Contacts of the strand formed by residues 229 - 238 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASP* 4.2 10.8 - - + +
190A LEU 3.4 18.2 - - - +
191A ASN* 4.0 16.1 + - + +
224A ILE* 4.9 2.2 - - - -
227A GLY 4.3 2.8 + - - -
228A ASP* 1.3 81.5 + - - +
230A TYR* 1.3 73.1 + - - +
231A SER* 3.6 16.4 + - - -
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Residues in contact with TYR 230 (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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188A VAL* 3.7 8.7 - - + +
189A ASP* 3.5 1.7 - - - -
190A LEU* 2.9 63.3 + - + -
202A PHE* 4.2 17.0 - + - -
220A GLU* 2.5 27.4 + - - -
222A TRP* 3.6 38.8 - + - -
224A ILE* 4.1 19.1 - - + +
229A THR* 1.3 70.0 - - - +
231A SER* 1.3 62.8 + - - +
232A LYS* 3.1 42.3 + - + +
96B VAL* 3.9 12.5 - - + +
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Residues in contact with SER 231 (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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188A VAL 3.4 3.4 - - - -
189A ASP* 2.6 25.1 + - - -
229A THR* 3.6 15.3 + - - -
230A TYR* 1.3 80.2 - - - +
232A LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 232 (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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187A THR* 3.7 2.9 - - - -
188A VAL* 2.8 47.7 + - + +
189A ASP* 5.3 0.2 - - - +
202A PHE* 4.6 3.6 - - - -
217A ASN* 3.0 32.7 - - - +
220A GLU* 3.2 17.4 + - - -
230A TYR* 3.1 30.7 + - + +
231A SER* 1.3 79.1 + - - +
233A VAL* 1.3 69.3 + - - +
234A ARG* 4.0 13.7 - - - +
96B VAL* 3.5 14.7 - - + +
97B ASP 3.2 17.0 + - - -
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Residues in contact with VAL 233 (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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171A GLN* 3.9 9.0 - - - +
185A PRO* 4.0 12.6 - - + -
186A PHE 3.4 10.1 - - - +
187A THR* 4.4 10.1 - - + -
232A LYS* 1.3 85.1 - - - +
234A ARG* 1.3 68.9 + - - +
235A GLY 4.9 0.9 - - - +
1273A PEG 3.6 60.1 - - - +
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Residues in contact with ARG 234 (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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186A PHE* 2.8 42.7 + - - +
188A VAL* 4.4 11.2 - - + -
204A MET* 4.5 8.8 - - - +
216A VAL* 2.9 28.9 + - + +
217A ASN* 3.6 20.5 - - + +
232A LYS* 4.0 13.7 - - - +
233A VAL* 1.3 78.6 - - - +
235A GLY* 1.3 64.1 + - - +
97B ASP* 2.8 44.1 + - - -
98B THR* 3.6 13.3 + - - +
99B ALA 2.8 29.7 + - - -
100B GLN* 3.1 20.7 + - - +
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Residues in contact with GLY 235 (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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183A PHE* 3.6 24.4 - - - -
184A VAL 3.3 11.4 - - - -
185A PRO* 3.7 4.3 - - - -
216A VAL* 4.5 5.6 - - - +
233A VAL* 4.3 1.6 - - - +
234A ARG* 1.3 89.1 + - - +
236A ILE* 1.3 61.9 + - - +
100B GLN* 3.5 16.3 + - - +
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Residues in contact with ILE 236 (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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183A PHE* 3.5 5.0 - - - -
184A VAL 2.9 35.3 + - - +
186A PHE* 3.7 19.5 - - + -
206A ALA* 4.0 12.8 - - + -
214A ILE* 4.7 13.2 - - + -
215A PRO 5.6 0.4 - - - +
216A VAL* 4.0 31.6 - - + +
235A GLY* 1.3 75.2 - - - +
237A ASN* 1.3 72.0 + - - +
238A PHE* 3.6 43.3 + - + -
242A TYR* 4.9 4.0 - - + -
249A ILE* 4.4 5.2 - - + -
100B GLN* 5.1 0.4 - - - +
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Residues in contact with ASN 237 (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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182A GLY 3.5 16.4 + - - +
183A PHE* 3.9 20.7 - - + +
236A ILE* 1.3 75.4 - - - +
238A PHE* 1.3 62.8 + - - +
239A ASP* 3.0 26.8 + - - +
242A TYR* 3.4 16.5 + - - -
75B LYS* 5.5 4.4 - - - +
100B GLN* 4.9 16.4 - - + +
101B GLN* 5.9 2.3 + - - +
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Residues in contact with PHE 238 (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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177A VAL* 3.8 24.5 - - + -
181A GLY* 3.1 4.9 - - - -
182A GLY 2.7 39.2 + - - +
184A VAL* 4.0 15.0 - - + -
236A ILE* 3.6 41.3 - - + -
237A ASN* 1.3 69.5 - - - +
239A ASP* 1.3 66.6 + - - +
242A TYR* 3.8 15.3 - + + -
247A TYR* 3.6 41.5 - + + -
249A ILE* 4.0 10.5 - - + -
268A VAL* 3.7 31.9 - - + -
270A LYS* 4.7 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