Contacts of the strand formed by residues 201 - 205 (chain A) in PDB entry 3LKB
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 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 6.2 1.3 - + - -
137A ILE* 3.6 46.0 - - + -
140A GLU* 2.8 38.9 + - + +
141A LYS* 3.7 14.1 - - + +
144A ALA* 3.8 25.1 - - + -
145A LYS 3.3 4.1 + - - +
146A VAL* 3.2 6.4 - - + +
147A ALA 3.0 23.9 + - - -
199A VAL* 3.4 2.6 - - - +
200A GLU* 1.3 101.1 - - + +
202A VAL* 1.3 62.3 + - - +
203A VAL 4.1 0.2 - - - -
226A ARG* 3.2 34.8 - - + +
228A LEU* 4.0 5.6 - - + -
250A LEU* 6.2 0.7 - - + -
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Residues in contact with VAL 202 (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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147A ALA 3.4 9.0 - - - +
149A VAL* 4.0 22.4 - - + -
191A LEU* 5.6 0.9 - - + -
194A PHE* 4.0 11.4 - - + -
199A VAL* 4.0 7.6 - - + -
201A TYR* 1.3 77.8 - - - +
203A VAL* 1.3 65.1 + - - +
204A HIS* 3.7 21.5 + - + +
214A ILE* 5.9 0.9 - - + -
225A MET* 3.8 37.0 - - + -
226A ARG 2.6 10.5 + - - +
227A HIS* 3.3 15.9 - - + +
228A LEU* 2.9 27.9 + - - +
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Residues in contact with VAL 203 (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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130A VAL* 4.4 19.7 - - + -
133A LEU* 4.3 23.3 - - + -
134A LEU* 4.4 5.8 - - + -
137A ILE* 3.7 29.2 - - + -
146A VAL* 4.2 11.2 - - + -
147A ALA 2.9 7.1 + - - -
148A LEU* 3.4 24.1 - - + +
149A VAL 3.0 23.6 + - - +
150A VAL* 5.8 0.2 - - - +
202A VAL* 1.3 77.7 - - - +
204A HIS* 1.3 70.8 + - - +
205A GLN* 4.2 0.4 + - + -
228A LEU* 3.5 11.4 - - + +
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Residues in contact with HIS 204 (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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130A VAL* 5.3 0.2 - - - +
149A VAL* 3.3 26.8 - - + +
202A VAL* 3.7 15.1 + - + +
203A VAL* 1.3 78.1 - - - +
205A GLN* 1.3 60.2 + - - +
206A ASN* 3.9 1.1 - - - -
211A VAL* 3.6 41.1 - - + +
214A ILE* 3.8 26.4 - - + +
215A LEU* 4.7 0.2 - - + -
227A HIS* 3.1 39.6 - + + +
228A LEU 2.7 21.9 + - - +
229A GLY* 3.3 0.7 - - - -
230A ALA* 3.2 25.5 + - - +
233A THR* 3.5 6.5 - - + +
249A PHE* 4.2 3.2 - - + -
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Residues in contact with GLN 205 (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 TYR* 3.1 38.7 - - - +
130A VAL* 5.2 2.9 - - + -
149A VAL 2.9 9.3 + - - -
150A VAL* 3.4 15.8 - - + +
151A HIS* 3.0 25.5 + - - +
155A PHE* 2.9 35.2 + - + +
156A GLY* 3.4 19.1 - - - +
159A PRO* 3.9 17.1 - - + +
203A VAL 4.2 0.4 + - - -
204A HIS* 1.3 72.2 - - - +
206A ASN* 1.3 62.8 + - - +
230A ALA* 3.3 25.4 - - + +
231A HIS 5.0 0.2 + - - -
232A TYR 5.6 1.2 + - - -
233A THR* 4.3 0.2 - - - -
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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