Contacts of the strand formed by residues 216 - 220 (chain F) in PDB entry 3STJ
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 GLY 216 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE 3.5 0.3 - - - +
177F GLN* 3.2 8.2 - - - +
178F THR* 2.9 43.0 + - - -
180F ALA 5.2 1.9 + - - -
182F ILE* 4.2 14.8 - - - -
204F ALA 3.8 5.2 - - - -
205F ILE* 4.2 8.5 - - - -
214F GLY 3.9 0.4 - - - -
215F ILE* 1.3 74.5 - - - +
217F PHE* 1.3 63.3 + - - -
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Residues in contact with PHE 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E LEU* 4.3 7.6 - - + -
164F ARG* 4.5 5.6 - - + -
167F LEU* 3.7 28.5 - - + -
169F LEU* 4.2 10.3 - - + -
175F PHE* 3.7 31.2 - - + -
176F ILE 3.3 3.4 - - - -
177F GLN* 3.5 30.1 - - + -
178F THR* 5.6 0.2 - - - -
182F ILE* 4.9 1.7 - - - +
202F ASN* 3.8 4.4 - - - +
203F THR 2.9 27.2 + - - -
204F ALA* 2.8 34.1 + - + +
205F ILE* 4.2 1.3 - - - -
206F LEU* 3.8 23.3 - - + -
215F ILE* 3.4 33.9 - - + -
216F GLY* 1.3 78.1 - - - -
218F ALA* 1.3 54.8 + - - +
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Residues in contact with ALA 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F PHE* 3.4 8.5 - - - -
176F ILE* 2.9 36.1 + - + +
178F THR* 5.5 1.6 - - + -
191F LEU* 3.9 21.1 - - + -
200F GLY* 4.3 2.9 - - - -
201F ILE 3.1 24.5 - - - +
202F ASN* 3.8 14.8 - - - +
203F THR 4.2 0.4 - - - +
217F PHE* 1.3 74.3 - - - +
219F ILE* 1.4 63.8 + - - +
220F PRO 3.5 0.3 - - - -
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Residues in contact with ILE 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASN* 3.7 16.4 - - - +
111F SER* 3.2 26.9 - - - +
112F ASP 3.7 5.2 - - - +
113F ILE* 3.5 29.4 - - + -
172F LEU 6.0 1.3 - - - +
175F PHE* 3.9 16.2 - - + -
200F GLY* 3.1 1.7 - - - -
201F ILE* 2.7 37.8 + - + +
203F THR* 3.2 23.5 + - + +
218F ALA* 1.4 69.2 - - - +
220F PRO* 1.3 81.7 - - + +
223F MET* 4.0 19.5 - - + -
224F ALA* 4.2 1.9 - - + +
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Residues in contact with PRO 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F SER* 3.5 22.0 - - - +
174F ASN* 3.1 45.1 - - - +
176F ILE* 3.6 13.9 - - + +
199F ILE 3.6 7.0 - - - +
218F ALA 3.5 4.9 - - - +
219F ILE* 1.3 89.5 - - + +
221F SER* 1.4 59.9 + - - +
222F ASN* 3.3 1.1 - - + +
223F MET* 3.1 21.6 + - + +
224F ALA* 2.9 24.1 + - - +
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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