Contacts of the strand formed by residues 241 - 247 (chain E) in PDB entry 5HMG
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 ASP 241 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169E PRO* 3.6 2.1 - - - +
170E ASN 2.8 23.9 + - - -
206E THR* 3.4 13.6 + - - -
207E ARG* 2.9 49.3 + - - +
208E ARG* 3.7 23.1 + - - +
237E VAL* 3.8 10.7 - - + -
238E LYS* 3.1 27.2 + - + +
239E PRO 3.2 1.6 + - - +
240E GLY* 1.3 79.9 - - - +
242E VAL* 1.3 76.8 + - - +
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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
----------------------------------------------------------
221C PRO* 4.2 12.2 - - + +
167E THR* 3.1 28.3 - - + +
168E MET 3.9 2.5 - - - -
169E PRO* 4.0 20.2 - - + -
206E THR* 3.1 29.3 - - - +
207E ARG* 3.6 29.2 - - - +
237E VAL* 4.1 4.0 - - - -
240E GLY 4.7 0.4 - - - +
241E ASP* 1.3 86.4 + - - +
243E LEU* 1.3 60.1 + - - +
244E VAL* 4.5 0.7 - - + -
2I NAG 3.8 24.9 - - + -
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Residues in contact with LEU 243 (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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125E PHE* 4.4 6.1 - - + -
167E THR* 3.1 7.6 + - - -
168E MET* 2.9 41.7 + - + +
178E TYR* 3.7 40.8 - - + -
180E TRP* 6.3 0.4 - - + -
204E VAL* 3.5 29.4 - - + -
205E SER 3.5 8.1 - - - +
206E THR* 4.3 0.9 - - + -
235E THR* 3.9 18.8 - - + -
237E VAL* 4.0 13.6 - - + +
242E VAL* 1.3 73.7 - - - +
244E VAL* 1.3 60.3 + - - +
245E ILE* 3.8 29.2 - - + -
254E PRO* 5.0 0.2 - - + -
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Residues in contact with VAL 244 (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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219C SER* 3.3 30.7 - - - +
220C ARG 4.6 0.7 - - - -
221C PRO* 3.6 35.0 - - + -
165E ASN* 4.3 13.2 - - - +
166E VAL 3.3 9.0 - - - +
167E THR* 3.4 24.2 - - - +
203E THR 3.8 0.3 - - - +
204E VAL* 3.5 2.9 - - - +
205E SER* 2.9 33.8 + - - +
242E VAL* 4.5 1.8 - - + -
243E LEU* 1.3 71.7 - - - +
245E ILE* 1.3 66.0 + - - +
1I NAG 4.2 14.1 - - - +
2I NAG 4.8 0.9 - - + -
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Residues in contact with ILE 245 (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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125E PHE* 4.1 14.4 - - + -
127E TRP* 4.2 7.9 - - + -
164E LEU* 3.9 2.4 - - + +
165E ASN* 3.5 1.7 + - - -
166E VAL* 2.9 40.6 + - + +
180E TRP* 5.9 1.3 - - + -
202E VAL* 4.9 0.9 - - + -
203E THR 3.7 2.5 - - - +
204E VAL* 4.1 21.5 - - + +
243E LEU* 3.8 26.9 - - + -
244E VAL* 1.3 76.6 - - - +
246E ASN* 1.3 62.3 + - - +
251E LEU* 3.9 34.8 - - + -
254E PRO* 3.5 35.7 - - + -
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Residues in contact with ASN 246 (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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218C GLY* 4.0 8.6 - - - -
219C SER* 3.5 33.0 + - - +
163E VAL* 3.9 17.0 - - - +
164E LEU 3.1 11.0 + - - +
165E ASN* 2.9 28.4 + - - +
201E ARG* 4.0 15.9 + - - -
202E VAL* 3.7 0.7 - - - +
203E THR* 2.8 41.5 + - - +
244E VAL* 4.0 0.6 - - + -
245E ILE* 1.3 74.1 - - - +
247E SER* 1.3 67.4 + - - +
1I NAG 6.0 0.4 - - - +
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Residues in contact with SER 247 (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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161E TYR* 4.2 1.8 + - - -
162E PRO 3.7 0.9 - - - +
163E VAL* 3.4 2.3 - - - -
164E LEU* 2.7 45.8 + - - +
201E ARG* 2.9 16.7 + - - +
202E VAL* 3.8 3.9 - - - +
246E ASN* 1.3 81.6 + - - +
248E ASN* 1.3 56.6 + - - +
249E GLY* 2.9 25.8 + - - -
251E LEU* 3.7 33.6 - - - +
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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