Contacts of the strand formed by residues 233 - 242 (chain A) in PDB entry 5AJI
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 ILE 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ILE 3.6 1.2 - - - +
191A GLY* 3.2 2.3 - - - -
192A VAL* 2.8 42.7 + - + +
193A ALA 4.6 1.6 - - - +
194A TYR* 3.2 55.4 - - + +
198A ILE* 5.8 2.9 - - + -
225A LEU* 3.4 15.7 - - + -
227A GLU 3.7 2.9 - - - -
228A LEU* 4.1 14.4 - - + -
232A SER* 1.3 72.5 - - - +
234A ASN* 1.3 61.1 + - - +
235A PHE* 3.1 36.3 - - + -
258B LYS* 3.9 18.4 - - + -
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Residues in contact with ASN 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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189A ILE* 4.2 19.6 - - + +
190A ILE 3.3 4.5 - - - +
191A GLY* 3.4 8.5 - - - -
225A LEU* 3.8 1.1 - - - +
226A ASN* 2.7 34.2 + - + +
227A GLU* 2.9 55.5 + - + +
229A GLY* 4.4 4.4 - - - -
232A SER* 2.8 31.0 + - - -
233A ILE* 1.3 74.2 - - - +
235A PHE* 1.3 57.6 + - - +
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Residues in contact with PHE 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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188A PHE 3.6 0.5 - - - +
189A ILE* 3.3 6.1 - - - -
190A ILE* 2.7 42.8 + - + +
192A VAL* 3.7 16.4 - - + -
196A SER* 5.7 0.7 - - - -
198A ILE* 4.2 22.2 - - + -
201A VAL* 3.4 38.4 - - + -
202A LYS* 4.1 20.6 - - + -
205A LEU* 4.2 19.1 - - + -
224A ARG* 3.2 20.2 - - - +
225A LEU* 3.5 21.1 - - + -
226A ASN* 4.5 0.7 - - - -
233A ILE* 3.1 30.7 - - + -
234A ASN* 1.3 72.7 - - - +
236A VAL* 1.3 62.1 + - - +
237A VAL* 5.0 0.2 - - - -
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Residues in contact with VAL 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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187A GLU* 3.8 19.5 - - + -
188A PHE 3.4 4.0 - - - +
189A ILE* 4.3 7.2 - - + -
222A THR* 3.9 5.8 - - + +
223A VAL* 3.4 1.9 - - - +
224A ARG* 2.9 41.1 + - + +
226A ASN* 3.9 30.7 - - + +
235A PHE* 1.3 74.7 - - - +
237A VAL* 1.3 67.5 + - - +
238A ARG* 3.6 31.6 - - + +
251B TRP* 3.9 22.7 - - + +
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Residues in contact with VAL 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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187A GLU* 3.3 4.0 - - - -
188A PHE* 2.8 60.0 + - + +
190A ILE* 4.7 8.3 - - + -
205A LEU* 3.8 36.3 - - + -
209A ILE* 4.1 25.1 - - + -
222A THR 3.2 10.1 - - - +
223A VAL* 4.1 12.1 - - + -
235A PHE 4.9 0.9 - - - +
236A VAL* 1.3 79.7 - - - +
238A ARG* 1.3 64.7 + - - +
239A VAL* 4.3 6.5 - - + -
253A VAL* 5.9 1.1 - - + -
257A ILE* 5.6 1.1 - - + -
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Residues in contact with ARG 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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185A ARG* 3.1 35.0 - - - +
186A ASN 3.3 3.1 - - - -
187A GLU* 2.7 32.2 + - + -
220A GLU* 3.4 29.1 + - - +
221A MET* 3.5 3.5 + - - -
222A THR* 2.9 37.8 + - - -
226A ASN* 5.2 6.3 + - - +
236A VAL* 3.6 20.2 - - + +
237A VAL* 1.3 78.8 - - - +
239A VAL* 1.3 65.9 + - - +
247B GLN* 4.2 10.3 + - - +
251B TRP* 3.7 28.2 - - - -
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Residues in contact with VAL 239 (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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185A ARG* 4.2 1.2 - - - +
186A ASN* 3.1 32.9 + - + +
188A PHE* 3.8 28.5 - - + -
209A ILE* 3.7 35.2 - - + -
215A ILE* 3.8 35.4 - - + -
220A GLU 4.0 4.3 - - - -
221A MET* 4.2 6.3 - - - -
237A VAL* 4.3 4.7 - - + -
238A ARG* 1.3 83.0 - - - +
240A TRP* 1.3 65.4 + - - +
241A SER* 4.0 3.1 + - - -
249A VAL* 5.3 1.3 - - + -
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Residues in contact with TRP 240 (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 VAL* 3.7 28.7 - - + -
184A ARG* 3.3 29.2 - - - -
185A ARG* 3.3 20.0 - - + +
215A ILE* 3.5 5.5 - - - +
216A LEU* 2.9 29.0 + - + -
219A ARG* 3.8 42.6 - - + +
220A GLU* 3.2 46.8 + - + +
239A VAL* 1.3 71.3 - - - +
241A SER* 1.3 63.6 + - - +
156B ARG* 5.4 7.0 - - - -
157B THR 5.1 1.1 - - - -
158B ALA 3.4 26.7 - - - -
160B GLY* 3.9 16.8 - - - -
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Residues in contact with SER 241 (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 VAL* 3.4 2.8 - - - +
184A ARG 2.9 29.6 + - - +
186A ASN* 4.0 9.0 + - - -
214A ARG 3.3 16.1 + - - -
215A ILE* 4.4 2.1 - - - +
216A LEU* 3.5 13.7 - - - -
239A VAL 4.0 2.5 + - - -
240A TRP* 1.3 76.9 + - - +
242A ASN* 1.3 68.7 + - - +
245A ASP* 4.1 1.6 - - - -
246A LEU* 4.4 7.8 - - - +
249A VAL* 3.8 32.0 - - - +
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Residues in contact with ASN 242 (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 PRO* 3.4 9.5 - - - +
183A VAL* 4.0 13.8 - - - +
214A ARG 4.4 0.4 + - - -
216A LEU* 3.9 18.0 - - - +
241A SER* 1.3 75.5 - - - +
243A SER* 1.3 67.6 + - - +
244A GLY* 4.3 4.7 - - - +
245A ASP* 2.8 34.1 + - - +
246A LEU* 3.0 11.1 + - - +
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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