Contacts of the strand formed by residues 250 - 255 (chain E) in PDB entry 1FZB
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 THR 250 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E GLU* 3.9 9.7 + - - +
211E CYS* 3.0 34.0 + - - +
227E ILE* 4.7 4.7 - - + -
238E VAL* 3.7 29.2 - - + -
248E GLY 3.5 1.8 + - - -
249E TRP* 1.3 70.9 - - - +
251E VAL* 1.3 62.9 + - - +
252E ILE* 3.3 15.8 + - + +
302E LEU* 4.4 10.8 - - + -
453E LYS* 3.2 0.9 - - - -
454E ILE* 2.9 44.2 + - - +
455E ARG* 5.6 0.7 - - - -
456E PRO* 6.1 0.2 - - - +
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Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E VAL* 3.9 3.3 - - - +
239E TYR* 3.1 39.7 + - + +
241E ASP* 4.1 5.8 - - + +
249E TRP 3.1 7.2 + - - +
250E THR* 1.3 75.7 - - - +
252E ILE* 1.3 64.7 + - - +
253E GLN 3.8 16.8 - - - +
254E ASN* 4.2 9.4 - - + -
289E PRO* 5.5 1.6 - - + -
292E TYR* 2.7 47.1 + - + +
451E SER* 5.5 1.3 - - - -
452E MET 4.1 2.2 - - - +
453E LYS* 3.8 26.0 - - - +
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Residues in contact with ILE 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E THR* 3.3 19.4 + - + +
251E VAL* 1.3 76.8 - - - +
253E GLN* 1.3 62.3 + - + +
292E TYR* 4.6 2.2 - - - -
293E TRP* 3.9 4.3 - - + -
294E LEU* 3.2 51.8 + - + +
299E ILE* 3.5 35.4 - - + +
302E LEU* 4.0 3.4 - - + -
310E LEU* 5.4 1.6 - - + -
329E PHE* 5.7 3.8 - - + -
452E MET* 2.6 41.8 + - + +
453E LYS* 4.5 2.2 - - - +
454E ILE* 3.8 31.4 - - + -
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Residues in contact with GLN 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E VAL* 3.7 6.4 - - - +
252E ILE* 1.3 82.0 - - - +
254E ASN* 1.3 68.5 - - - +
255E ARG* 3.1 25.5 - - - +
262E PHE* 4.4 3.1 - - + -
292E TYR* 3.2 14.8 - - - +
293E TRP* 3.5 21.8 - - + -
412E PRO* 3.3 9.3 - - - +
413E ASN* 3.2 19.5 - - - +
450E MET* 3.7 4.9 + - - +
451E SER* 3.5 12.3 - - - +
452E MET* 3.0 60.4 + - + +
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Residues in contact with ASN 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E VAL* 4.2 14.4 - - + -
253E GLN* 1.3 79.5 - - - +
255E ARG* 1.3 79.9 + - - +
256E GLN* 3.5 31.2 + - - +
262E PHE* 3.9 0.2 - - - -
289E PRO* 3.8 14.7 + - + +
290E GLY 2.9 28.7 + - - +
291E GLU* 3.1 26.0 - - - +
292E TYR* 3.1 14.4 + - + -
449E LYS* 6.0 0.3 - - - +
450E MET 3.7 6.8 - - - +
451E SER* 4.0 10.3 - - - -
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Residues in contact with ARG 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E GLN* 3.1 20.6 - - - +
254E ASN* 1.3 79.9 - - - +
256E GLN* 1.3 65.3 - - - +
258E GLY* 5.4 0.2 - - - -
260E VAL 4.7 4.0 + - - -
262E PHE* 3.2 48.3 - - - +
291E GLU* 3.6 10.9 + - - +
412E PRO 2.5 33.9 + - - +
413E ASN* 3.5 6.9 - - - +
414E GLY 3.4 21.8 + - - -
416E TYR* 3.7 35.5 - - + +
435E VAL* 3.3 18.7 - - + +
448E ARG 4.5 0.2 - - - -
449E LYS* 3.5 4.0 - - - +
450E MET* 2.7 42.8 + - + +
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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