Contacts of the strand formed by residues 156 - 161 (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 GLN 156 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ILE* 3.4 31.0 - - + +
19K GLY* 4.1 4.9 - - - +
20K SER* 3.2 19.2 + - - +
21K ASP* 3.0 30.1 + - - +
22K ALA* 4.5 0.7 - - - -
139K THR* 3.3 8.5 - - - +
140K GLY 2.9 29.9 + - - +
144K LEU* 3.9 21.8 - - + +
152K PRO* 3.8 23.2 - - + +
153K SER 5.4 0.4 - - - +
154K VAL* 2.8 21.4 + - - +
155K LEU* 1.3 80.3 + - - +
157K VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 157 (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 THR* 5.5 5.6 - - - +
16K ILE* 4.1 2.4 - - - +
19K GLY* 3.3 2.8 - - - -
20K SER* 2.8 50.8 + - - +
21K ASP 4.4 0.9 - - - +
22K ALA* 4.1 15.0 - - + -
26K MET* 4.3 15.5 - - + -
137K ARG* 3.3 43.5 - - + +
138K VAL 3.2 7.2 - - - +
139K THR* 3.7 9.2 - - + -
156K GLN* 1.3 78.3 - - - +
158K VAL* 1.3 66.1 + - - +
159K ASN* 4.7 1.3 - - - +
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Residues in contact with VAL 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ILE* 3.6 21.1 - - + -
17K VAL 4.2 1.1 - - - +
18K GLU 4.1 13.5 - - - +
19K GLY* 4.2 0.4 - - - -
137K ARG* 3.4 3.3 - - - +
138K VAL* 2.8 53.8 + - + -
157K VAL* 1.3 75.8 - - - +
159K ASN* 1.3 63.8 + - - +
160K LEU* 3.8 24.2 + - + -
187K ARG 4.3 3.6 - - - +
188K GLY* 3.6 28.0 - - - -
189K ASP 4.4 6.3 - - - +
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Residues in contact with ASN 159 (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 GLU* 3.2 85.0 + - + +
135K LYS* 4.8 1.1 - - + -
136K GLY 3.0 7.0 - - - +
137K ARG* 3.1 36.5 + - - +
157K VAL* 5.3 1.1 - - - -
158K VAL* 1.3 75.0 - - - +
160K LEU* 1.3 62.3 + - - +
184K TYR* 3.3 23.7 + - - -
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Residues in contact with LEU 160 (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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135K LYS* 4.1 2.2 - - - -
136K GLY* 2.8 31.5 + - - +
138K VAL* 4.0 6.9 - - + +
158K VAL* 3.8 27.6 - - + -
159K ASN* 1.3 80.8 - - - +
161K PRO* 1.3 67.1 - - + +
162K ILE 3.9 0.3 + - - -
183K ALA* 4.2 7.4 - - + +
184K GLY* 4.0 40.6 - - + +
188K GLY* 3.4 25.4 - - - +
189K ASP* 4.2 12.6 - - - +
199K PHE* 4.0 6.9 - - + -
228K TYR* 3.5 25.6 - - + +
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Residues in contact with PRO 161 (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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133K GLY* 4.0 14.4 - - - +
134K TYR 3.4 6.1 - - - +
135K LYS* 3.9 17.0 - - + -
160K LEU* 1.3 86.5 - - + +
162K ILE* 1.3 67.8 - - - +
183K ALA* 3.1 2.4 - - - -
184K GLY* 2.8 88.9 + - + +
186K GLU* 4.3 7.2 - - - +
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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