Contacts of the strand formed by residues 220 - 226 (chain A) in PDB entry 4FUL
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 ILE 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.9 32.1 - - + -
219A CYS* 1.3 78.9 - - - +
221A PHE* 1.3 64.5 + - - +
222A ILE* 3.6 26.0 - - + -
233A ILE 3.5 0.9 - - - +
234A LYS 4.0 0.2 - - - -
235A VAL* 2.7 40.2 + - + +
237A PRO* 4.1 15.9 - - + -
287A ILE* 3.8 29.4 - - + -
288A LYS* 4.6 4.3 - - + -
293A VAL* 4.6 13.7 - - + -
297A LEU* 4.6 10.1 - - + -
303A ILE* 3.8 14.6 - - + -
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 5.1 13.5 - - - -
219A CYS* 3.8 30.3 - - + -
220A ILE* 1.3 74.4 - - - +
222A ILE* 1.4 59.6 + - - +
223A VAL* 5.4 2.3 - - + +
232A THR* 4.2 20.4 - - + -
233A ILE 3.6 4.5 - - - -
234A LYS* 3.9 29.2 - - + -
302A GLU* 5.4 0.3 - - - -
303A ILE* 3.6 28.3 + - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE* 3.6 27.4 - - + +
221A PHE* 1.4 72.1 - - - +
223A VAL* 1.3 63.9 + - - +
224A ILE* 3.4 26.5 - - + +
232A THR* 3.6 0.4 - - - -
233A ILE 2.9 30.0 + - - +
235A VAL* 3.8 29.2 - - + -
244A ILE* 4.9 5.4 - - + -
272A LEU* 5.3 5.8 - - + -
281A LEU* 5.5 3.4 - - + -
287A ILE* 4.9 14.6 - - + -
293A VAL* 5.2 1.6 - - + -
303A ILE* 3.4 35.4 - - + +
305A VAL* 4.0 18.6 - - + -
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Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PHE* 5.4 2.5 - - + +
222A ILE* 1.3 73.2 - - - +
224A ILE* 1.3 60.2 + - - +
225A HIS* 3.3 25.5 - - + +
230A SER* 3.9 17.3 - - - +
231A GLN 3.7 9.6 - - - +
232A THR* 3.8 21.3 - - + +
302A GLU* 5.0 13.2 - - + +
303A ILE 2.9 13.1 + - - +
304A HIS* 3.4 28.5 - - + +
305A VAL* 2.9 32.0 + - - +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ILE* 3.4 32.1 - - + +
223A VAL* 1.3 70.3 - - - +
225A HIS* 1.3 69.5 + - - +
226A ARG* 6.1 0.2 - - + -
230A SER* 3.4 1.0 - - - -
231A GLN* 2.9 35.1 + - - +
233A ILE* 4.0 24.5 - - + -
244A ILE* 4.8 8.5 - - + -
248A PHE* 3.7 41.2 - - + -
272A LEU* 4.1 15.7 - - + -
305A VAL* 3.7 18.6 - - + -
307A LEU* 4.2 17.7 - - + +
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Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 3.3 19.1 - - + +
224A ILE* 1.3 76.9 - - - +
226A ARG* 1.4 70.7 + - - +
227A SER 4.9 8.0 + - - +
228A THR 5.7 0.4 + - - -
229A THR 3.5 7.9 + - - +
230A SER* 3.6 18.9 - - - +
275A CYS* 4.0 8.2 - - - -
304A HIS* 2.7 33.5 + + - -
305A VAL 3.2 23.5 + - - +
306A VAL* 3.9 14.1 - - + -
307A LEU* 3.5 20.4 + - - +
823A LEU* 3.8 18.9 - - + +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS* 1.4 78.5 - - - +
227A SER* 1.3 69.3 + - - +
229A THR* 2.7 40.6 + - - +
248A PHE* 6.4 2.2 - - + -
270A PHE* 3.3 35.5 - - - -
307A LEU* 3.5 43.5 + - + +
308A ASP* 4.7 2.0 - - - +
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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