Contacts of the strand formed by residues 300 - 309 (chain B) in PDB entry 4IF8
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 SER 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLN* 4.3 5.8 - - - +
249B VAL 3.2 30.6 + - - +
298B LEU 4.6 3.1 + - - -
299B LEU* 1.3 80.2 + - - +
301B ARG* 1.4 68.8 + - - +
302B ARG* 3.5 7.7 + - - +
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Residues in contact with ARG 301 (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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246B ILE* 5.8 13.2 - - + -
247B TYR 4.0 6.3 - - - -
248B GLN* 3.8 33.5 - - + +
300B SER* 1.4 73.6 - - - +
302B ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 302 (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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245B GLY 3.6 0.5 - - - +
246B ILE* 3.7 8.6 - - - +
247B TYR 3.0 36.3 + - - +
249B VAL* 5.3 9.2 - - + -
300B SER* 4.0 8.7 - - - +
301B ARG* 1.3 75.2 - - - +
303B VAL* 1.4 70.8 + - + +
304B VAL* 3.4 9.2 - - + +
382B LEU* 3.5 43.7 - - - +
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Residues in contact with VAL 303 (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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244B SER* 4.4 14.4 - - - +
245B GLY* 3.7 12.8 - - - +
246B ILE* 5.0 5.6 - - + +
302B ARG* 1.4 76.5 - - + +
304B VAL* 1.3 62.8 + - - +
305B ASP* 5.2 3.5 - - - +
382B LEU 3.3 20.2 + - - +
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Residues in contact with VAL 304 (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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244B SER* 3.4 3.9 - - - -
245B GLY 3.2 27.7 + - - +
247B TYR* 3.8 10.1 - - + -
249B VAL* 3.5 27.8 - - + -
260B LEU* 4.6 0.2 - - + -
302B ARG* 3.4 20.2 - - + +
303B VAL* 1.3 77.2 - - - +
305B ASP* 1.3 64.2 + - - +
306B VAL* 3.5 23.9 + - + +
382B LEU* 3.4 21.5 - - + +
384B VAL* 3.8 29.8 - - + +
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Residues in contact with ASP 305 (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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242B PHE* 3.8 29.6 - - + -
243B ARG 4.1 3.6 - - - -
244B SER* 3.2 20.3 + - - -
303B VAL* 5.2 4.0 - - - +
304B VAL* 1.3 72.3 - - - +
306B VAL* 1.3 60.9 + - - +
307B SER* 3.9 1.2 + - - -
382B LEU 3.4 12.5 + - - +
383B VAL* 4.1 21.2 - - + +
384B VAL 3.5 21.5 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 4.7 5.7 - - + -
241B MET 3.5 0.9 - - - +
242B PHE* 3.4 9.5 - - - -
243B ARG 3.1 30.4 + - - +
247B TYR* 3.7 39.3 - - + -
260B LEU* 3.7 28.9 - - + -
262B ILE* 4.1 5.4 - - + -
304B VAL* 3.7 20.2 - - + +
305B ASP* 1.3 71.2 - - - +
307B SER* 1.4 63.1 + - - +
308B VAL* 3.6 23.7 + - + -
384B VAL 3.9 7.4 - - - +
386B ILE* 4.8 0.2 - - + -
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Residues in contact with SER 307 (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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226B GLU* 4.9 6.6 + - - -
240B MET* 3.8 18.5 - - - +
241B MET 3.3 6.2 + - - -
242B PHE* 3.5 21.5 - - - +
305B ASP 3.9 1.5 + - - -
306B VAL* 1.4 68.6 - - - +
308B VAL* 1.4 59.8 + - - +
384B VAL 3.2 7.5 + - - -
385B LYS* 3.6 35.6 + - - +
386B ILE* 3.0 31.5 + - - +
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Residues in contact with VAL 308 (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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214B TRP* 5.8 2.0 - - + -
218B PHE* 4.7 8.7 - - + -
240B MET* 3.7 3.8 - - - -
241B MET* 2.7 53.3 + - + +
262B ILE* 3.6 29.4 - - + -
272B PHE* 3.7 24.9 - - + -
306B VAL* 3.6 14.6 - - + -
307B SER* 1.4 76.2 - - - +
309B PRO* 1.4 77.3 - - + +
360B MET* 3.7 9.0 - - + -
386B ILE* 3.8 10.5 - - + -
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Residues in contact with PRO 309 (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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228B PHE* 3.8 13.2 - - + -
238B VAL* 4.4 6.1 - - + -
239B PRO 3.6 9.0 - - - +
240B MET* 3.9 8.5 - - - -
241B MET* 3.4 2.8 - - - +
308B VAL* 1.4 89.3 - - + +
310B ARG* 1.3 62.1 + - - +
311B LEU* 4.4 1.3 - - - +
360B MET* 3.4 23.9 - - - +
386B ILE* 3.3 34.8 - - + +
390B TYR* 3.7 20.0 - - + +
411B PRO* 3.6 22.9 - - + -
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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