Contacts of the strand formed by residues 242 - 250 (chain A) in PDB entry 4HBT
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 THR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A PHE* 6.1 1.1 - - + -
67A ALA* 3.8 12.3 - - + +
69A CYS* 3.9 9.6 - - - -
172A ALA* 3.3 13.6 - - + +
237A SER* 3.1 8.2 - - - -
238A GLY 3.0 28.7 + - - +
239A GLY 2.7 22.1 + - - -
240A TYR 4.0 0.7 - - - -
241A GLY* 1.3 76.2 - - - +
243A THR* 1.3 62.7 + - - +
244A ASN* 3.6 24.7 - - - +
263A PHE 3.2 13.9 - - - +
264A THR* 2.7 21.8 + - - +
272A SER* 5.7 0.7 - - - -
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Residues in contact with THR 243 (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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236A GLY 3.6 6.3 - - - +
237A SER* 5.6 2.7 - - - -
241A GLY 2.9 15.7 + - - -
242A THR* 1.3 74.5 + - - +
244A ASN* 1.3 66.0 + - - +
263A PHE* 2.8 33.0 + - - +
272A SER* 3.7 7.7 - - - -
273A ARG* 3.1 24.8 + - - +
274A ARG* 3.6 43.5 - - + +
277A LEU* 3.4 12.6 - - + +
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Residues in contact with ASN 244 (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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66A PHE* 5.3 0.7 - - - +
67A ALA 2.8 28.3 + - - +
68A MET* 3.1 18.6 + - - +
69A CYS* 4.3 3.0 - - - +
71A THR* 3.8 9.4 - - + -
220A SER* 4.9 0.3 + - - -
235A THR* 3.3 6.4 - - - +
236A GLY 2.8 29.2 + - - +
242A THR* 3.6 15.6 - - - +
243A THR* 1.3 83.6 - - - +
245A ASP* 1.3 64.3 + - - +
261A THR 3.4 4.7 - - - -
262A TYR* 3.3 25.2 - - + +
263A PHE 3.2 15.8 + - - -
277A LEU* 3.4 7.9 - - - +
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Residues in contact with ASP 245 (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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71A THR* 4.4 0.2 - - - -
217A GLY 4.4 0.9 - - - +
220A SER* 3.3 10.3 - - - -
221A ILE* 2.9 45.6 + - + +
222A GLN 4.6 0.2 + - - -
233A ASP* 2.5 34.6 - - - +
234A LYS 3.1 18.1 - - - +
235A THR* 3.5 2.4 - - - +
244A ASN* 1.3 77.4 - - - +
246A ILE* 1.3 68.1 + - - +
261A THR* 2.9 33.5 + - - +
277A LEU* 3.9 13.5 - - + -
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Residues in contact with ILE 246 (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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71A THR* 4.0 25.1 - - + +
74A VAL* 4.0 18.2 - - + -
186A MET* 4.0 20.4 - - + -
190A LEU* 4.0 22.7 - - + -
211A MET* 4.2 1.5 - - + +
233A ASP* 3.1 3.7 - - - +
234A LYS* 2.9 46.8 + - + +
245A ASP* 1.3 81.2 + - - +
247A ALA* 1.3 61.3 + - - +
259A LEU 3.4 4.0 - - - -
260A VAL* 3.8 18.6 - - + -
262A TYR* 3.7 28.0 - - + +
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Residues in contact with ALA 247 (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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190A LEU* 3.6 11.3 - - - +
221A ILE* 3.8 20.9 - - + -
231A VAL* 4.1 6.1 - - + -
232A GLY 3.2 11.0 - - - +
233A ASP* 3.8 10.5 - - + -
246A ILE* 1.3 76.4 - - - +
248A VAL* 1.3 59.8 + - - +
249A ILE* 4.1 18.3 - - + +
257A LEU 4.0 0.2 - - - +
258A ILE* 3.4 4.2 - - - -
259A LEU* 2.8 35.1 + - - +
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Residues in contact with VAL 248 (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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190A LEU* 4.1 1.9 - - + +
194A THR* 3.8 32.5 - - + +
195A LEU* 4.0 11.9 - - + -
208A VAL* 5.3 2.7 - - + -
211A MET* 5.1 6.5 - - + -
231A VAL* 3.5 3.5 - - - +
232A GLY* 2.9 45.6 + - - +
247A ALA* 1.3 73.8 - - - +
249A ILE* 1.3 63.2 + - - +
250A TRP* 3.6 41.1 - - + -
256A PRO* 4.8 1.3 - - + -
257A LEU 3.5 5.8 - - - +
258A ILE* 3.7 17.3 - - + -
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Residues in contact with ILE 249 (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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221A ILE* 4.2 7.2 - - + -
225A LEU* 3.9 27.8 - - + -
229A TRP* 3.7 30.1 - - + -
230A VAL 3.4 8.1 - - - +
231A VAL* 4.4 4.7 - - + -
247A ALA* 4.1 10.8 - - + -
248A VAL* 1.3 79.6 - - - +
250A TRP* 1.3 64.4 + - - +
251A PRO* 3.4 9.0 - - + +
256A PRO* 3.1 6.8 - - - +
257A LEU* 2.8 52.8 + - + +
259A LEU* 3.9 30.7 - - + +
285A THR* 5.3 0.9 - - + -
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Residues in contact with TRP 250 (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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194A THR 5.4 0.2 - - - -
195A LEU* 4.1 12.5 - - + +
208A VAL* 3.7 28.3 - - + -
212A LYS* 4.3 14.1 - - + -
228A SER 4.9 0.2 - - - +
229A TRP* 3.7 1.0 - - - -
230A VAL* 2.8 60.0 + - + +
232A GLY 4.2 7.6 - - - -
248A VAL* 3.6 46.7 - - + -
249A ILE* 1.3 74.4 - - - +
251A PRO* 1.3 69.5 - - - +
252A LYS 3.7 0.2 + - - -
254A ARG 5.4 2.7 - - - +
256A PRO* 3.8 28.1 - - + +
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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