Contacts of the helix formed by residues 329 - 333 (chain C) in PDB entry 3UGV
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 329 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C LEU* 5.0 0.2 - - - -
35C LEU* 4.2 16.8 - - + -
51C TYR* 3.6 40.4 - - + +
53C GLU* 3.8 11.4 + - - +
308C GLU* 6.0 0.2 - - - +
326C GLN* 4.8 4.5 - - - +
327C SER* 3.1 1.0 - - - +
328C TRP* 1.3 76.6 - - - +
330C ASP* 1.3 67.0 + - - +
331C PRO* 3.4 2.7 - - - -
332C ILE* 3.2 24.8 - - + +
333C LEU* 3.9 6.0 - - + +
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Residues in contact with ASP 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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308C GLU* 4.7 7.8 - - - +
325C TRP* 4.8 7.4 + - - -
326C GLN 4.6 2.4 - - - +
327C SER* 3.1 36.6 + - - +
329C ALA* 1.3 76.8 - - - +
331C PRO* 1.3 68.8 - - + +
333C LEU* 2.8 29.3 + - - +
336C PRO* 3.6 37.3 - - + +
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Residues in contact with PRO 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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17C LEU* 4.0 21.3 - - + -
18C LYS 5.9 2.5 - - - +
327C SER 3.6 7.6 - - - +
328C TRP 3.8 6.5 - - - +
329C ALA 3.4 3.6 - - - -
330C ASP* 1.3 94.7 - - + +
332C ILE* 1.3 61.0 + - - +
333C LEU 3.3 3.6 + - - +
357C ASP* 3.8 6.9 - - - +
360C VAL* 3.7 34.3 - - + +
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Residues in contact with ILE 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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15C VAL* 4.4 9.0 - - + -
17C LEU* 4.3 20.9 - - + -
35C LEU* 3.6 23.1 - - + -
37C LEU* 4.5 14.4 - - + -
51C TYR* 4.6 9.9 - - + -
329C ALA* 3.2 18.6 - - + +
330C ASP 2.9 2.2 + - - -
331C PRO* 1.3 74.5 - - - +
333C LEU* 1.3 75.9 + - + +
356C TRP* 3.4 26.4 - - + -
357C ASP* 3.1 22.9 + - - +
360C VAL* 4.3 13.5 - - + -
361C VAL* 4.3 15.9 - - + +
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Residues in contact with LEU 333 (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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51C TYR* 4.8 4.7 - - + +
308C GLU* 3.6 33.4 - - + +
329C ALA* 3.9 9.0 - - + +
330C ASP* 2.8 24.8 + - - +
331C PRO 4.0 4.0 - - - +
332C ILE* 1.3 98.1 - - + +
334C GLN* 1.3 66.6 + - - +
335C GLU 4.2 9.0 - - - +
336C PRO* 3.8 24.0 - - + +
337C TYR* 6.2 0.2 - - + -
354C LEU* 4.1 26.7 - - + -
355C ASP 3.6 4.9 - - - +
356C TRP* 3.6 19.3 - - + -
357C ASP* 4.4 4.7 - - - +
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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