Contacts of the helix formed by residues 324 - 334 (chain C) in PDB entry 4UQJ
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 324 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS* 5.6 0.7 - - - -
322C PRO 3.4 6.1 + - - -
323C TRP* 1.3 70.3 - - - +
325C GLN* 1.3 60.1 + - - +
326C GLY 3.0 2.5 + - - -
327C VAL* 3.2 28.5 + - - +
328C GLU* 4.1 5.2 + - - +
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Residues in contact with GLN 325 (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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305C GLU 5.4 1.1 - - - +
306C ILE* 4.2 27.3 - - + +
323C TRP* 2.9 30.8 + - + +
324C GLY* 1.3 76.5 - - - +
326C GLY* 1.3 58.3 + - - +
327C VAL 3.4 0.2 - - - -
328C GLU* 3.6 10.9 + - - +
329C ILE* 3.2 26.2 + - - +
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Residues in contact with GLY 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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93C HIS* 3.5 19.4 - - - +
95C SER* 4.4 0.5 + - - -
109C PHE* 3.3 15.3 - - - -
323C TRP* 2.9 21.7 + - - -
325C GLN* 1.3 77.0 - - - +
327C VAL* 1.3 64.4 + - - +
328C GLU 3.2 0.7 - - - -
329C ILE* 3.2 11.4 + - - +
330C GLU 3.2 17.7 + - - -
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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
----------------------------------------------------------
93C HIS* 3.5 28.0 - - + +
109C PHE* 4.1 8.9 - - + -
324C GLY* 3.2 19.2 + - - +
326C GLY* 1.3 77.2 - - - +
328C GLU* 1.3 65.4 + - + +
330C GLU* 3.6 9.4 + - - +
331C ARG* 3.3 20.3 + - + +
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Residues in contact with GLU 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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299C LEU* 4.6 6.9 - - + +
304C ILE* 4.1 38.4 - - + +
306C ILE* 4.8 6.5 - - + -
324C GLY 4.8 7.0 - - - +
325C GLN* 3.6 10.9 + - - +
326C GLY 3.2 0.8 - - - -
327C VAL* 1.3 79.3 - - + +
329C ILE* 1.3 63.7 + - - +
330C GLU 3.1 1.8 - - - -
331C ARG* 3.3 11.8 + - - +
332C ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 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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71C TYR* 3.3 36.1 - - + +
72C ALA* 4.8 4.5 - - + -
95C SER* 3.6 17.3 - - - +
295C ALA* 6.5 0.2 - - + -
299C LEU* 4.5 7.0 - - + -
306C ILE* 4.3 22.4 - - + -
323C TRP* 3.7 25.6 - - + -
325C GLN 3.2 17.7 - - - +
326C GLY* 3.2 9.3 + - - +
328C GLU* 1.3 77.4 - - - +
330C GLU* 1.3 60.9 + - - +
332C ALA* 3.4 6.9 + - + +
333C LEU* 3.2 30.9 + - + +
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Residues in contact with GLU 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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95C SER* 3.8 6.7 + - - +
108C PRO* 4.0 9.9 - - - +
109C PHE* 3.4 59.0 + - + +
110C VAL 5.7 0.2 - - - +
111C ILE* 5.1 7.4 - - + +
326C GLY 3.2 11.5 + - - +
327C VAL* 3.7 12.9 - - - +
328C GLU 3.1 0.4 - - - -
329C ILE* 1.3 73.7 - - - +
331C ARG* 1.3 58.7 + - - +
332C ALA 2.9 9.8 + - - -
333C LEU* 3.3 4.5 + - - +
334C LYS* 3.0 30.1 + - + +
349C GLN 4.3 13.5 - - - +
350C ASN 5.1 1.6 - - - +
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Residues in contact with ARG 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* 3.3 11.6 + - + +
328C GLU* 3.3 17.6 + - - +
330C GLU* 1.3 78.5 - - - +
332C ALA* 1.3 57.5 + - - +
334C LYS* 4.5 4.6 - - - +
335C GLN* 3.1 26.4 + - - +
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Residues in contact with ALA 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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295C ALA* 3.9 13.7 - - + +
298C ASN* 5.3 4.9 + - + +
299C LEU* 3.4 39.9 - - + -
328C GLU 3.1 10.8 + - - +
329C ILE* 3.5 7.0 - - + +
330C GLU 2.9 0.6 - - - -
331C ARG* 1.3 77.0 - - - +
333C LEU* 1.3 67.0 + - - +
335C GLN* 3.0 14.4 + - - +
336C VAL* 3.1 17.5 + - - +
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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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72C ALA* 5.0 3.4 - - + -
95C SER* 3.5 31.6 - - - -
97C ILE* 3.7 27.1 - - + -
111C ILE* 3.8 21.1 - - + -
291C VAL* 4.1 12.6 - - + +
292C MET* 4.0 19.1 - - + -
295C ALA* 3.5 20.8 - - + +
329C ILE* 3.2 21.1 + - + +
330C GLU* 4.0 2.2 - - - +
332C ALA* 1.3 78.3 - - - +
334C LYS* 1.3 62.6 + - - +
336C VAL* 3.2 22.9 + - - +
347C PHE* 3.8 11.8 - - - -
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Residues in contact with LYS 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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111C ILE* 4.3 12.5 - - + +
330C GLU* 3.0 22.9 + - + +
331C ARG* 4.8 3.8 - - - -
333C LEU* 1.3 76.4 - - - +
335C GLN* 1.3 60.1 - - - +
336C VAL 3.3 1.3 + - - +
347C PHE* 3.6 34.0 + - + +
348C ASP 3.9 19.5 - - - +
349C GLN* 5.3 6.5 - - - +
350C ASN 6.1 0.2 - - - -
351C GLY* 5.7 1.1 - - - -
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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