Contacts of the strand formed by residues 201 - 205 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 6.1 1.3 - + - -
137B ILE* 3.7 44.2 - - + -
140B GLU* 3.3 31.3 + - + +
141B LYS* 3.3 27.7 - - + +
144B ALA* 3.6 32.1 - - + -
145B LYS 3.2 2.5 + - - -
146B VAL* 3.1 10.7 - - + +
147B ALA 2.8 31.4 + - - -
199B VAL* 3.2 2.6 - - - +
200B GLU* 1.3 93.2 - - + +
202B VAL* 1.3 59.0 + - - +
203B VAL 4.2 0.4 - - - -
226B ARG* 3.4 30.5 - - + +
228B LEU* 4.0 7.0 - - + -
250B LEU* 6.4 0.7 - - + -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ALA* 3.4 6.7 - - + +
149B VAL* 3.8 22.4 - - + -
191B LEU* 6.2 0.2 - - + -
194B PHE* 4.3 10.8 - - + -
199B VAL* 3.9 6.5 - - + -
201B TYR* 1.3 76.7 - - - +
203B VAL* 1.3 63.0 + - - +
204B HIS* 3.4 25.4 + - + +
214B ILE* 5.8 1.1 - - + -
225B MET* 3.6 41.1 - - + -
226B ARG 2.9 7.1 + - - -
227B HIS* 3.5 15.6 - - + +
228B LEU* 2.8 28.5 + - - +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 4.2 27.1 - - + +
133B LEU* 4.1 27.6 - - + -
134B LEU* 4.1 15.0 - - + -
137B ILE* 3.7 30.5 - - + -
146B VAL* 4.4 7.2 - - + -
147B ALA 2.8 9.7 + - - -
148B LEU* 3.2 18.1 - - + +
149B VAL 3.0 22.6 + - - -
202B VAL* 1.3 75.1 - - - +
204B HIS* 1.4 64.1 + - - +
205B GLN 4.2 0.3 + - - -
228B LEU* 3.5 8.1 - - + -
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Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B VAL* 3.4 25.7 - - + +
202B VAL* 3.4 17.7 + - + +
203B VAL* 1.4 76.3 - - - +
205B GLN* 1.3 59.8 + - - +
206B ASN* 3.9 2.2 - - + -
211B VAL* 3.7 43.0 - - + +
214B ILE* 4.1 21.3 - - + +
227B HIS* 2.9 40.1 - + + -
228B LEU 2.8 22.6 + - - +
229B GLY* 3.5 0.8 - - - -
230B ALA* 3.2 25.5 + - - +
233B THR* 3.5 5.9 - - + +
249B PHE* 4.1 4.6 - - + -
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Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 3.2 32.4 - - - +
130B VAL* 5.0 3.6 - - + -
149B VAL 2.9 10.1 + - - -
150B VAL* 3.2 15.4 - - + +
151B HIS* 3.0 25.5 + - - +
155B PHE* 2.9 36.5 + - - +
156B GLY* 3.2 22.0 - - - +
159B PRO* 3.7 19.5 - - + +
203B VAL 4.2 0.6 + - - -
204B HIS* 1.3 71.7 - - - +
206B ASN* 1.3 62.4 + - - +
230B ALA* 3.2 24.2 - - + +
231B HIS 5.1 0.2 + - - -
232B TYR* 5.6 1.9 + - - +
233B THR* 4.4 0.4 - - - +
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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