Contacts of the helix formed by residues 306 - 320 (chain B) in PDB entry 1U0C
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 ASN 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B LYS 4.2 0.4 + - - -
305B TYR* 1.3 74.7 - - - +
307B LYS* 1.3 61.9 + - - +
308B GLU* 2.5 47.2 + - - +
309B PHE* 2.7 34.6 + - + +
310B LEU* 3.2 8.5 + - - +
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Residues in contact with LYS 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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8A GLU* 3.0 33.4 + - - -
305B TYR 3.4 3.9 + - - -
306B ASN* 1.3 72.7 + - - +
308B GLU* 1.3 69.1 - - + +
310B LEU* 3.1 11.7 + - - +
311B LEU* 3.0 28.1 + - + +
394B PHE* 3.8 32.1 - - + -
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Residues in contact with GLU 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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7A LYS* 2.5 42.2 + - - -
11A LEU* 4.0 28.6 - - + +
94A PHE* 5.4 2.8 - - - -
306B ASN* 2.5 21.0 + - - +
307B LYS* 1.3 77.2 - - + +
309B PHE* 1.3 60.1 + - - +
311B LEU* 3.4 5.7 + - + +
312B TYR* 3.1 25.6 + - - +
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Residues in contact with PHE 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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96A LYS* 4.8 11.4 - - - +
305B TYR* 3.7 41.3 - + + -
306B ASN* 2.7 26.1 + - + +
307B LYS 3.1 0.2 - - - -
308B GLU* 1.3 78.7 - - - +
310B LEU* 1.3 62.6 + - + +
312B TYR* 3.9 5.8 - + - +
313B LEU* 3.1 59.9 + - + +
358B LEU* 4.4 6.3 - - + -
361B GLU* 3.0 44.4 - - + -
362B ILE* 4.0 13.0 - - + -
387B PHE* 4.7 0.9 - + - -
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Residues in contact with LEU 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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305B TYR* 3.9 28.3 - - + +
306B ASN 3.2 15.5 + - - +
307B LYS* 3.1 10.1 + - - +
309B PHE* 1.3 93.2 - - + +
311B LEU* 1.3 55.4 + - - +
313B LEU* 4.4 1.8 - - - -
314B ALA* 2.6 38.1 + - - +
387B PHE* 4.5 6.1 - - + -
390B GLN* 3.5 35.0 - - + +
391B LEU* 3.7 22.4 - - + +
394B PHE* 3.7 23.8 - - + -
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Residues in contact with LEU 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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8A GLU* 3.8 51.4 - - + +
11A LEU* 3.9 23.6 - - + -
12A TYR* 3.3 25.1 - - + +
307B LYS* 3.0 28.3 + - + +
308B GLU* 3.7 8.7 - - + +
310B LEU* 1.3 77.3 - - - +
312B TYR* 1.3 62.7 + - - +
314B ALA* 3.4 5.5 + - - +
315B GLY 3.2 16.3 + - - -
394B PHE* 3.5 30.5 - - + -
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Residues in contact with TYR 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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11A LEU* 3.4 22.4 + - + +
14A ALA* 4.0 1.3 - - + -
15A GLY* 3.2 35.2 - - - -
18A ASP* 2.7 30.0 + - - +
94A PHE* 3.3 29.2 - - + -
96A LYS* 3.3 48.1 - - + +
308B GLU 3.1 13.8 + - - +
309B PHE* 3.9 6.1 - + - +
311B LEU* 1.3 80.1 - - - +
313B LEU* 1.3 64.7 + - + +
315B GLY 3.1 2.9 + - - -
316B PHE* 2.9 29.1 + + + -
354B PHE* 3.6 22.7 - + - -
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Residues in contact with LEU 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 PHE* 3.1 49.6 + - + +
310B LEU 3.9 2.5 - - - +
312B TYR* 1.3 80.6 - - + +
314B ALA* 1.3 62.3 + - - +
315B GLY 3.0 1.3 - - - -
316B PHE* 3.6 15.1 - - + +
317B VAL* 2.7 50.2 + - + +
343B PHE* 5.0 1.3 - - + -
345B VAL* 5.2 0.2 - - + -
354B PHE* 5.5 1.3 - - + -
358B LEU* 3.8 28.0 - - + -
362B ILE* 4.1 7.4 - - + -
387B PHE* 3.6 30.5 - - + -
391B LEU* 4.3 5.8 - - + -
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Residues in contact with ALA 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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12A TYR* 4.1 2.9 - - + -
310B LEU 2.6 22.9 + - - +
311B LEU 3.6 3.6 - - - +
313B LEU* 1.3 71.5 - - - +
315B GLY* 1.3 58.7 + - - +
318B ASP* 2.8 33.3 + - - +
391B LEU* 3.8 7.3 - - + +
394B PHE* 3.3 42.8 - - + +
395B LEU* 3.7 18.6 - - + +
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Residues in contact with GLY 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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12A TYR* 3.4 39.4 - - - -
16A PHE* 3.2 22.2 - - - -
311B LEU 3.2 4.0 + - - -
312B TYR 3.1 3.9 + - - -
313B LEU 3.0 0.6 - - - -
314B ALA* 1.3 81.0 - - - +
316B PHE* 1.3 63.1 + - - +
318B ASP 3.3 0.9 + - - -
319B GLY 3.1 15.4 + - - -
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Residues in contact with PHE 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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15A GLY* 3.3 20.8 - - - +
18A ASP* 3.7 20.0 - - + -
19A GLY 4.1 1.3 - - - -
97A LEU* 3.7 21.8 - - + -
312B TYR* 2.9 20.3 + - + +
313B LEU* 3.0 16.6 + - + +
315B GLY* 1.3 75.9 - - - +
317B VAL* 1.3 53.7 + - - +
319B GLY* 3.0 2.1 + - - -
320B ASP* 2.7 40.7 + - + -
321B GLY 3.7 0.2 + - - -
345B VAL* 3.0 39.7 - - + -
347B GLU* 3.3 28.5 - - + -
354B PHE* 3.5 29.8 - + - -
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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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313B LEU* 2.7 25.6 + - + +
314B ALA 3.7 3.4 - - - +
316B PHE* 1.3 74.0 - - - +
318B ASP* 1.3 63.2 + - - +
319B GLY 2.8 4.5 - - - -
321B GLY* 2.8 32.4 + - - +
323B ILE* 4.0 22.9 - - + -
343B PHE* 3.3 42.8 - - + -
345B VAL* 4.1 10.1 - - + -
391B LEU* 4.3 6.5 - - + -
395B LEU* 4.1 14.8 - - + -
398B LYS* 3.4 8.6 - - + -
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Residues in contact with ASP 318 (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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12A TYR* 2.6 26.0 + - - +
16A PHE* 3.5 16.1 - - + -
20A ASP* 4.2 2.3 - - - +
47A GLU* 4.8 1.4 - - - +
314B ALA 2.8 19.3 + - - +
315B GLY 3.7 4.3 - - - +
317B VAL* 1.3 76.0 - - - +
319B GLY* 1.3 59.8 + - - +
395B LEU* 3.6 7.0 - - - +
396B LYS 2.5 29.6 + - - -
397B LEU* 2.8 25.2 + - + +
398B LYS* 3.1 39.9 + - - +
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Residues in contact with GLY 319 (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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16A PHE* 4.1 5.6 - - - -
19A GLY* 4.6 2.0 - - - -
20A ASP* 3.5 26.0 - - - -
602A MG 2.3 30.4 - - - -
315B GLY 3.1 9.2 + - - -
316B PHE 3.0 6.1 + - - -
317B VAL 2.8 2.2 - - - -
318B ASP* 1.3 79.8 - - - +
320B ASP* 1.3 52.8 + - - -
321B GLY 3.5 1.2 + - - +
398B LYS* 5.5 0.5 - - - -
565D G 2.7 11.4 + - - +
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Residues in contact with ASP 320 (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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19A GLY* 3.3 15.9 - - - +
20A ASP* 3.5 0.3 - - - +
316B PHE* 2.7 20.5 + - + +
319B GLY* 1.3 71.4 - - - -
321B GLY* 1.3 61.2 + - - +
344B GLN 4.3 0.2 - - - +
345B VAL* 4.5 1.8 - - - -
346B THR* 3.1 35.0 + - - +
347B GLU* 2.3 28.9 - - - +
601B MG 2.5 18.0 - - - -
603C MG 2.1 33.6 - - - -
564D C 3.6 6.2 - - - +
565D G 3.4 16.0 + - - +
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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