Contacts of the strand formed by residues 198 - 202 (chain K) in PDB entry 1BTH
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 PRO 198 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29K TRP* 4.3 12.1 - - + +
30K GLN* 3.3 27.1 - - - +
44K ALA 4.1 4.5 - - - +
45K SER* 3.3 25.6 - - - +
137K ARG 3.3 9.9 - - - +
138K VAL* 3.6 14.9 - - - +
139K THR* 3.9 9.6 + - - +
197K GLY* 1.4 84.4 - - - +
199K PHE* 1.3 59.5 + - - +
200K VAL* 3.8 16.1 - - + +
209K GLN* 3.5 26.0 - - - +
211K GLY 3.7 0.2 - - - +
213K VAL* 4.9 1.1 - - - -
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Residues in contact with PHE 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K GLY* 3.6 33.9 - - - -
137K ARG 3.2 5.6 - - - -
138K VAL* 3.5 25.6 - - + -
160K LEU* 4.0 9.4 - - + -
162K ILE* 4.2 10.1 - - + -
181K PHE* 3.6 30.3 - + - -
183K ALA* 3.7 25.1 - - + -
198K PRO* 1.3 73.6 - - - +
200K VAL* 1.3 58.4 + - - +
201K MET* 4.2 15.7 - - + -
209K GLN* 3.6 1.4 - - - -
210K MET* 2.8 29.2 + - + -
211K GLY* 2.8 24.9 + - - +
228K TYR* 3.6 22.4 - + + -
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Residues in contact with VAL 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K TRP* 4.0 16.8 - - + +
121K VAL* 3.8 26.0 - - + -
136K GLY* 3.2 6.1 - - - -
137K ARG* 2.7 55.0 + - + +
198K PRO* 4.0 14.4 - - + +
199K PHE* 1.3 74.7 - - - +
201K MET* 1.3 65.8 + - - +
207K TRP* 3.5 28.1 - - + -
208K TYR 3.0 15.0 - - - +
209K GLN* 4.0 6.1 - - - -
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Residues in contact with MET 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J TYR* 3.5 23.1 - - + -
129K LEU* 3.3 47.7 - - - +
130K LEU* 4.6 1.1 - - - -
134K TYR* 3.9 2.9 - - + -
135K LYS 3.1 22.4 - - - +
136K GLY* 4.0 7.6 - - - -
162K ILE* 3.8 23.6 - - + -
199K PHE* 4.2 5.2 - - + -
200K VAL* 1.3 80.3 - - - +
202K LYS* 1.3 60.7 + - - +
203K SER 3.8 1.2 + - - -
206K ARG 3.9 0.2 - - - +
207K TRP* 3.5 6.2 - - - -
208K TYR* 2.9 32.7 + - - +
210K MET* 3.5 30.3 - - + -
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Residues in contact with LYS 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J GLU* 2.8 20.0 + - - +
12J LEU 5.4 2.2 + - - -
13J GLU* 5.2 2.8 + - - +
14J TYR* 2.5 75.1 - - + +
129K LEU* 4.5 1.6 - - - -
201K MET* 1.3 74.8 - - - +
203K SER* 1.3 68.2 + - - +
204K PRO 3.4 0.3 - - - -
205K ASN* 3.0 45.8 + - - +
206K ARG 3.7 7.2 - - - +
207K TRP* 3.7 38.2 - - + +
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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