Contacts of the strand formed by residues 250 - 258 (chain B) in PDB entry 5FS9
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 GLN 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PRO 4.5 0.3 - - - +
130B SER* 3.9 15.1 - - - +
242B MET* 3.1 41.3 - - + +
243B VAL 3.2 8.1 - - - +
244B LYS* 3.9 27.9 - - + +
248B GLY 4.1 4.9 - - - +
249B SER* 1.3 79.4 - - - +
251B ILE* 1.3 66.9 + - - +
252B THR 4.3 0.2 - - - -
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Residues in contact with ILE 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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128B ALA* 3.9 21.5 - - + -
129B PRO 3.5 21.3 - - - +
130B SER 3.4 5.6 - - - +
132B VAL* 4.0 23.1 - - + -
135B LEU* 4.9 4.0 - - + -
160B LEU* 3.8 21.5 - - + -
162B VAL* 4.6 5.6 - - + -
228B LEU* 4.5 2.2 - - + -
242B MET* 3.4 1.4 - - - -
243B VAL* 2.9 43.8 + - + +
245B LEU* 4.2 25.1 - - + -
249B SER* 4.9 0.4 - - - +
250B GLN* 1.3 78.6 - - - +
252B THR* 1.3 77.4 + - - +
253B TYR* 4.6 1.2 - - - -
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Residues in contact with THR 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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130B SER 2.8 15.8 + - - +
131B HIS* 2.8 29.0 - - - +
132B VAL 2.9 24.9 + - - +
240B ASP 4.3 6.5 - - - +
241B ASN* 3.1 10.3 - - - +
242B MET* 3.7 35.7 - - + -
251B ILE* 1.3 78.7 - - - +
253B TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 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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131B HIS* 4.0 4.4 + - - -
132B VAL 3.2 9.4 - - - +
135B LEU* 3.7 39.3 - - + -
236B LEU* 3.7 26.7 - - + +
238B VAL* 4.3 5.7 - - - -
241B ASN* 2.9 55.9 + - + +
242B MET* 3.6 8.3 - - - -
243B VAL* 4.2 2.9 - - + -
251B ILE 4.6 0.7 - - - -
252B THR* 1.3 75.7 - - - +
254B GLU* 1.3 65.1 + - - +
255B LYS 3.8 11.7 - - - +
256B CYS* 3.5 28.9 - - + -
432B ASN* 3.6 23.8 - - - -
433B ILE* 3.8 15.8 - - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B HIS* 2.9 34.7 - - + +
132B VAL 3.3 0.8 + - - -
133B PRO* 3.1 32.9 + - + +
241B ASN* 5.9 0.2 - - - -
253B TYR* 1.3 76.2 - - - +
255B LYS* 1.3 72.4 + - + +
432B ASN* 3.2 25.5 + - - +
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Residues in contact with LYS 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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133B PRO 2.8 7.4 + - - +
134B PHE* 3.5 18.7 - - + -
135B LEU 3.0 23.6 + - - -
253B TYR* 3.8 4.4 - - - +
254B GLU* 1.3 88.8 - - + +
256B CYS* 1.3 60.9 + - - +
431B SER 5.6 0.9 - - - -
432B ASN* 3.7 9.9 - - + -
434B TRP* 3.7 28.6 - - + -
469B MET* 3.0 42.1 + - + +
470B THR* 5.1 1.8 - - - +
471B GLY 5.4 2.0 - - - +
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Residues in contact with CYS 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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135B LEU* 3.2 16.4 - - - +
137B ILE* 3.7 30.1 - - - -
236B LEU* 4.8 5.8 - - - -
253B TYR* 3.5 33.4 - - + +
255B LYS* 1.3 73.9 - - - +
257B LEU* 1.3 66.8 + - - +
258B ILE* 4.5 7.6 - - - -
432B ASN 2.9 10.0 + - - +
433B ILE* 3.3 9.0 - - + -
434B TRP* 3.0 28.6 + - - +
469B MET* 3.7 3.8 - - - -
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Residues in contact with LEU 257 (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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135B LEU 2.9 6.5 + - - +
136B LEU* 3.8 22.9 - - + -
137B ILE* 2.7 35.2 + - - +
142B ALA 4.3 5.2 - - - +
143B ALA* 4.4 1.3 - - - -
146B ALA* 3.4 32.5 - - + -
256B CYS* 1.3 75.3 - - - +
258B ILE* 1.3 65.3 + - - +
259B ALA* 4.2 15.5 - - + -
434B TRP* 3.4 24.9 - - + +
436B ALA* 3.8 17.7 - - + +
465B ALA* 3.7 24.2 - - + -
469B MET* 3.7 7.5 - - - +
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.1 18.6 - - + -
236B LEU* 4.1 11.4 - - + -
256B CYS* 4.5 2.2 - - - -
257B LEU* 1.3 74.5 - - - +
259B ALA* 1.3 61.4 + - - +
260B THR* 3.8 20.0 - - + +
406B LEU* 5.3 4.9 - - + -
412B LEU* 3.6 30.7 - - + -
421B PHE* 3.7 36.1 - - + -
433B ILE* 3.8 17.7 - - + -
434B TRP 2.8 14.3 + - - +
435B VAL* 3.2 14.6 - - + +
436B ALA 3.0 24.8 + - - -
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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