Contacts of the strand formed by residues 301 - 306 (chain B) in PDB entry 3IFS
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 PHE 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ILE* 3.8 26.7 - - + -
270A MSE 4.0 21.1 - - + -
301A PHE* 4.6 2.5 - + - -
303A SER* 3.6 32.8 - - - -
314A LEU* 5.0 10.3 - - + -
317A TYR* 3.6 34.8 - + - +
318A VAL* 5.8 0.9 - - + -
325A LEU* 3.8 19.1 - - + -
267B THR 2.8 17.7 + - - +
268B ILE* 3.5 9.6 - - + +
269B GLU 2.9 25.1 + - - +
299B GLY 3.5 2.2 + - - -
300B ILE* 1.3 70.8 - - - +
302B PRO* 1.3 83.1 - - + +
303B SER* 3.5 13.3 + - - -
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Residues in contact with PRO 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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314A LEU* 3.8 20.5 - - + +
317A TYR* 4.3 11.0 - - + -
258B ARG* 5.9 1.1 - - - +
269B GLU 3.7 3.8 - - - +
285B TRP* 3.5 26.0 - - + -
286B LYS* 3.6 23.7 - - - +
289B PHE* 4.7 4.9 - - + -
290B GLY* 3.8 25.8 - - - +
300B ILE* 3.3 11.9 - - + +
301B PHE* 1.3 99.8 - - + +
303B SER* 1.3 60.7 - - - +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.5 23.9 - - - -
303A SER* 4.8 3.7 + - - -
268B ILE* 4.0 13.7 - - - -
269B GLU 2.8 14.8 + - - +
270B MSE 3.9 15.5 - - - +
271B LEU 2.9 18.5 + - - -
285B TRP* 3.4 7.6 - - - -
286B LYS* 4.3 5.8 - - - +
301B PHE* 3.5 7.7 + - - -
302B PRO* 1.3 75.1 - - - +
304B SER* 1.3 73.5 + - - +
314B LEU* 5.7 1.2 - - - +
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Residues in contact with SER 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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286A LYS* 5.1 7.8 + - - -
270B MSE 4.5 4.8 - - - +
271B LEU* 3.3 18.4 - - - +
273B ASN* 6.4 0.2 - - - -
282B ALA* 3.9 24.1 - - - +
283B GLU* 4.4 1.9 + - - -
286B LYS* 3.3 27.8 + - - +
303B SER* 1.3 84.5 + - - +
305B ALA* 1.3 63.5 + - - +
306B ASN* 5.7 1.0 + - - -
310B ASP* 4.9 0.5 - - - +
314B LEU* 5.0 5.9 - - - +
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Residues in contact with ALA 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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270B MSE 3.7 14.6 - - + -
271B LEU 3.1 5.7 + - - +
272B ILE* 3.4 25.7 - - + -
273B ASN* 3.2 25.1 + - - -
304B SER* 1.3 79.5 - - - +
306B ASN* 1.3 66.4 + - - +
307B PHE* 3.8 12.5 + - + -
310B ASP* 3.5 15.3 - - + +
314B LEU* 4.9 5.2 - - + -
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Residues in contact with ASN 306 (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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283A GLU* 5.8 2.0 + - - -
273B ASN* 2.8 34.3 + - - +
276B PRO* 5.4 9.2 - - + -
279B GLN* 3.8 40.5 + - - +
282B ALA* 5.6 1.7 - - - +
304B SER* 5.7 1.6 + - - -
305B ALA* 1.3 75.0 - - - +
307B PHE* 1.3 61.8 + - - +
309B THR* 3.3 12.2 - - + +
310B ASP* 2.8 43.9 + - - +
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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