Contacts of the helix formed by residues 304 - 317 (chain B) in PDB entry 3ZUU
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 SER 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ARG* 4.4 0.9 - - - +
303B GLN* 1.3 72.9 - - - +
305B ILE* 1.3 63.2 + - - +
306B GLU* 2.8 34.5 + - - -
307B GLU* 2.6 40.0 + - - +
308B ILE* 3.0 18.7 + - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE* 3.7 44.0 - - + -
70B ARG* 3.5 24.1 - - - +
303B GLN 3.5 3.2 + - - -
304B SER* 1.3 72.5 - - - +
306B GLU* 1.3 67.2 + - + +
308B ILE* 3.4 6.3 - - + +
309B MET* 2.8 49.0 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B SER* 2.8 33.4 + - - -
305B ILE* 1.3 90.0 + - + +
307B GLU* 1.3 55.8 + - - +
309B MET* 3.2 10.1 + - - +
310B GLN* 2.9 24.7 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B GLY 4.9 0.7 - - - +
303B GLN* 3.2 28.2 + - + +
304B SER* 2.6 38.4 + - - +
306B GLU* 1.3 75.9 - - - +
308B ILE* 1.3 60.9 + - - +
310B GLN* 3.1 11.7 + - + +
311B ILE* 2.5 45.0 + - + +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 4.6 9.4 - - + -
67B ILE* 3.9 26.5 - - + -
70B ARG* 3.5 36.6 - - - +
80B PHE* 4.2 9.0 - - + -
83B VAL* 5.1 5.3 - - + +
303B GLN* 3.5 39.9 - - + +
304B SER 3.0 13.7 + - - +
305B ILE* 3.4 8.3 - - - +
307B GLU* 1.3 76.7 - - - +
309B MET* 1.3 57.7 + - - +
311B ILE* 3.1 11.8 + - + +
312B ILE* 2.9 42.2 + - + +
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 4.1 33.4 - - + +
67B ILE* 3.7 31.9 - - + -
305B ILE* 2.8 31.9 + - + +
306B GLU* 3.4 7.6 - - - +
308B ILE* 1.3 75.2 - - - +
310B GLN* 1.3 62.6 + - - +
312B ILE* 3.4 7.0 + - - +
313B ALA* 3.0 25.6 + - - +
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU 2.9 12.9 + - - +
307B GLU* 3.1 15.4 + - + +
309B MET* 1.3 77.1 - - - +
311B ILE* 1.3 56.3 + - + +
313B ALA* 3.4 7.9 - - - +
314B GLU* 2.9 57.0 + - - +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.7 26.7 - - + +
84B ILE* 4.7 0.4 - - - -
85B LEU* 3.6 36.6 - - + +
90B LEU* 5.0 1.5 - - + +
303B GLN* 3.3 29.4 - - - +
307B GLU* 2.5 32.1 + - + +
308B ILE* 3.3 8.7 - - - +
310B GLN* 1.3 72.1 - - + +
312B ILE* 1.3 65.4 + - - +
314B GLU* 3.5 11.8 + - - +
315B ALA* 2.9 25.1 + - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 3.3 22.1 - - + +
59B ASP 5.0 1.3 - - - +
62B VAL* 5.4 2.2 - - + -
63B LYS* 3.5 52.0 - - + +
66B ILE* 4.5 16.2 - - + -
67B ILE* 4.8 2.9 - - + -
83B VAL* 5.4 5.8 - - + -
90B LEU* 5.3 5.4 - - + -
308B ILE* 2.9 33.4 + - + +
309B MET* 3.7 10.8 - - - +
311B ILE* 1.3 75.6 - - + +
313B ALA* 1.3 64.8 + - - +
315B ALA* 3.0 8.8 + - - +
316B THR* 2.9 23.5 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B MET 3.0 18.6 + - - +
310B GLN* 3.4 12.8 - - - +
312B ILE* 1.3 71.5 - - - +
314B GLU* 1.3 55.2 + - - +
315B ALA 2.6 14.7 + - - -
316B THR* 2.6 27.1 + - - -
317B VAL* 4.1 5.7 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 3.7 21.4 + - - +
85B LEU* 4.0 22.6 - - + +
310B GLN* 2.9 44.9 + - - +
311B ILE* 3.7 12.4 - - - +
313B ALA* 1.3 76.5 - - - +
315B ALA* 1.3 58.4 + - - +
316B THR 3.8 0.2 + - - -
317B VAL* 3.9 11.3 - - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 3.1 28.2 - - + +
58B ILE* 3.2 24.9 - - + +
85B LEU* 3.3 20.2 - - + -
90B LEU* 4.4 11.0 - - + -
311B ILE 2.9 18.3 + - - +
312B ILE* 3.2 8.5 - - - +
313B ALA 2.6 5.5 + - - -
314B GLU* 1.3 72.2 - - - +
316B THR* 1.3 59.3 + - - -
317B VAL 3.1 7.7 + - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY* 2.9 31.7 - - - +
56B GLU* 5.3 2.2 - - - +
58B ILE* 3.2 32.8 + - - +
312B ILE* 2.9 16.6 + - - +
313B ALA* 2.6 22.3 + - - -
315B ALA* 1.3 70.2 - - - +
317B VAL* 1.3 61.5 + - - +
318B PRO* 3.9 1.7 - - - +
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 2.8 36.0 + - - +
55B GLY 4.5 0.2 - - - -
313B ALA 4.7 6.3 - - - +
314B GLU* 3.9 12.7 + - - +
315B ALA 3.1 3.7 - - - -
316B THR* 1.3 84.9 - - - +
318B PRO* 1.3 60.0 - - + +
319B PRO* 5.1 1.3 - - + -
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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