Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 4F5G
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 LEU 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 4.2 21.8 - - + +
12A PHE* 3.9 24.9 - - + -
124B LEU* 3.9 21.5 - - + -
130B VAL* 4.7 0.4 - - + -
182B GLY* 5.0 1.5 - - - +
183B ASP 2.8 16.0 + - - +
184B VAL* 3.1 18.5 - - + +
185B VAL 3.0 21.0 + - - -
215B GLY 3.9 0.4 + - - -
216B TRP* 1.3 71.7 - - - +
218B PRO* 1.3 68.8 - - - +
245B HIS* 4.4 1.6 - - + -
247B GLU* 3.7 46.4 - - + +
248B LEU* 3.9 8.1 - - - +
249B ILE* 4.0 9.0 - - + -
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Residues in contact with PRO 218 (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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185B VAL* 3.4 10.5 - - + +
187B PHE* 5.1 1.1 - - + -
211B SER* 3.5 14.6 - - - +
216B TRP* 3.4 8.5 - - + +
217B LEU* 1.3 88.8 - - + +
219B LEU* 1.3 58.3 + - - +
220B ILE* 4.1 7.0 - - + -
241B PHE* 3.4 39.9 - - + -
245B HIS* 3.6 7.2 - - + -
247B GLU 3.5 19.5 - - - +
248B LEU* 3.5 15.5 - - + +
249B ILE 3.1 22.2 + - - +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.9 23.3 - - + -
120B ALA* 4.3 11.2 - - + -
124B LEU* 5.0 2.7 - - + -
147B PHE* 4.0 27.1 - - + -
184B VAL* 3.6 22.9 - - + -
185B VAL 2.9 7.7 + - - +
186B LEU* 3.1 16.8 - - + +
187B PHE 2.9 24.6 + - - +
217B LEU 3.5 0.6 + - - -
218B PRO* 1.3 74.3 - - - +
220B ILE* 1.3 77.9 + - - +
221B ASP 4.0 0.7 - - - +
249B ILE* 3.2 34.8 - - + +
251B ALA* 4.4 5.8 - - + -
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Residues in contact with ILE 220 (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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187B PHE* 3.4 28.5 - - + -
189B GLY* 3.7 28.9 - - - +
204B TRP* 4.7 3.6 - - + -
218B PRO* 4.7 6.5 - - + -
219B LEU* 1.3 81.2 - - - +
221B ASP* 1.3 64.7 + - - +
222B ILE* 4.3 2.7 - - + -
238B LEU* 4.2 34.8 - - + -
241B PHE* 4.4 23.8 - - + -
248B LEU* 5.4 5.6 - - + -
249B ILE 2.9 11.5 + - - +
250B VAL* 3.3 15.7 - - + +
251B ALA 2.8 26.3 + - - -
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Residues in contact with ASP 221 (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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117B LEU* 3.8 11.8 - - + +
143B HIS* 2.5 30.1 + - + +
186B LEU* 3.9 22.9 - - + -
187B PHE 3.0 6.6 + - - +
188B HIS* 3.3 8.9 - - + +
189B GLY 2.8 22.2 + - - -
190B CYS 5.5 0.3 - - - +
219B LEU* 3.8 3.2 + - - -
220B ILE* 1.3 70.9 - - - +
222B ILE* 1.3 64.2 + - - +
223B ALA 3.9 3.6 + - - -
251B ALA* 3.5 9.2 - - - +
256B LLP 2.7 41.6 + - - +
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Residues in contact with ILE 222 (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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92B LEU* 3.6 24.2 - - + -
189B GLY* 4.3 17.9 - - - +
190B CYS* 4.4 6.5 - - - +
220B ILE* 4.3 2.2 - - + +
221B ASP* 1.3 75.9 + - - +
223B ALA* 1.3 59.5 + - - +
225B GLN* 3.9 41.2 + - + +
234B ASP 4.0 20.0 - - - +
235B ALA* 4.7 2.7 - - - -
238B LEU* 4.3 15.5 - - + -
250B VAL* 3.7 18.2 - - + -
251B ALA 2.9 12.6 + - - +
252B SER* 3.3 4.6 - - - -
253B SER 3.1 21.2 + - - +
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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