Contacts of the strand formed by residues 243 - 251 (chain A) in PDB entry 3LEZ
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 THR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE* 3.9 38.8 - - + -
241A GLY 3.8 4.4 + - - -
242A TRP* 1.3 74.1 - - - +
244A VAL* 1.3 64.2 + - - +
262A ILE* 3.5 2.9 - - - +
263A TRP* 2.8 56.8 + - + -
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Residues in contact with VAL 244 (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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225A ILE* 3.4 16.9 - - - +
234A ILE* 4.2 17.5 - - + -
235A ARG* 3.0 52.3 + - + +
238A VAL* 3.6 40.2 - - + -
242A TRP 4.0 3.5 + - - +
243A THR* 1.3 81.5 - - - +
245A GLY* 1.3 75.3 + - - +
246A ASP* 4.3 4.5 - - + -
261A ILE 3.4 7.2 - - - +
262A ILE* 4.3 8.3 - - + -
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Residues in contact with GLY 245 (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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224A LEU* 3.3 28.5 - - - -
225A ILE* 3.7 7.0 - - - -
244A VAL* 1.3 75.8 - - - +
246A ASP* 1.3 62.2 + - - +
260A GLY* 3.0 3.7 - - - -
261A ILE* 2.9 35.6 + - - +
263A TRP* 4.0 7.4 - - - -
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Residues in contact with ASP 246 (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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140A ILE* 4.7 1.0 - - - +
224A LEU* 3.1 23.8 + - - +
227A ASN* 3.0 38.1 + - - +
230A GLY* 3.7 4.7 - - - -
234A ILE* 4.8 2.9 - - + -
235A ARG* 2.9 38.3 + - - -
244A VAL* 4.3 9.2 - - + -
245A GLY* 1.3 75.7 - - - +
247A LYS* 1.3 60.2 + - - +
248A THR* 3.4 8.1 - - - +
258A ASP* 2.5 32.2 - - - +
259A ILE 3.1 14.1 - - - +
260A GLY* 4.0 1.3 - - - -
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Residues in contact with LYS 247 (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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85A SER* 3.5 20.3 - - - +
86A THR* 3.5 10.0 - - - +
88A LYS* 4.0 4.3 - - - -
89A PRO* 3.5 38.1 - - + -
139A ALA 3.4 22.7 - - - -
140A ILE* 3.5 25.4 + - + +
143A SER* 2.9 26.5 + - - -
224A LEU* 4.2 4.5 - - + +
227A ASN* 4.3 1.6 - - - +
229A THR* 4.6 2.0 + - - -
246A ASP* 1.3 74.7 - - - +
248A THR* 1.3 86.8 + - - +
258A ASP* 3.2 5.3 - - - -
259A ILE* 2.8 35.2 + - + -
305A EPE 3.1 7.9 + - - -
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Residues in contact with THR 248 (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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85A SER* 3.5 7.3 - - - -
86A THR* 3.8 3.1 - - - -
229A THR* 2.7 29.2 + - - +
230A GLY* 3.7 15.3 - - - -
233A LEU* 4.0 11.0 - - + -
246A ASP* 3.4 17.7 - - - +
247A LYS* 1.3 101.1 + - - +
249A GLY* 1.3 60.5 + - - +
256A ARG* 4.0 4.9 - - - +
257A ASN 3.4 7.4 - - - -
258A ASP* 3.5 9.9 - - - +
305A EPE 2.5 31.6 + - - -
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Residues in contact with GLY 249 (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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84A THR* 3.3 16.6 - - - -
85A SER 4.0 5.6 - - - -
86A THR* 3.8 5.4 - - - +
248A THR* 1.3 77.0 - - - +
250A ALA* 1.3 60.8 + - - -
256A ARG* 3.1 12.5 + - - -
257A ASN* 2.9 33.9 + - - -
305A EPE 3.4 9.2 - - - -
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Residues in contact with ALA 250 (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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84A THR* 3.2 18.2 + - - -
85A SER* 4.7 1.1 + - - +
183A ASN* 3.7 7.8 + - - -
249A GLY* 1.3 75.4 - - - +
251A GLY* 1.3 58.9 + - - +
255A THR 3.2 8.3 - - - +
256A ARG* 3.8 13.0 - - - +
286A TYR* 3.9 25.4 - - + +
305A EPE 3.7 24.6 + - - +
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Residues in contact with GLY 251 (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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84A THR* 3.9 9.9 - - - -
183A ASN* 3.8 13.5 - - - -
250A ALA* 1.3 76.4 - - - +
252A GLY* 1.3 69.3 + - - +
254A GLY* 3.8 4.3 + - - -
255A THR* 3.1 20.0 + - - +
284A ALA 5.5 0.2 - - - +
286A TYR* 5.5 2.3 - - - -
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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