Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 4BU2
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A TYR 4.2 1.3 - - - -
168A ILE* 3.3 2.6 - - - -
169A THR 2.8 30.0 + - - -
189A GLN* 3.0 17.8 + - - -
191A GLU 3.4 3.6 - - - -
193A GLU 3.5 15.3 - - - -
194A LYS* 3.1 36.3 + - - +
244A THR* 3.6 10.4 - - - +
250A HIS* 1.3 75.8 - - - +
252A THR* 1.3 72.3 + - - +
253A HIS* 4.6 1.7 + - - -
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Residues in contact with THR 252 (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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81A PHE* 3.9 20.0 - - + +
82A LYS 5.4 0.2 - - - -
83A LEU* 4.9 0.3 - - - +
166A VAL* 4.4 9.0 - - + -
167A TYR 3.3 4.0 - - - -
168A ILE* 3.6 21.1 - - + +
189A GLN* 3.7 2.0 + - - -
190A LEU* 2.8 36.0 + - + -
191A GLU* 2.8 41.4 + - - +
250A HIS* 3.1 17.5 + - - -
251A SER* 1.3 82.5 + - - +
253A HIS* 1.3 62.5 + - - +
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Residues in contact with HIS 253 (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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166A VAL* 3.4 5.0 - - - +
167A TYR* 2.8 57.6 + + + +
187A ILE* 3.5 20.6 - - + -
188A LEU 3.2 18.2 - - - +
189A GLN* 3.6 19.8 + - - +
190A LEU* 4.0 5.6 - - - -
194A LYS* 4.3 12.0 + - + +
196A TRP* 4.0 12.7 + + - -
251A SER* 4.6 2.6 + - - -
252A THR* 1.3 75.3 - - - +
254A VAL* 1.3 61.0 + - - +
255A THR* 3.4 15.9 - - - -
701A AKG 3.0 41.7 + - + -
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Residues in contact with VAL 254 (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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80A LEU* 5.3 0.4 - - + -
140A PRO* 4.3 3.1 - - + -
147A LEU* 4.4 19.1 - - + -
164A SER* 3.7 26.0 - - - +
165A ASN 3.2 15.0 - - - +
166A VAL* 3.8 17.7 - - + -
186A PHE 3.7 1.2 - - - +
187A ILE* 3.6 1.9 - - - -
188A LEU* 3.1 44.3 + - + -
190A LEU* 4.0 17.2 - - + +
253A HIS* 1.3 77.0 - - - +
255A THR* 1.3 62.7 + - - +
256A ILE* 4.7 10.3 - - + -
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Residues in contact with THR 255 (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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164A SER* 3.1 5.1 - - - -
165A ASN* 2.7 30.6 + - - -
167A TYR* 3.4 9.4 - - - -
185A VAL* 3.7 28.5 - - + -
186A PHE 4.0 1.6 - - - -
187A ILE* 3.7 8.1 - - + +
253A HIS* 3.4 11.1 + - - -
254A VAL* 1.3 72.8 - - - +
256A ILE* 1.3 63.0 + - - +
257A SER* 3.6 3.4 + - - +
701A AKG 2.8 24.7 + - - +
902A EDO 3.6 31.5 + - - -
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Residues in contact with ILE 256 (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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45A LEU* 5.5 3.1 - - + -
147A LEU* 4.8 9.4 - - + -
150A ILE* 4.3 23.6 - - + -
151A GLN* 4.5 8.3 - - + +
154A LEU* 3.8 15.5 - - + -
162A VAL* 3.5 29.4 - - + -
163A GLY 3.5 5.2 - - - +
164A SER* 4.1 12.3 - - - -
184A GLU 3.6 1.0 - - - +
185A VAL* 3.4 2.2 - - - -
186A PHE* 2.8 50.4 + - + +
188A LEU* 4.3 25.6 - - + -
254A VAL* 4.7 9.4 - - + -
255A THR* 1.3 71.9 - - - +
257A SER* 1.3 58.9 + - - +
258A THR* 6.2 0.2 - - - -
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Residues in contact with SER 257 (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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161A LEU 3.9 0.2 - - - +
162A VAL* 3.5 3.7 - - - -
163A GLY* 3.0 36.1 + - - +
164A SER* 4.9 0.5 + - - -
165A ASN* 5.3 2.9 + - - -
183A VAL* 3.3 34.5 - - - +
184A GLU 3.1 6.1 - - - -
185A VAL* 4.2 7.4 - - - -
255A THR 3.6 4.6 + - - -
256A ILE* 1.3 76.1 - - - +
258A THR* 1.3 64.5 + - - +
902A EDO 4.5 11.5 + - - -
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Residues in contact with THR 258 (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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59A TRP* 4.3 7.2 - - + -
158A PHE* 4.4 18.0 - - + +
160A SER* 3.2 11.3 + - - -
161A LEU 2.6 22.4 + - - -
162A VAL* 3.4 17.5 - - - +
183A VAL* 3.4 5.1 - - - +
184A GLU* 2.9 42.9 + - + +
186A PHE* 5.0 5.8 - - + -
257A SER* 1.3 78.4 - - - +
259A TYR* 1.3 82.6 + - + +
260A GLN* 3.2 5.0 + - - -
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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