Contacts of the strand formed by residues 288 - 295 (chain A) in PDB entry 5PJP
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 ASN 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TYR* 5.3 0.2 - - - -
181A TYR 4.6 2.3 - - - +
182A PHE* 3.3 8.5 - - - +
183A GLY* 2.9 44.4 + - - +
204A LEU* 3.9 15.3 - - + +
206A LEU 3.1 15.9 - - - +
207A GLY* 4.2 0.4 - - - -
208A GLU 2.9 26.4 + - - +
209A PRO 3.4 9.5 + - - -
210A LYS* 4.5 3.5 + - - +
284A ASN* 3.0 29.1 + - - +
286A GLY 3.7 5.6 + - - -
287A PHE* 1.4 83.9 - - - +
289A CYS* 1.3 62.9 + - - +
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Residues in contact with CYS 289 (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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66A ILE* 5.3 0.9 - - + -
144A LEU* 3.6 26.9 - - + -
180A LEU* 4.7 3.6 - - - -
181A TYR 3.3 5.6 - - - -
182A PHE* 3.4 36.3 - - + -
204A LEU* 3.6 5.3 - - - +
205A HIS* 2.8 35.0 + - - +
206A LEU* 2.9 27.1 + - + +
287A PHE* 5.4 0.9 - - + -
288A ASN* 1.3 77.2 - - - +
290A ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 290 (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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180A LEU* 3.3 4.0 - - - -
181A TYR* 2.8 41.5 + - + +
202A ASN* 3.7 20.6 - - - +
203A TYR 3.2 12.6 - - - +
204A LEU* 4.0 6.1 - - + -
205A HIS* 4.3 3.8 - - - +
210A LYS* 3.9 24.9 - - - +
288A ASN* 4.3 0.6 + - - +
289A CYS* 1.3 75.9 - - - +
291A GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 291 (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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143A SER* 2.6 34.2 + - - -
144A LEU 2.8 16.6 + - - -
145A PHE* 3.3 22.2 - - + -
154A LEU* 3.5 10.2 - - + +
155A GLY 4.3 0.2 + - - -
178A PRO* 3.5 21.1 - - + +
179A TYR 3.2 10.3 - - - +
180A LEU* 3.7 7.0 - - + +
181A TYR* 4.8 0.2 - - - -
202A ASN* 3.3 1.6 - - - -
203A TYR 2.8 33.8 + - - +
205A HIS* 2.8 36.9 + - + +
290A ALA* 1.3 74.8 - - - +
292A ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 292 (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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154A LEU* 4.4 1.8 - - - -
178A PRO* 3.5 2.4 - - - +
179A TYR* 2.8 32.8 + - - +
181A TYR* 3.9 11.4 - - + -
201A ILE 3.0 13.0 - - - +
202A ASN* 3.9 7.2 - - - +
291A GLU* 1.3 76.3 - - - +
293A ILE* 1.3 63.7 + - - +
404A OGA 3.7 13.7 - - - +
412A EDO 3.7 27.2 - - - +
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Residues in contact with ILE 293 (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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154A LEU* 3.6 27.6 - - + +
155A GLY* 5.6 0.4 - - - -
157A LEU* 3.8 23.3 - - + -
176A ASN* 3.6 28.9 - - - +
177A THR* 3.6 33.0 - - - +
178A PRO* 3.7 5.6 - - + -
179A TYR* 5.5 0.4 - - + -
200A SER* 3.4 1.4 - - - -
201A ILE* 3.0 48.5 + - + +
292A ALA* 1.3 77.0 - - - +
294A ASN* 1.3 73.1 + - - +
412A EDO 4.0 8.7 - - - -
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Residues in contact with ASN 294 (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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157A LEU* 5.3 0.2 - - - +
160A ILE* 4.1 5.6 - - + -
176A ASN* 3.1 25.5 + - - +
179A TYR* 6.1 0.2 - - - -
194A GLU* 2.9 35.8 + - - +
195A ASP* 4.9 11.8 + - - +
198A LEU* 4.1 24.3 - - + +
199A TYR 3.0 16.6 + - - +
200A SER* 3.7 4.2 - - - -
293A ILE* 1.3 84.1 - - - +
295A PHE* 1.3 63.3 + - - +
412A EDO 3.4 18.6 + - - -
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Residues in contact with PHE 295 (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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31A PHE* 4.0 30.3 - + + -
32A ASP* 5.8 1.3 - - - -
35A ILE* 4.2 15.5 - - + -
157A LEU* 4.5 13.0 - - + -
158A GLY 5.0 9.2 - - - +
160A ILE* 3.9 10.8 - - - -
176A ASN* 5.0 0.4 - - - -
198A LEU* 3.5 5.1 - - - +
199A TYR* 3.1 74.8 + + + +
200A SER 3.8 18.6 - - - -
201A ILE* 3.8 27.1 - - + -
273A VAL* 4.2 4.5 - - + -
294A ASN* 1.3 75.6 - - - +
296A ALA* 1.3 72.3 + - - +
297A THR* 4.0 12.8 - - + -
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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