Contacts of the strand formed by residues 215 - 220 (chain B) in PDB entry 5FA5
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 PRO 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B THR* 3.9 10.0 + - - -
186B CYS* 3.6 36.6 - - + +
187B SER 3.5 21.3 - - - +
188B GLU* 6.1 0.2 - - - +
190B ASN* 3.8 17.7 - - - +
191B ARG 4.0 7.0 - - - +
192B ILE* 3.7 29.4 - - + -
213B TYR 3.6 2.2 - - - +
214B LEU* 1.4 84.3 - - + +
216B THR* 1.4 60.9 + - - +
217B SER 5.4 0.2 - - - +
230B PHE* 4.2 11.2 - - + -
231B GLY 3.6 6.7 - - - +
232B ASP* 4.5 0.7 - - - -
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Residues in contact with THR 216 (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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171B THR* 3.3 28.8 - - + +
172B CYS* 4.0 6.4 - - - +
186B CYS* 4.2 3.8 - - - -
214B LEU* 4.0 11.7 - - + +
215B PRO* 1.4 77.0 - - - +
217B SER* 1.3 57.3 + - - +
231B GLY 2.8 16.0 + - - -
232B ASP 3.4 12.0 - - - -
233B GLU* 4.0 12.3 - - + +
257B CYS* 3.7 21.6 - - - -
258B VAL 2.8 24.4 + - - +
259B THR* 4.5 5.3 - - - +
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B CYS* 4.4 6.5 - - - -
186B CYS* 4.3 1.1 - - - -
215B PRO 3.9 0.6 - - - -
216B THR* 1.3 78.3 + - - +
218B LEU* 1.4 66.9 + - - +
230B PHE* 3.2 10.4 - - - +
231B GLY* 3.0 37.0 + - - +
258B VAL* 3.0 27.5 + - - +
259B THR 3.8 14.1 - - - -
260B GLY* 3.9 11.0 - - - -
261B LEU* 3.4 8.9 - - - +
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Residues in contact with LEU 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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172B CYS* 3.7 32.7 - - - +
173B VAL 4.6 0.2 - - - +
174B ALA* 4.1 18.5 - - + +
184B LEU* 3.8 23.8 - - + +
185B SER 3.7 28.0 - - - +
186B CYS* 3.8 18.4 - - + -
192B ILE* 4.4 9.6 - - + -
217B SER* 1.4 82.4 - - - +
219B ALA* 1.3 63.0 + - - +
228B PHE* 4.3 17.9 - - + -
229B VAL 3.5 3.6 - - - +
230B PHE* 3.9 17.5 - - + -
261B LEU* 4.4 6.6 + - - +
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Residues in contact with ALA 219 (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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174B ALA* 5.1 2.2 - - - -
184B LEU* 5.5 0.4 - - - -
218B LEU* 1.3 76.5 - - - +
220B TRP* 1.3 62.5 + - - +
228B PHE* 3.3 3.4 - - - +
229B VAL* 2.8 55.8 + - + +
261B LEU* 3.4 25.1 - - + +
262B VAL* 5.1 0.9 - - - -
263B PHE* 3.7 13.8 - - + +
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Residues in contact with TRP 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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174B ALA* 2.8 31.7 + - + +
175B ALA 3.1 26.0 + - - -
176B SER* 3.8 6.7 - - - -
177B PRO* 3.6 27.2 - - + +
182B VAL* 3.8 25.1 - - + -
183B PHE* 4.2 4.7 - - - -
184B LEU* 3.6 29.0 - - + +
194B LEU* 3.5 24.2 - - + -
219B ALA* 1.3 74.9 - - - +
221B HIS* 1.3 65.5 + - - +
222B PRO* 3.6 2.4 - - - +
224B GLN 5.3 0.2 - - - -
225B SER 3.6 24.2 - - - -
226B GLU* 4.8 7.4 - - - -
227B VAL 3.7 20.9 - - - -
228B PHE* 4.0 10.1 - + + -
242B THR* 5.0 3.1 - - - -
263B PHE* 3.3 13.4 - - - -
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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