Contacts of the strand formed by residues 242 - 250 (chain A) in PDB entry 3H90
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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74A GLY* 5.3 3.5 - - - -
76A GLY* 5.9 0.3 - - - -
238A GLN* 3.4 1.1 - - - +
239A SER* 3.0 34.2 + - - -
241A PRO* 1.3 83.6 - - + +
243A ARG* 1.3 60.8 + - - +
244A PHE* 3.7 20.7 - - - -
277A GLY* 3.4 31.0 - - - +
278A SER* 5.1 0.9 - - - -
279A ASP* 5.6 1.6 - - - -
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Residues in contact with ARG 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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210A LEU* 4.2 15.3 - - + -
214A GLU* 2.9 39.8 + - - -
237A ARG 3.4 9.6 - - - +
238A GLN* 3.4 30.4 + - + +
241A PRO 3.8 9.5 + - - +
242A THR* 1.3 76.7 - - - +
244A PHE* 1.3 63.4 + - - +
245A ILE* 4.0 2.1 + - + +
275A PHE* 3.7 26.6 - - - +
276A PRO* 4.8 10.1 + - - +
278A SER* 3.1 22.7 + - - +
279A ASP* 2.9 27.0 + - - +
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Residues in contact with PHE 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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73A PHE* 3.7 26.5 - + + -
74A GLY 4.0 21.1 - - - -
235A ARG 4.4 0.8 - - - -
236A THR* 3.3 6.6 - - - -
237A ARG* 2.6 69.7 + - + +
239A SER* 3.6 29.8 - - - -
242A THR* 3.7 25.1 - - - -
243A ARG* 1.3 74.9 - - - +
245A ILE* 1.3 63.7 + - - +
246A GLN* 5.7 4.7 - - - +
279A ASP* 3.4 37.9 - - + +
73C PHE* 5.8 1.1 - - + -
235C ARG* 4.3 2.7 - - - -
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Residues in contact with ILE 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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210A LEU* 4.5 9.0 - - + -
218A ILE* 3.8 30.3 - - + -
234A LEU* 4.0 20.4 - - + -
235A ARG 3.5 2.9 - - - -
236A THR* 4.1 5.6 - - + -
243A ARG* 4.8 0.7 - - + -
244A PHE* 1.3 80.6 - - - +
246A GLN* 1.3 69.7 + - - +
247A ILE* 5.3 5.4 - - + -
271A ILE* 3.6 29.6 - - + -
275A PHE* 4.6 5.2 - - + -
278A SER* 3.7 22.7 - - - +
279A ASP 3.0 7.1 + - - +
280A VAL* 3.2 20.7 - - + +
281A ILE* 2.9 27.3 + - - +
282A ILE* 6.3 0.2 - - + -
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Residues in contact with GLN 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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73A PHE* 6.2 0.2 - - - -
233A ASP* 4.0 0.9 - - - -
234A LEU* 3.2 9.6 - - - +
235A ARG* 2.9 70.1 + - + +
237A ARG* 5.4 3.4 - - - +
244A PHE* 5.7 2.6 - - - +
245A ILE* 1.3 78.5 - - - +
247A ILE* 1.3 62.8 + - - +
281A ILE* 3.2 25.5 - - + +
73C PHE* 3.6 29.2 - - - -
246C GLN* 4.1 18.6 - - - +
279C ASP* 4.7 0.9 - - - +
281C ILE* 3.8 28.5 - - + +
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Residues in contact with ILE 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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218A ILE* 4.9 2.5 - - + -
219A ILE* 5.9 3.6 - - + -
222A VAL* 4.1 22.2 - - + -
231A ALA* 3.9 20.9 - - + -
232A HIS 4.6 1.3 - - - +
233A ASP 2.8 16.2 - - - +
234A LEU* 4.0 25.1 - - + -
245A ILE* 5.4 4.5 - - + -
246A GLN* 1.3 79.1 - - - +
248A HIS* 1.3 77.3 + - - +
249A LEU* 3.8 9.9 - - + -
271A ILE* 5.7 1.3 - - + -
281A ILE 3.3 2.2 + - - +
282A ILE* 3.4 31.5 - - + -
283A HIS* 2.9 25.3 + - - +
281C ILE* 4.7 1.1 - - - +
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Residues in contact with HIS 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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231A ALA* 3.1 9.0 - - - +
232A HIS* 2.9 48.9 + + + +
233A ASP* 3.1 32.7 + - + +
247A ILE* 1.3 81.0 - - - +
249A LEU* 1.3 62.7 + - - +
283A HIS* 3.0 34.3 - + + +
285A ASP* 3.0 4.5 + - - +
293A ZN 2.1 33.7 - - - -
281C ILE* 4.5 13.4 - - + +
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Residues in contact with LEU 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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222A VAL* 3.6 27.8 - - + -
228A VAL* 3.9 15.5 - - + -
230A GLY 3.8 1.3 - - - -
231A ALA* 4.2 1.8 - - + -
247A ILE* 3.8 24.0 - - + -
248A HIS* 1.3 76.4 - - - +
250A GLU* 1.3 59.9 + - - +
251A MET* 3.2 25.5 + - + +
264A ALA* 3.8 17.3 - - - -
267A VAL* 3.9 23.6 - - + -
282A ILE* 3.5 21.3 - - + -
283A HIS 2.9 8.2 + - - +
284A GLN* 3.5 1.9 - - - -
285A ASP* 2.8 27.6 + - - +
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Residues in contact with GLU 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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228A VAL* 4.9 0.6 - - - +
229A SER* 3.0 33.7 + - - +
230A GLY* 2.7 37.0 + - - +
231A ALA 3.6 6.1 + - - +
232A HIS* 3.0 45.0 + - + +
249A LEU* 1.3 72.0 - - - +
251A MET* 1.3 63.4 + - - +
285A ASP* 3.3 7.2 - - + -
286A PRO 3.9 12.1 - - - +
289A VAL* 3.8 23.3 - - + +
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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