Contacts of the strand formed by residues 269 - 274 (chain A) in PDB entry 3EWS
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 GLN 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A MET* 3.0 39.0 + - - +
131A PRO* 3.8 22.0 - - + +
132A GLN 2.7 37.4 + - - +
133A ASN* 3.6 4.0 - - - -
151A ALA* 4.8 3.1 - - - +
155A GLN* 4.6 7.6 + - - +
237A LYS 3.0 16.4 + - - +
238A VAL* 3.7 15.4 - - + +
239A PHE* 2.9 30.5 + - - +
267A ASN 3.5 3.0 + - - -
268A CYS* 1.3 69.8 - - - +
270A MET* 1.3 59.2 + - - +
271A LEU* 3.4 28.7 + - + +
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Residues in contact with MET 270 (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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133A ASN* 2.7 34.3 + - - +
134A LEU 2.9 25.6 + - - +
239A PHE* 3.6 11.9 - - + -
261A GLN* 3.5 26.0 - - - +
264A LEU* 4.1 24.2 - - + -
265A PRO 3.9 18.4 - - - +
266A ARG* 4.5 9.2 - - - +
268A CYS* 3.3 20.9 - - + +
269A GLN* 1.3 73.6 - - - +
271A LEU* 1.3 63.8 + - - +
288A VAL 4.4 1.8 - - - +
289A VAL* 3.6 20.6 - - + +
290A PRO* 4.0 11.7 - - + -
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Residues in contact with LEU 271 (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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126A MET* 3.0 32.3 - - + -
134A LEU* 3.4 20.0 - - + +
148A PHE* 4.5 0.4 - - + -
151A ALA* 4.3 6.7 - - + -
238A VAL* 3.8 26.0 - - + -
239A PHE* 2.9 10.1 + - - +
240A VAL* 3.3 13.3 - - + +
241A LEU* 2.7 32.9 + - - +
269A GLN* 3.4 33.9 - - + +
270A MET* 1.3 84.2 - - - +
272A LEU* 1.3 55.6 + - - +
273A PHE* 3.5 18.8 - - + -
289A VAL* 4.6 1.6 - - - -
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Residues in contact with LEU 272 (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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134A LEU 2.9 8.0 + - - +
135A ILE* 3.4 12.8 - - + -
136A ALA 2.9 24.8 + - - +
241A LEU* 3.4 32.5 - - + +
244A ALA* 3.8 25.1 - - + -
271A LEU* 1.3 74.7 - - - +
273A PHE* 1.3 72.1 + - - +
274A SER* 4.5 4.9 - - - -
277A PHE* 5.2 2.0 - - + -
281A VAL* 5.5 0.2 - - + -
284A PHE* 4.0 10.5 - - + -
285A ALA* 3.8 38.6 - - + -
288A VAL* 4.6 2.2 - - + -
289A VAL* 3.6 20.1 - - + +
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Residues in contact with PHE 273 (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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122A ALA* 5.3 2.9 - - + -
126A MET* 3.3 26.7 - - + -
134A LEU* 4.1 8.7 - - + -
136A ALA* 3.2 29.4 - - + -
144A LYS* 3.8 42.0 - - + -
147A ALA* 4.8 5.8 - - + -
148A PHE* 3.5 30.1 - + + -
240A VAL* 4.3 6.7 - - + -
241A LEU 3.0 6.3 + - - +
242A ASP* 4.3 14.1 - - - +
243A GLU 3.5 6.1 + - - -
244A ALA* 3.0 25.1 + - - +
271A LEU* 3.5 26.2 - - + -
272A LEU* 1.3 80.3 - - - +
274A SER* 1.3 63.9 + - - +
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Residues in contact with SER 274 (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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136A ALA 3.0 8.3 + - - +
137A GLN* 3.1 6.3 - - - -
138A SER 2.8 25.5 + - - +
144A LYS* 3.7 7.6 - - - +
243A GLU* 5.0 1.3 - - - +
244A ALA* 3.8 11.4 - - - -
245A ASP* 3.4 15.9 + - - +
272A LEU* 4.5 5.2 - - - -
273A PHE* 1.3 78.6 - - - +
275A ALA* 1.3 61.3 + - - +
276A THR 2.7 25.6 + - - -
277A PHE* 4.6 7.4 - - - -
281A VAL* 3.3 15.0 - - - +
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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