Contacts of the strand formed by residues 236 - 242 (chain E) 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 VAL 236 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E VAL* 3.8 24.0 - - + -
229E SER 3.4 3.1 - - - -
230E VAL* 4.5 4.9 - - + -
234E GLY 4.3 2.5 - - - +
235E VAL* 1.3 81.8 - - - +
237E THR* 1.3 64.4 + - - +
238E CYS 3.5 23.1 - - - +
239E MET* 4.5 10.5 - - + -
256E MET* 4.4 16.2 - - + +
260E LYS* 5.8 1.8 - - + -
232F GLY* 4.2 7.2 + - - -
233F LEU* 4.3 1.6 - - - +
234F THR* 4.1 24.0 - - - +
237F TRP* 2.9 38.1 + - + +
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Residues in contact with THR 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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111E ARG 4.5 7.0 - - - +
112E ILE* 3.8 28.3 - - - +
114E ASN 6.2 0.2 - - - -
115E ASN* 3.6 19.6 + - + +
198E PRO* 4.6 3.4 - - - +
229E SER* 2.9 20.9 + - - -
231E THR* 4.3 15.6 - - - +
235E VAL* 4.0 5.1 - - - +
236E VAL* 1.3 76.1 - - - +
238E CYS* 1.3 59.8 + - + +
229F GLY* 3.3 38.0 + - - +
231F GLY* 5.6 5.0 - - - -
237F TRP* 3.2 16.5 - - - -
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Residues in contact with CYS 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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111E ARG* 3.4 38.6 - - + +
112E ILE* 3.7 27.6 - - + -
227E LEU* 4.4 1.8 - - - -
228E VAL* 3.5 1.4 - - - -
229E SER* 3.0 28.2 + - - -
236E VAL* 3.5 9.0 - - - +
237E THR* 1.3 83.1 - - + +
239E MET* 1.3 71.6 + - - +
240E ARG* 4.2 16.4 - - - -
227F GLY 3.6 6.1 - - - +
228F SER* 4.6 4.5 - - - +
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Residues in contact with MET 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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226E LEU* 4.2 16.6 - - + -
227E LEU 3.4 5.6 - - - +
228E VAL* 4.7 4.9 - - + +
236E VAL* 4.5 6.5 - - + -
238E CYS* 1.3 80.5 - - - +
240E ARG* 1.3 58.9 + - - +
252E ILE* 4.6 10.3 - - - -
256E MET* 3.1 33.9 - - + -
211F LEU* 3.9 27.6 - - + -
225F LEU* 3.3 39.9 - - + +
226F LEU 3.6 0.6 - - - +
227F GLY 3.5 18.0 + - - -
237F TRP* 4.0 18.8 - - + -
241F VAL* 4.0 17.7 - - + -
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Residues in contact with ARG 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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104E GLU* 3.5 30.5 + - - +
108E THR* 4.4 20.0 - - - +
111E ARG* 5.4 4.9 - - - +
149E PHE* 5.4 0.6 - - - -
226E LEU* 3.2 9.6 - - - +
227E LEU* 2.9 56.1 + - + +
238E CYS* 4.2 10.5 - - - -
239E MET* 1.3 74.6 - - - +
241E LYS* 1.3 73.3 + - - +
242E VAL* 3.5 24.7 - - - +
121F GLU* 5.3 11.6 + - - +
124F LEU* 4.4 11.5 - - - +
125F ALA* 5.4 0.8 - - - +
128F GLU* 3.2 30.4 + - - -
225F LEU* 4.4 4.7 - - - +
226F LEU* 3.9 27.0 - - + +
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Residues in contact with LYS 241 (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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224E ALA* 4.0 19.3 - - - +
225E SER 3.7 7.9 - - - +
226E LEU* 4.3 3.1 - - + -
240E ARG* 1.3 85.4 + - - +
242E VAL* 1.3 66.2 + - - +
243E GLY 3.6 14.5 + - - +
245E GLY 2.6 30.1 + - - -
247E LEU* 3.8 32.5 - - + -
128F GLU* 2.9 19.3 + - + +
222F VAL* 5.5 2.0 - - + -
223F ALA* 2.8 26.2 + - - +
224F GLY* 4.1 8.1 - - - -
225F LEU* 3.7 34.5 + - + +
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Residues in contact with VAL 242 (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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104E GLU* 4.1 9.9 - - - +
149E PHE* 5.4 7.0 - - + -
202E THR* 5.8 0.4 - - + -
224E ALA* 3.7 0.3 - - - -
225E SER* 2.7 70.6 + - - +
227E LEU* 4.4 16.4 - - + -
240E ARG* 3.5 21.1 - - - +
241E LYS* 1.3 79.1 - - - +
243E GLY* 1.3 61.8 + - - +
128F GLU* 3.3 20.9 - - - +
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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