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423C GLY 4.4 1.6 - - - +
424C TYR* 3.7 22.6 - - + -
425C THR* 3.0 40.9 + - - +
427C GLU* 1.3 81.1 - - + +
429C LEU* 1.3 57.5 + - - +
431C ALA* 3.5 5.8 + - - +
432C MET* 3.1 35.6 + - - +
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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 VAL* 5.1 0.7 - - + -
321C ILE* 3.4 31.2 - - + -
346C THR* 4.4 5.2 - - + -
356C TRP* 3.9 23.3 - - + -
361C TRP* 3.5 27.6 - - + -
422C LEU* 4.1 11.7 - - + -
424C TYR* 4.6 7.4 - - + +
425C THR 2.8 18.3 + - - +
426C PRO 3.9 2.7 - - - +
428C GLU* 1.3 70.0 - - - +
430C HIS* 1.3 68.9 + - + +
432C MET* 3.2 22.5 + - + +
433C LEU* 2.9 46.2 + - + +
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Residues in contact with HIS 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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356C TRP* 4.0 30.8 - + + +
358C GLY* 3.6 33.8 + - - -
360C GLY 3.1 29.6 + - - -
361C TRP* 4.9 1.1 - + - -
426C PRO* 2.8 44.9 + - + +
427C GLU* 3.8 7.4 + - - +
429C LEU* 1.3 74.6 - - + +
431C ALA* 1.3 58.0 + - - +
433C LEU* 3.1 2.2 + - - -
434C ASP 2.8 24.8 + - - -
435C VAL* 3.1 30.9 + - + +
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Residues in contact with ALA 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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427C GLU 3.1 16.3 + - - +
428C GLU* 3.7 6.5 - - - +
430C HIS* 1.3 76.7 - - - +
432C MET* 1.3 63.5 + - + +
434C ASP* 2.9 17.6 + - - +
435C VAL 5.2 0.2 - - - +
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Residues in contact with MET 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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320C VAL* 3.3 45.3 - - + +
321C ILE* 3.5 22.2 - - + -
348C LYS* 3.5 18.0 + - - -
424C TYR* 3.9 30.5 - - + -
428C GLU* 3.1 28.7 + - - +
429C LEU* 3.2 19.0 + - + +
431C ALA* 1.3 77.0 - - + +
433C LEU* 1.3 59.3 + - + +
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Residues in contact with LEU 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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320C VAL* 3.3 28.3 - - + -
345C LEU 3.3 21.5 - - - +
346C THR* 3.6 26.5 - - - -
347C ASP 4.1 1.3 - - - +
348C LYS* 3.4 20.7 - - + +
351C GLN* 3.2 24.3 + - - +
356C TRP* 3.7 12.6 - - + +
429C LEU* 2.9 42.6 + - + +
430C HIS 3.4 0.2 - - - -
432C MET* 1.3 77.4 - - + +
434C ASP* 1.3 74.8 + - - +
435C VAL* 4.0 7.6 - - + -
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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