Contacts of the strand formed by residues 135 - 140 (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 LYS 135 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J SER* 2.8 127.6 + - + +
133K GLY 4.3 1.1 - - - +
134K TYR* 1.3 73.5 - - - +
136K GLY* 1.3 60.2 + - - +
159K ASN 4.8 1.8 - - - +
160K LEU 3.3 5.4 - - - +
161K PRO* 3.9 19.7 - - + -
184K TYR* 3.4 27.2 - - - +
186K LYS* 5.0 7.1 - - - +
201K MET* 3.1 9.1 - - - +
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Residues in contact with GLY 136 (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 LEU* 4.2 6.7 - - - -
135K LYS* 1.3 74.9 - - - +
137K ARG* 1.3 60.2 + - - -
159K ASN* 3.0 5.9 - - - +
160K LEU 2.8 33.4 + - - -
199K PHE* 3.6 24.0 - - - -
200K VAL 3.2 12.6 - - - -
201K MET* 4.0 2.0 - - - -
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Residues in contact with ARG 137 (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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4J ARG* 3.6 9.1 - - - +
14J LEU* 2.7 80.3 + - + +
26K MET* 3.8 14.3 + - - +
27K SER* 5.2 2.2 - - - -
136K GLY* 1.3 72.8 - - - -
138K VAL* 1.3 67.6 + - - +
139K THR* 4.5 7.4 + - + -
157K VAL* 3.3 29.0 - - + +
158K VAL 3.4 2.7 - - - +
159K ASN* 3.1 17.3 + - - +
198K PRO 3.3 2.3 - - - +
199K PHE* 3.2 6.3 - - - -
200K VAL* 2.7 50.3 + - + +
207K TRP* 3.2 27.8 - - + -
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Residues in contact with VAL 138 (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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16K ILE* 3.8 17.9 - - + +
137K ARG* 1.3 78.3 - - - +
139K THR* 1.3 68.4 + - - +
157K VAL* 3.2 4.5 - - - +
158K VAL* 2.8 45.9 + - + +
160K LEU* 4.0 13.7 - - + -
190K ALA* 4.2 9.6 - - + -
198K PRO 3.6 5.6 - - - +
199K PHE* 3.5 27.1 - - + -
213K VAL* 3.8 27.6 - - + -
228K TYR* 3.8 15.0 - - + +
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Residues in contact with THR 139 (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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16K ILE* 3.9 5.6 - - - +
22K ALA* 5.2 1.3 - - + -
26K MET* 5.5 0.2 - - - -
27K SER* 3.3 26.8 + - - +
29K TRP* 5.6 0.9 + - - -
30K GLN* 2.7 31.3 + - - +
137K ARG* 4.5 6.0 + - + -
138K VAL* 1.3 87.1 - - - +
140K GLY* 1.3 59.2 + - - +
155K LEU* 4.0 9.9 - - + -
156K GLN 3.3 15.0 - - - +
157K VAL* 3.7 18.4 - - + -
194K ASP* 4.2 4.0 - - - +
197K GLY* 4.5 6.2 - - - -
198K PRO* 3.9 17.3 + - - +
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Residues in contact with GLY 140 (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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16K ILE* 3.7 4.1 + - - +
30K GLN* 4.3 7.9 - - - -
139K THR* 1.3 77.1 - - - +
141K TRP* 1.3 62.6 + - - -
142K GLY 3.4 0.2 - - - -
155K LEU* 3.4 10.6 - - - +
156K GLN* 2.9 35.3 + - - +
193K GLY 5.4 0.4 - - - -
194K ASP* 3.1 20.6 - - - -
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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