Contacts of the strand formed by residues 241 - 251 (chain A) in PDB entry 2B4M
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 TYR 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.8 24.7 - - + -
103A THR 3.6 12.3 - - - +
105A LYS* 4.1 11.7 - - - +
210A TRP* 3.6 28.4 - + + -
213A ILE* 3.9 14.6 - - + -
214A ALA* 5.1 2.9 - - - -
226A LEU* 4.4 9.6 - - + +
234A ALA* 3.9 27.2 + - - +
237A TYR* 3.0 31.6 - - + -
238A LYS 4.4 10.5 - - - +
239A GLY 3.7 1.2 - - - -
240A LYS* 1.3 79.9 + - - +
242A ASP* 1.3 79.0 + - - +
243A ASP* 3.9 18.5 + - + +
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Residues in contact with ASP 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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102A ILE* 3.1 7.8 - - - +
103A THR* 2.8 51.4 + - - +
104A ARG 3.6 4.8 - - - +
105A LYS* 3.9 12.9 + - - +
106A GLY 3.3 23.6 + - - -
107A PHE 4.3 2.4 + - - -
108A SER* 4.8 3.8 + - - -
109A LYS* 4.1 11.2 + - - -
241A TYR* 1.3 81.8 - - - +
243A ASP* 1.3 58.6 + - - +
244A ILE* 3.8 14.3 + - + -
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Residues in contact with ASP 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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100A HIS* 2.5 39.1 + - - +
101A THR 3.8 4.3 - - - +
102A ILE* 4.0 7.2 - - - -
226A LEU* 4.1 8.1 - - - +
241A TYR* 3.9 16.8 + - + +
242A ASP* 1.3 70.3 - - - +
244A ILE* 1.3 61.1 + - - +
245A GLY 3.3 18.2 + - - +
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Residues in contact with ILE 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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101A THR* 3.0 20.8 + - + +
103A THR* 3.6 30.1 - - + +
108A SER* 4.0 15.7 - - - +
115A ALA* 3.9 32.3 - - + +
118A LEU* 3.9 16.6 - - + -
119A SER* 3.1 27.4 - - - +
242A ASP* 3.9 22.2 - - + -
243A ASP* 1.3 76.4 - - - +
245A GLY* 1.3 57.3 + - - +
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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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100A HIS* 3.4 1.9 - - - +
101A THR* 2.7 39.9 + - - -
118A LEU 5.1 0.2 - - - -
119A SER* 4.4 11.9 - - - -
121A PHE 5.9 0.9 - - - -
243A ASP* 3.3 13.5 + - - +
244A ILE* 1.3 80.9 - - - +
246A THR* 1.3 59.8 + - - -
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Residues in contact with THR 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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98A GLU* 3.3 20.1 + - + +
99A ILE 3.5 11.7 - - - +
100A HIS* 3.1 24.6 + - - -
119A SER 5.4 0.6 + - - +
121A PHE 3.6 9.3 - - - +
122A LYS* 3.7 15.6 - - - +
245A GLY* 1.3 69.5 - - - -
247A SER* 1.3 62.9 + - - +
248A MET 3.6 21.1 - - - +
249A THR* 4.2 9.2 - - + -
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Residues in contact with SER 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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99A ILE* 2.8 33.2 + - - +
100A HIS* 4.3 2.0 + - - +
101A THR* 4.1 8.8 + - - -
121A PHE* 3.5 48.4 - - - -
122A LYS* 3.9 2.1 - - - +
123A TRP* 3.2 30.8 + - - +
184A SER* 6.0 0.3 - - - -
222A LEU* 5.0 2.4 + - - +
245A GLY 4.1 1.4 - - - -
246A THR* 1.3 73.0 - - - +
248A MET* 1.3 63.7 + - - +
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Residues in contact with MET 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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74A PRO* 4.4 10.8 - - - -
98A GLU* 3.1 7.8 - - - +
99A ILE* 2.7 52.3 + - + -
123A TRP* 3.6 33.0 - - + +
124A THR* 3.4 25.4 - - - +
125A GLN* 3.6 33.0 - - + +
128A MET* 3.8 21.3 - - + -
246A THR* 3.5 4.0 - - - +
247A SER* 1.3 82.1 + - - +
249A THR* 1.3 75.9 + - - +
251A VAL* 4.5 1.8 - - + -
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Residues in contact with THR 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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97A GLU 3.9 0.7 - - - -
98A GLU* 3.9 20.6 - - - +
125A GLN* 4.8 3.8 + - - +
246A THR* 4.2 14.8 - - + -
248A MET* 1.3 92.8 - - - +
250A GLY* 1.3 68.4 + - - +
251A VAL* 3.1 5.6 + - - +
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Residues in contact with GLY 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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96A ALA* 5.6 3.4 - - - +
97A GLU 3.5 7.1 + - - -
125A GLN* 3.6 11.8 + - - -
249A THR* 1.3 77.9 + - - +
251A VAL* 1.3 64.2 + - - +
252A LYS* 3.5 18.1 + - - +
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Residues in contact with VAL 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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74A PRO* 3.5 25.8 - - + -
96A ALA 5.6 0.2 + - - -
97A GLU* 3.4 51.5 + - + +
98A GLU* 4.1 2.5 - - - -
99A ILE* 4.0 25.6 - - + -
125A GLN* 4.0 2.0 - - - +
225A TRP* 3.4 30.1 - - + -
248A MET* 4.2 3.6 - - + +
249A THR 3.1 11.8 + - - +
250A GLY* 1.3 72.7 - - - +
252A LYS* 1.3 62.6 + - - +
253A MET* 5.2 0.7 - - - -
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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