Contacts of the strand formed by residues 247 - 256 (chain B) in PDB entry 1P4A
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 MET 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.6 1.8 - - + -
122B PHE* 3.1 45.3 - - + -
125B VAL* 3.5 38.1 - - + -
126B PHE* 4.2 10.1 - - + -
229B ILE 2.8 13.9 + - - +
230B GLY* 3.4 1.9 - - - -
231B VAL* 2.9 27.0 + - - +
246B TYR* 1.3 77.2 - - - +
248B SER* 1.3 62.5 + - - +
249B LEU* 3.9 13.2 - - + -
268B ASN* 3.3 5.8 - - - +
269B PHE* 3.8 19.3 - - + -
272B PHE* 3.6 29.4 - - + -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B VAL* 3.3 17.0 - - - -
234B GLU* 2.4 43.4 + - - -
246B TYR* 4.4 2.7 - - - -
247B MET* 1.3 74.6 - - - +
249B LEU* 1.3 64.1 + - - +
250B LEU 3.9 6.7 - - - -
267B GLY* 3.5 1.2 - - - -
268B ASN* 2.8 25.0 + - - -
269B PHE* 3.2 26.2 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 4.8 4.0 - - + -
84B VAL* 3.3 28.7 - - + +
87B LEU* 5.3 1.6 - - + -
118B VAL* 4.1 22.7 - - + -
121B LEU* 3.7 35.7 - - + -
122B PHE* 4.4 6.7 - - + -
231B VAL 3.2 12.8 + - - +
232B LEU* 3.3 31.2 - - + +
247B MET* 3.9 22.2 - - + -
248B SER* 1.3 76.5 - - - +
250B LEU* 1.3 60.6 + - + +
267B GLY 2.7 20.1 + - - -
269B PHE* 3.5 16.5 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.5 27.1 - - + +
87B LEU* 4.0 29.4 - - + -
88B GLY* 3.6 24.2 - - - -
91B LEU* 3.7 27.6 - - + -
232B LEU* 2.9 10.7 + - + +
233B VAL* 3.3 15.1 - - + -
234B GLU* 2.9 29.5 + - - +
248B SER* 3.9 2.1 - - - -
249B LEU* 1.3 81.9 - - + +
251B THR* 1.3 61.9 + - - +
264B ILE* 3.8 9.0 - - + -
265B GLN 3.8 13.5 - - - +
266B ASN* 4.7 1.1 - - - +
267B GLY* 3.4 4.0 - - - +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B VAL* 4.6 1.3 - - - -
234B GLU* 3.3 24.8 + - + +
236B GLU* 3.9 30.1 - - + +
250B LEU* 1.3 72.6 - - - +
252B LEU* 1.3 61.9 + - - +
253B SER* 3.3 9.7 + - - +
264B ILE* 3.3 7.3 - - - +
265B GLN* 2.7 41.4 + - - +
266B ASN 3.0 20.8 + - - -
267B GLY* 3.4 10.0 - - - -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 3.6 20.4 - - - +
103B VAL* 3.5 24.0 - - + -
205B PHE* 4.0 14.8 - - + -
233B VAL* 3.9 14.3 - - + +
234B GLU 2.8 14.2 + - - +
235B ALA* 3.7 8.4 - - + +
236B GLU* 3.4 18.0 + - - +
251B THR* 1.3 70.0 - - - +
253B SER* 1.3 61.4 - - - +
254B THR 4.0 8.3 - - - +
255B ILE* 4.2 15.0 - - + -
262B ILE* 3.9 28.7 - - + -
263B GLU 3.7 13.9 - - - +
264B ILE* 4.1 7.6 - - + -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLU* 3.3 42.7 - - - +
251B THR* 3.3 5.0 + - - -
252B LEU* 1.3 74.6 - - - +
254B THR* 1.3 67.0 + - - +
263B GLU* 3.1 23.5 + - - +
265B GLN* 3.4 37.4 + - - +
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 3.3 4.8 + - - +
253B SER* 1.3 86.2 + - - +
255B ILE* 1.3 68.6 + - - +
256B ASN* 5.8 1.1 - - + -
261B SER* 4.8 10.8 - - - +
262B ILE* 3.4 2.6 - - - -
263B GLU* 2.8 66.9 + - + +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 4.0 22.4 - - + -
101B GLY* 3.6 34.8 - - - +
102B TYR 3.5 24.5 - - - +
103B VAL* 4.0 7.0 - - + -
207B LYS* 5.9 2.7 - - - +
252B LEU* 4.2 11.9 - - + -
254B THR* 1.3 78.2 - - - +
256B ASN* 1.3 69.4 + - - +
257B MET 5.0 0.9 - - - +
261B SER* 3.6 8.5 - - - +
262B ILE* 3.9 22.0 - - + -
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Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 4.4 3.0 - - - +
254B THR* 5.8 1.3 - - + -
255B ILE* 1.3 79.2 - - - +
257B MET* 1.3 56.0 + - - +
258B LYS* 2.8 35.4 + - - +
259B GLU* 2.9 37.6 - - - +
260B LYS* 2.8 30.7 + - - -
261B SER* 3.0 31.3 + - - +
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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