Contacts of the strand formed by residues 237 - 243 (chain A) in PDB entry 4ERH
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 SER 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU* 5.2 0.2 + - - -
231A LEU* 4.4 1.2 - - - +
235A ASP 4.7 2.4 + - - -
236A GLY* 1.3 76.3 - - - -
238A VAL* 1.3 68.7 + - - +
239A VAL* 5.5 6.9 - - - +
277A LYS* 3.4 9.9 - - - -
316A GLU 3.6 1.1 - - - +
317A VAL* 3.4 4.7 - - - +
318A LYS* 3.0 53.9 + - - +
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Residues in contact with VAL 238 (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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228A LEU* 4.4 9.0 - - + +
231A LEU* 3.6 25.6 - - + -
237A SER* 1.3 81.5 - - - +
239A VAL* 1.3 68.1 + - - +
240A VAL* 4.5 3.6 - - + -
268A LEU* 5.0 4.5 - - + -
273A ILE* 4.4 12.6 - - + -
277A LYS 2.9 9.8 + - - +
278A ILE* 3.2 31.7 - - + -
279A SER* 3.1 24.4 + - - -
315A ILE* 4.0 23.6 - - + -
316A GLU 3.4 3.4 - - - +
317A VAL* 4.3 10.1 - - + -
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Residues in contact with VAL 239 (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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237A SER* 5.5 7.0 - - - +
238A VAL* 1.3 78.7 - - - +
240A VAL* 1.3 64.3 + - - +
241A LEU* 3.8 29.4 + - + +
279A SER* 3.6 13.9 - - - +
281A ARG* 3.9 32.5 - - - +
314A GLU 3.8 0.7 - - - +
315A ILE* 3.3 5.2 - - - +
316A GLU* 2.8 56.5 + - + +
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Residues in contact with VAL 240 (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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238A VAL* 4.5 3.4 - - + -
239A VAL* 1.3 75.1 - - - +
241A LEU* 1.3 62.4 + - - +
261A ALA* 3.3 35.8 - - - +
264A VAL* 3.9 19.7 - - + -
265A VAL* 3.7 22.4 - - + -
268A LEU* 4.6 1.3 - - + -
278A ILE* 4.3 15.0 - - + -
279A SER 2.9 9.3 + - - +
280A ALA* 3.5 0.7 - - - -
281A ARG* 2.9 27.7 + - - +
313A VAL* 3.7 20.9 - - + -
314A GLU 3.5 2.7 - - - +
315A ILE* 4.0 11.2 - - + -
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Residues in contact with LEU 241 (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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239A VAL* 3.8 18.6 - - + +
240A VAL* 1.3 74.1 - - - +
242A GLY* 1.3 59.8 + - - +
243A PHE* 3.6 28.7 - - + -
261A ALA* 4.3 1.1 - - - -
281A ARG* 3.5 35.4 - - + +
283A MSE 4.0 19.7 - - + -
313A VAL* 3.2 7.3 - - - -
314A GLU* 2.6 52.8 + - + +
316A GLU* 3.9 28.9 - - + +
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Residues in contact with GLY 242 (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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241A LEU* 1.3 71.7 - - - +
243A PHE* 1.3 59.4 + - - -
257A SER* 3.5 26.3 + - - -
260A ARG* 5.6 0.9 - - - -
261A ALA* 3.7 7.5 - - - +
281A ARG 2.9 13.3 + - - -
283A MSE 2.8 32.7 + - - +
284A GLY 3.4 2.8 + - - -
312A ARG 4.2 1.8 - - - -
313A VAL* 4.6 9.4 - - - -
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Residues in contact with PHE 243 (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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202A SER* 4.0 4.0 + - - -
241A LEU* 3.6 32.1 - - + -
242A GLY* 1.3 74.6 - - - -
244A THR* 1.3 61.1 + - - +
250A ASP* 3.8 7.6 - - - +
257A SER* 4.2 5.8 - - - -
260A ARG* 5.5 1.9 + - - -
283A MSE 3.4 33.4 - - + -
284A GLY 3.4 7.0 - - - +
286A SER 3.4 18.2 - - - -
287A ASN* 4.1 17.7 - - + -
310A ASP 3.5 2.9 - - - +
312A ARG* 2.9 81.5 + - + +
313A VAL* 5.8 0.2 - - - +
314A GLU* 3.8 23.3 - - + -
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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