Contacts of the strand formed by residues 229 - 238 (chain I) in PDB entry 5U0A
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 GLY 229 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11I THR* 3.5 4.1 + - - -
12I LEU* 2.9 29.5 + - - +
193I THR* 4.6 4.7 - - - -
195I HIS* 3.3 17.5 - - - -
228I ALA* 1.3 78.0 - - - +
230I THR* 1.3 66.0 + - - -
231I PHE* 3.6 11.2 + - - -
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Residues in contact with THR 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ILE* 4.6 14.6 - - - -
11I THR* 3.8 21.8 - - - +
193I THR* 4.3 0.2 - - - -
194I VAL* 3.0 39.0 + - - +
195I HIS* 3.3 13.5 + - + -
229I GLY* 1.3 72.5 - - - -
231I PHE* 1.3 65.3 + - - +
310I TYR* 4.0 27.0 - - + +
311I THR* 4.2 15.9 - - + +
314I ALA* 4.8 1.8 - - - +
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Residues in contact with PHE 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I ALA 3.7 0.3 - - - +
9I ILE* 3.4 6.8 - - - +
10I GLN 2.9 36.0 + - - +
12I LEU* 3.4 38.1 - - + -
17I ILE* 4.4 15.5 - - + -
36I THR* 3.8 22.0 - - + -
38I VAL* 3.4 31.6 - - + -
43I TRP* 4.6 4.0 - + - -
191I ALA* 4.4 13.2 - - + -
192I PHE 3.3 6.1 - - - +
193I THR* 3.1 38.8 - - + -
194I VAL* 4.7 1.1 - - - -
228I ALA* 5.6 1.3 - - - -
229I GLY* 4.2 11.2 - - - -
230I THR* 1.3 74.2 - - - +
232I TYR* 1.3 59.4 + - - +
233I ARG* 4.1 7.0 + - + +
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Residues in contact with TYR 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I HIS* 3.0 20.3 + - + -
8I ALA 3.6 2.5 - - - -
9I ILE* 3.8 14.4 - - + -
190I HIS 4.5 0.7 - - - +
191I ALA* 3.2 23.0 - - - -
192I PHE* 2.7 40.7 + + + +
194I VAL* 4.3 5.2 - - + -
230I THR 3.8 1.4 + - - -
231I PHE* 1.3 72.1 - - - +
233I ARG* 1.3 74.6 + - - +
234I TYR* 3.8 19.3 - - + +
295I SER* 5.1 0.4 - - - -
296I PHE* 2.9 30.5 + - + -
297I ALA* 3.8 20.9 - - + -
300I PHE* 3.4 35.7 - + + -
318I LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I HIS* 3.4 4.3 - - - -
8I ALA* 2.8 41.5 + - + +
10I GLN* 2.5 45.2 + - - -
43I TRP* 3.2 48.2 - - - +
188I PHE* 5.8 0.4 - - - -
189I ALA 5.7 0.4 - - - +
191I ALA* 3.8 19.0 - - + +
231I PHE* 4.5 7.2 - - + +
232I TYR* 1.3 85.9 - - - +
234I TYR* 1.3 61.9 + - - +
263I PHE* 2.4 69.1 + - + -
264I LEU 4.6 1.6 + - - -
266I THR 4.7 0.6 + - - -
281I PRO* 4.0 10.1 - - - +
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Residues in contact with TYR 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E ALA* 3.4 33.2 - - + -
278E MET* 4.7 2.5 - - + +
5I ASP* 3.6 15.1 - - + +
6I ILE 3.3 8.1 - - - -
7I HIS* 3.4 36.3 - + - -
188I PHE* 4.2 1.0 - - - -
189I ALA* 3.2 35.5 + - + +
232I TYR* 3.8 16.1 - - + +
233I ARG* 1.3 76.8 - - - +
235I ALA* 1.3 68.8 + - - +
236I ASN* 2.4 35.9 + - - -
263I PHE* 4.1 5.4 - - - -
293I PRO* 3.3 13.2 - - - +
294I ILE 3.5 8.5 + - - -
295I SER* 3.6 28.2 + - - -
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Residues in contact with ALA 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL 3.9 0.2 - - - +
5I ASP* 3.2 4.5 - - - +
6I ILE* 2.9 41.5 + - + +
187I GLN 3.1 11.9 - - - +
188I PHE* 4.2 13.2 - - + -
234I TYR* 1.3 82.0 - - - +
236I ASN* 1.3 65.2 + - - +
259I PHE* 4.2 9.4 - - + -
263I PHE* 3.8 23.1 - - + -
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Residues in contact with ASN 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E MET* 4.1 2.8 - - - +
3I PHE* 5.4 4.0 - - + -
4I VAL 3.5 3.6 - - - +
5I ASP* 3.0 12.8 - - - +
186I VAL* 3.2 10.4 - - - +
187I GLN* 2.5 65.7 + - + +
234I TYR* 2.4 42.2 + - - -
235I ALA* 1.3 71.9 - - - +
237I VAL* 1.3 70.4 + - - +
238I ASN 4.2 1.1 - - - +
259I PHE* 4.7 0.5 - - - -
293I PRO* 3.2 23.3 - - + +
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Residues in contact with VAL 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I PHE* 3.5 3.7 - - - -
4I VAL* 2.8 43.6 + - + +
6I ILE* 6.2 0.2 - - + -
169I LEU* 5.1 1.3 - - + -
185I ALA 3.3 8.3 - - - +
186I VAL* 3.7 8.7 - - + -
236I ASN* 1.3 82.0 - - - +
238I ASN* 1.3 61.5 + - - +
239I LEU* 3.3 15.3 + - + +
242I LEU* 4.4 11.2 - - + -
256I VAL* 3.9 27.1 - - + -
259I PHE* 3.5 35.2 - - + -
260I LEU* 4.4 8.3 - - + -
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Residues in contact with ASN 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I THR 3.8 6.9 - - - +
3I PHE* 3.6 32.7 - - + -
185I ALA* 2.8 19.1 + - - +
236I ASN* 4.2 1.0 - - - +
237I VAL* 1.3 69.3 - - - +
239I LEU* 1.3 64.1 + - - +
240I ASP* 3.3 20.9 + - - +
241I ARG* 3.1 39.4 + - + +
242I LEU* 3.0 21.5 + - - +
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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