Contacts of the strand formed by residues 234 - 240 (chain E) in PDB entry 3K75
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 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E LEU* 4.0 3.4 - - - -
229E SER* 4.0 1.2 - - - +
231E GLY* 2.7 36.3 + - - -
233E THR* 1.3 86.1 + - - +
235E PHE* 1.3 62.7 + - - +
236E MET* 3.4 36.0 + - + +
256E ASP* 3.5 13.5 + - - +
257E ILE 3.4 4.5 - - - +
258E ARG* 3.3 61.7 - - + +
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Residues in contact with PHE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 4.0 6.0 - - + +
215E VAL* 3.6 35.7 - - + -
219E GLN* 5.7 0.4 - - - -
224E ILE* 3.6 39.5 - - + -
226E ASP 4.3 0.2 - - - -
227E THR* 3.6 30.5 - - + -
229E SER 3.6 8.1 - - - -
230E LYS* 3.9 16.4 - - + -
231E GLY 4.5 0.7 - - - +
234E LYS* 1.3 74.6 - - - +
236E MET* 1.3 61.2 + - - +
237E GLY* 3.7 26.7 - - - -
255E ILE* 4.3 7.9 - - + -
256E ASP* 3.6 4.0 - - - -
257E ILE* 2.9 51.4 + - + +
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Residues in contact with MET 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E HIS* 4.0 21.5 - - + +
228E LEU* 2.9 14.2 + - + -
229E SER* 2.7 50.4 + - - +
234E LYS* 3.4 39.2 - - + +
235E PHE* 1.3 80.4 - - - +
237E GLY* 1.3 57.8 + - - +
254E ARG* 3.1 30.1 - - - +
255E ILE 4.0 3.1 - - - -
256E ASP* 3.9 6.1 - - - +
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Residues in contact with GLY 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASP 3.5 9.9 - - - -
228E LEU* 3.7 11.1 - - - +
235E PHE* 3.7 12.2 - - - -
236E MET* 1.3 75.0 - - - +
238E VAL* 1.3 65.1 + - - +
254E ARG* 3.1 13.8 + - - +
255E ILE* 3.0 35.3 + - - -
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Residues in contact with VAL 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ILE* 3.9 24.0 - - + -
142E TYR* 3.9 13.5 - - + -
146E PHE* 3.6 28.9 - - + -
224E ILE* 3.0 12.0 - - - +
225E THR* 2.7 43.2 + - - +
226E ASP* 2.8 21.5 + - + +
228E LEU* 4.3 5.2 - - + -
237E GLY* 1.3 78.1 - - - +
239E CYS* 1.3 59.1 + - - +
252E HIS* 3.9 13.7 - - + -
253E ARG 3.5 11.4 - - - +
255E ILE* 4.1 1.7 - - - +
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Residues in contact with CYS 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E MET* 5.1 9.4 - - - -
223E PHE* 2.8 55.9 - - + +
224E ILE* 3.9 3.1 - - + -
225E THR* 3.9 5.6 - - - +
238E VAL* 1.3 75.9 - - - +
240E GLN* 1.3 59.2 + - - +
252E HIS* 3.8 1.6 - - - -
253E ARG* 3.0 46.8 + - - +
254E ARG 5.2 0.2 - - - -
255E ILE* 4.0 24.2 - - + -
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Residues in contact with GLN 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E MET* 6.1 0.2 - - - -
222E ARG 4.2 4.7 - - - +
223E PHE* 2.7 36.5 + - - +
225E THR* 3.6 16.5 - - + +
239E CYS* 1.3 76.1 - - - +
241E LEU* 1.3 75.5 + - - +
242E PRO* 3.8 2.1 - - - +
249E GLU* 3.4 25.7 - - - +
250E TYR 2.5 30.6 + - - +
251E PRO 3.6 9.4 - - - +
252E HIS* 3.7 31.1 + - - +
253E ARG* 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