Contacts of the strand formed by residues 231 - 236 (chain C) in PDB entry 6D6Q
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 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C MET* 3.0 10.9 - - - +
227C ASP* 2.8 40.6 + - + -
229C GLU* 3.3 34.1 + - + +
230C GLY* 1.3 83.1 - - - +
232C LEU* 1.3 67.4 + - - +
178D ARG* 5.3 9.7 - - - +
200D LEU* 4.1 27.3 - - + +
201D TYR 3.3 16.4 - - - +
202D SER* 4.8 6.1 - - - +
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 3.7 29.6 - - + -
225C VAL 3.3 12.6 - - - +
226C MET* 3.3 27.1 - - + -
227C ASP* 5.2 1.6 - - - -
230C GLY 5.3 0.4 - - - +
231C LYS* 1.3 77.4 - - - +
233C CYS* 1.3 60.1 + - - +
234C CYS 4.6 1.6 - - - +
235C LEU* 5.1 1.1 - - + -
252C MET* 3.5 26.9 - - + -
200D LEU* 3.1 8.7 - - - +
201D TYR* 2.9 72.6 + - + +
202D SER 4.7 0.2 - - - -
203D ASP* 4.7 8.7 - - + +
206D LEU* 4.6 4.5 - - + -
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Residues in contact with CYS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP 4.5 0.2 - - - -
112C VAL* 3.8 23.8 - - - -
115C ASN* 3.5 15.0 + - - +
116C SER* 3.2 45.5 - - - +
193C PRO* 5.1 0.9 - - + -
225C VAL* 3.1 25.2 + - + -
227C ASP* 5.0 4.9 - - + +
231C LYS 4.5 0.2 + - - -
232C LEU* 1.3 73.2 - - - +
234C CYS* 1.3 61.4 + - - +
197D THR* 4.1 4.8 - - - +
199D GLY 3.1 20.2 - - - +
200D LEU* 4.4 3.4 - - + -
201D TYR* 5.0 0.9 - - - -
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Residues in contact with CYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 3.4 33.0 - - + -
111C ASP* 5.1 8.7 - - + +
112C VAL* 4.0 9.4 - - + -
224C ILE* 3.4 6.4 - - - +
225C VAL* 2.9 59.8 + - - +
232C LEU* 3.7 2.0 - - - +
233C CYS* 1.3 83.7 - - - +
235C LEU* 1.3 59.7 + - - +
236C HIS* 4.9 1.8 - - + +
197D THR* 3.4 14.8 - - + +
201D TYR* 4.5 2.9 - - - -
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Residues in contact with LEU 235 (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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222C LEU* 4.3 12.6 - - + -
223C THR 3.6 6.5 - - - +
224C ILE* 3.9 28.0 - - + -
232C LEU* 5.1 0.7 - - + -
234C CYS* 1.3 72.4 - - - +
236C HIS* 1.3 54.5 + - - +
237C LYS* 3.3 4.2 + - + -
248C LEU* 4.2 22.7 - - + -
183D PHE* 4.9 2.2 - - + -
192D LEU* 5.3 4.5 - - + -
195D SER* 2.8 54.8 + - - +
196D SER* 4.5 2.6 - - - -
197D THR* 3.3 11.9 - - + +
201D TYR* 3.2 23.8 - - - +
206D LEU* 4.0 22.4 - - + -
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Residues in contact with HIS 236 (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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104C VAL* 4.5 21.6 - - + +
108C PHE* 3.9 32.1 - + + -
149C LEU* 4.5 17.9 - - + +
221C THR* 6.5 0.4 - - + -
222C LEU* 3.5 3.3 - - - +
223C THR* 2.8 49.6 + - - +
234C CYS* 3.8 1.3 - - + -
235C LEU* 1.3 70.3 - - - +
237C LYS* 1.3 59.7 + - - +
238C PRO* 3.4 36.6 - - + +
93D SER* 4.8 4.0 - - - -
96D ARG* 5.9 1.8 + - - -
97D LEU* 4.5 21.8 - - + +
195D SER 4.2 1.7 + - - -
196D SER* 6.0 0.2 - - - +
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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