Contacts of the helix formed by residues 330 - 344 (chain C) in PDB entry 4D10
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 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C GLN* 4.7 7.1 - - - +
323C ALA* 3.3 21.7 - - - +
328C LEU 4.7 0.3 - - - -
329C SER* 1.3 76.3 + - - +
331C PRO* 1.3 74.1 - - - +
332C GLN* 3.1 13.2 + - - -
333C GLU* 3.7 7.8 + - - +
334C ALA 3.7 5.0 + - - -
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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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319C LEU* 3.6 43.2 - - + +
320C GLN* 3.6 22.7 - - + +
323C ALA* 4.3 0.4 - - - -
330C GLY* 1.3 82.4 - - - +
332C GLN* 1.3 78.8 + - - +
333C GLU 3.5 0.2 - - - -
334C ALA* 3.4 3.3 + - + +
335C GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 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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329C SER 5.0 0.7 - - - +
330C GLY* 3.1 14.7 - - - -
331C PRO* 1.3 97.8 - - + +
333C GLU* 1.3 59.6 + - + +
335C GLU* 3.3 8.8 + - - +
336C LYS* 3.0 37.7 + - - +
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Residues in contact with GLU 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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328C LEU* 4.0 33.5 - - + +
329C SER 4.3 6.3 + - - +
330C GLY 3.7 6.5 + - - +
332C GLN* 1.3 77.9 - - + +
334C ALA* 1.3 60.7 + - - +
336C LYS* 3.6 30.6 + - - +
337C TYR* 3.0 55.8 + - - -
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Residues in contact with ALA 334 (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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319C LEU* 3.7 31.0 - - + +
322C MET* 4.2 18.8 - - + +
323C ALA 4.4 4.3 - - - +
328C LEU* 4.1 15.1 - - + +
330C GLY 3.7 6.2 + - - +
331C PRO 3.4 10.7 + - - +
332C GLN 3.3 0.2 - - - -
333C GLU* 1.3 77.0 - - - +
335C GLU* 1.3 59.4 + - - +
337C TYR* 3.5 1.7 + - - +
338C VAL* 2.9 35.0 + - - +
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Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 3.7 21.3 - - + +
331C PRO 2.9 16.9 + - - +
332C GLN* 3.6 7.9 - - - +
334C ALA* 1.3 76.8 - - - +
336C LYS* 1.3 57.4 + - - +
338C VAL* 3.5 3.1 + - - +
339C LEU* 2.9 33.8 + - + +
351C ILE* 4.0 32.9 - - + +
353C GLN* 3.2 36.1 + - - +
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Residues in contact with LYS 336 (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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332C GLN* 3.0 22.7 + - - +
333C GLU* 3.6 34.5 + - - +
335C GLU* 1.3 75.7 - - - +
337C TYR* 1.3 60.7 + - + +
339C LEU* 3.3 7.3 + - - +
340C HIS* 2.9 51.1 + - + +
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Residues in contact with TYR 337 (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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300C SER* 4.6 16.5 - - - -
303C TYR* 3.8 33.2 - - + -
304C LYS* 4.6 17.5 - - + -
307C ILE* 3.7 28.7 - - + -
328C LEU* 3.7 24.5 - - + +
333C GLU* 3.0 42.1 + - - +
334C ALA* 3.9 4.7 - - - +
336C LYS* 1.3 78.4 - - + +
338C VAL* 1.3 58.0 + - - +
340C HIS* 3.5 11.8 + + + +
341C MET* 2.9 36.3 + - - +
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Residues in contact with VAL 338 (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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307C ILE* 4.5 11.2 - - + -
322C MET* 3.5 32.3 - - + -
334C ALA 2.9 22.1 + - - +
335C GLU* 4.0 4.5 - - - +
337C TYR* 1.3 74.6 - - + +
339C LEU* 1.3 59.6 - - - +
341C MET* 3.2 7.6 + - - +
342C ILE* 2.9 52.7 + - + +
347C ILE* 4.9 3.8 - - + -
349C ALA* 4.6 6.3 - - + -
351C ILE* 3.9 16.6 - - + -
358C VAL* 4.3 20.2 - - + -
360C PHE* 5.8 1.1 - - + -
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Residues in contact with LEU 339 (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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335C GLU* 2.9 23.1 + - + +
336C LYS* 3.7 5.8 - - - +
338C VAL* 1.3 76.2 - - - +
340C HIS* 1.3 68.8 + - + +
342C ILE* 3.4 9.6 + - + +
343C GLU* 3.0 27.3 + - + +
351C ILE* 4.1 20.2 - - + +
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Residues in contact with HIS 340 (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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304C LYS* 5.5 7.0 - - - +
336C LYS* 2.9 44.9 + - + +
337C TYR* 3.7 12.1 - + - +
339C LEU* 1.3 79.1 - - + +
341C MET* 1.3 59.0 + - + +
343C GLU* 3.3 13.3 + - - +
344C ASP* 2.9 44.7 + - - +
346C GLU* 4.5 0.2 - - - -
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Residues in contact with MET 341 (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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304C LYS* 3.4 46.7 - - + +
307C ILE* 3.8 33.4 - - + -
308C GLN* 3.8 20.0 - - + -
337C TYR* 2.9 23.0 + - - +
338C VAL* 3.7 4.5 - - - +
340C HIS* 1.3 74.0 - - - +
342C ILE* 1.3 62.9 + - - +
345C GLY 3.2 1.9 + - - -
346C GLU* 2.8 53.0 + - + +
347C ILE* 3.2 31.7 + - + -
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Residues in contact with ILE 342 (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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338C VAL* 2.9 40.8 + - + +
339C LEU* 3.8 9.2 - - + +
341C MET* 1.3 73.0 - - - +
343C GLU* 1.3 65.5 + - - +
345C GLY* 3.2 12.6 + - - -
347C ILE* 3.9 24.0 - - + +
349C ALA 3.4 31.9 - - - +
350C SER* 4.5 1.3 - - - +
351C ILE* 4.0 17.0 - - + -
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C LEU* 3.0 20.2 + - + +
340C HIS* 3.3 13.5 + - - +
342C ILE* 1.3 80.3 - - - +
344C ASP* 1.3 67.2 + - - +
345C GLY* 3.2 1.3 + - - -
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Residues in contact with ASP 344 (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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304C LYS* 4.1 9.1 + - - -
340C HIS* 2.9 24.8 + - - +
343C GLU* 1.3 83.8 - - - +
345C GLY* 1.3 61.6 + - - +
346C GLU* 3.4 31.9 + - - +
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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