Contacts of the helix formed by residues 306 - 313 (chain A) in PDB entry 4KEU
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 LYS 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.7 1.2 - - - +
17A GLY* 3.9 13.2 + - - +
18A PHE* 3.8 44.4 - - + +
302A ALA* 2.8 30.8 + - + +
304A ILE 3.4 0.2 - - - -
305A PHE* 1.3 85.6 - - - +
307A GLU* 1.3 66.4 + - + +
308A ASN 3.4 0.9 - - - -
309A PRO* 3.4 3.8 - - - +
310A LYS* 3.1 23.7 + - - +
58B GLN* 5.4 6.2 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA 3.1 6.0 + - - +
303A THR* 3.6 25.8 - - + +
306A LYS* 1.3 79.9 - - + +
308A ASN* 1.3 59.3 + - - +
310A LYS* 3.1 29.5 + - - +
311A LYS* 2.9 50.3 + - - +
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Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 3.7 12.1 - - + -
248A SER 2.8 23.4 + - - +
249A ASP 3.2 19.1 + - - +
250A LYS 3.9 0.8 - - - -
251A ILE 2.5 32.4 + - - +
252A MET* 3.4 9.8 - - + +
303A THR* 2.7 27.6 + - - +
304A ILE* 3.6 6.4 - - - +
307A GLU* 1.3 71.2 - - - +
309A PRO* 1.3 65.6 - - + +
311A LYS* 3.1 19.1 + - - +
312A PHE* 2.8 30.7 + - - +
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Residues in contact with PRO 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.8 4.9 - - + -
19A THR* 3.9 30.7 - - + +
21A ILE* 4.4 11.4 - - + -
252A MET* 3.4 17.9 - - + -
304A ILE 3.1 20.4 - - - +
305A PHE* 3.6 19.7 - - - +
306A LYS 3.4 11.0 - - - +
308A ASN* 1.3 91.6 - - + +
310A LYS* 1.3 61.2 + - - +
312A PHE* 3.3 1.6 + - + +
313A PHE* 3.0 33.0 + - + -
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 3.6 35.8 - - - +
14A LYS* 3.8 28.4 - - - +
16A ILE* 4.9 5.3 - - + +
306A LYS 3.1 12.7 + - - +
307A GLU* 3.1 36.0 + - - +
309A PRO* 1.3 79.1 - - - +
311A LYS* 1.3 58.2 + - + +
313A PHE 3.3 3.5 + - - -
314A SER* 2.4 34.4 + - - +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY 4.8 3.0 - - - +
194A LYS* 4.8 1.6 - - - -
218A PHE* 4.1 13.1 - - + -
249A ASP* 3.3 24.5 + - - +
250A LYS* 5.3 3.0 - - - +
303A THR* 5.5 2.0 - - - +
307A GLU* 2.9 32.2 + - + +
308A ASN* 3.3 35.2 + - - +
310A LYS* 1.3 74.1 - - + +
312A PHE* 1.3 63.8 + - - +
314A SER* 3.1 23.9 + - - +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.1 11.0 - - + -
135A PHE* 5.3 0.2 - - + -
166A PRO* 3.3 41.2 - - + +
167A ILE 3.6 14.1 - - - -
168A ILE* 3.8 24.5 - - + -
193A GLY 4.1 7.0 - - - -
194A LYS* 3.1 28.5 + - - +
195A ILE 3.7 1.8 - - - -
196A LEU* 3.6 27.1 - - + -
218A PHE* 3.5 26.2 - + + -
252A MET* 3.6 10.5 - - + -
308A ASN 2.8 18.0 + - - +
309A PRO 3.4 4.7 - - - +
311A LYS* 1.3 78.5 - - - +
313A PHE* 1.3 81.4 + + - +
314A SER 3.4 0.2 - - - -
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.3 13.3 + - - -
3A ILE* 3.2 48.4 - - + +
13A SER* 4.4 6.4 - - - -
16A ILE* 5.2 11.7 - - + -
19A THR* 5.6 0.4 - - + -
21A ILE* 3.8 15.5 - - + -
65A VAL* 3.8 31.2 - - + -
91A VAL* 4.1 17.7 - - + -
134A GLY 3.6 20.9 - - - -
135A PHE* 4.3 3.8 - + - -
166A PRO* 3.7 16.6 - - + -
194A LYS* 3.7 5.7 + - - +
309A PRO* 3.0 30.2 + - + +
310A LYS* 3.6 3.6 - - - +
312A PHE* 1.3 96.2 - + - +
314A SER* 1.3 59.1 + - - +
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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