Contacts of the strand formed by residues 229 - 238 (chain H) in PDB entry 4BEI
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 229 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189H ASP* 4.2 6.2 + - - +
190H LEU 3.4 10.6 + - - -
191H ASN* 4.6 9.4 - - - +
224H ILE* 4.7 1.6 - - - -
227H GLY 5.1 2.7 - - - +
228H ASP* 1.3 83.1 - - - +
230H TYR* 1.3 69.2 + - - +
231H SER* 3.6 17.9 + - - -
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Residues in contact with TYR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G VAL* 3.9 12.5 - - + +
188H VAL* 3.7 7.8 - - + +
189H ASP* 3.5 2.4 - - - -
190H LEU* 2.9 63.1 + - + -
202H PHE* 4.2 16.8 - + - -
220H GLU* 2.5 27.8 + - - -
222H TRP* 3.6 39.7 - + + -
224H ILE* 4.1 19.3 - - + +
229H THR* 1.3 70.1 + - - +
231H SER* 1.3 63.0 + - - +
232H LYS* 3.1 42.2 + - + +
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Residues in contact with SER 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H VAL 3.3 3.4 - - - -
189H ASP* 2.6 25.6 + - - -
229H THR* 3.6 16.3 + - - -
230H TYR* 1.3 80.5 - - - +
232H LYS* 1.3 67.0 + - - +
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Residues in contact with LYS 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G VAL* 3.5 15.1 - - + +
97G ASP 3.2 17.4 + - - -
187H THR* 3.7 2.9 - - - -
188H VAL* 2.8 47.6 + - + +
189H ASP* 5.3 0.2 - - - +
202H PHE* 4.6 3.6 - - - -
217H ASN* 3.0 32.1 - - - +
220H GLU* 3.2 17.4 + - - -
230H TYR* 3.1 31.1 + - + +
231H SER* 1.3 79.7 + - - +
233H VAL* 1.3 71.8 + - - +
234H ARG* 4.0 13.7 - - - +
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Residues in contact with VAL 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H GLN* 3.9 24.2 - - - +
183H PHE* 6.5 0.2 - - + -
185H PRO* 4.0 14.6 - - + -
186H PHE 3.4 10.8 - - - +
187H THR* 4.4 16.6 - - + -
232H LYS* 1.3 86.1 - - - +
234H ARG* 1.3 68.2 + - - +
235H GLY 4.9 0.9 - - - +
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Residues in contact with ARG 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ASP* 2.9 40.5 + - - -
98G THR* 3.5 15.8 + - - +
99G ALA 2.7 29.9 + - - +
100G GLN* 3.7 14.1 + - - +
186H PHE* 2.8 42.3 + - - +
188H VAL* 4.4 11.4 - - + +
204H MET* 4.5 9.0 - - - +
216H VAL* 2.9 27.3 + - + +
217H ASN* 3.6 24.1 - - + +
232H LYS* 4.0 13.5 - - - +
233H VAL* 1.3 80.0 - - - +
235H GLY* 1.3 69.5 + - - +
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Residues in contact with GLY 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLN* 4.6 4.2 - - - +
183H PHE* 3.6 26.2 - - - -
184H VAL 3.4 11.2 - - - -
185H PRO* 3.7 5.1 - - - +
216H VAL* 4.5 6.6 - - - +
233H VAL* 4.3 1.4 - - - +
234H ARG* 1.3 97.8 + - - +
236H ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H PHE* 3.5 5.1 - - - -
184H VAL 2.9 35.8 + - - +
186H PHE* 3.7 19.3 - - + -
206H ALA* 4.0 12.8 - - + -
214H ILE* 4.7 13.0 - - + -
215H PRO 5.6 0.4 - - - +
216H VAL* 4.0 31.9 - - + +
235H GLY* 1.3 75.4 - - - +
237H ASN* 1.3 71.8 + - - +
238H PHE* 3.6 44.6 + - + -
242H TYR* 4.9 3.8 - - + -
249H ILE* 4.4 5.2 - - + -
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Residues in contact with ASN 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LYS* 5.5 3.6 - - - +
100G GLN* 5.5 10.3 + - + +
101G GLN* 5.9 3.2 + - - +
182H GLY 3.5 16.8 + - - +
183H PHE* 3.9 21.2 - - + +
235H GLY 4.4 0.4 + - - -
236H ILE* 1.3 74.6 - - - +
238H PHE* 1.3 62.9 + - - +
239H ASP* 3.0 27.0 + - - +
242H TYR* 3.4 16.1 + - - -
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Residues in contact with PHE 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H VAL* 3.8 25.4 - - + -
181H GLY* 3.1 4.7 - - - -
182H GLY 2.7 39.3 + - - +
184H VAL* 4.0 14.6 - - + -
236H ILE* 3.7 41.5 - - + -
237H ASN* 1.3 70.4 - - - +
239H ASP* 1.3 67.4 + - - +
242H TYR* 3.8 15.0 - + + -
247H TYR* 3.6 42.2 - + + -
249H ILE* 4.0 11.0 - - + -
268H VAL* 3.7 33.2 - - + -
270H LYS* 4.7 8.1 - - + -
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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