Contacts of the strand formed by residues 215 - 221 (chain F) in PDB entry 5GJQ
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 215 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F ALA* 5.3 0.4 - - + -
50F VAL 3.2 9.6 - - - +
51F GLU* 3.8 5.2 - - - -
52F LYS* 2.8 19.6 + - - -
199F LEU* 3.4 34.8 - - + -
202F LEU* 3.7 16.6 - - + -
206F MET* 3.5 31.0 - - + -
210F LEU* 3.7 22.2 - - + -
211F ASN 4.0 6.5 - - - +
212F ALA 4.0 3.3 - - - +
214F ASN* 1.3 82.8 - - - +
216F GLU* 1.3 64.8 + - - +
217F LEU* 5.0 0.9 - - + -
234F LEU* 3.9 29.4 - - + +
238F ILE* 5.5 2.2 - - + -
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Residues in contact with GLU 216 (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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49F ALA* 3.3 4.0 - - - +
50F VAL* 2.9 46.7 + - + +
52F LYS* 3.3 22.1 + - + +
64F ILE 3.6 17.2 - - - +
65F GLU* 4.0 4.2 - - - +
66F LYS* 2.4 36.4 + - - +
67F ILE* 2.8 22.4 + - + +
215F ILE* 1.3 73.1 - - - +
217F LEU* 1.3 64.2 + - - +
228F MET* 4.1 19.6 - - + +
229F PHE 6.1 0.9 - - - +
234F LEU* 4.9 4.0 - - + -
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Residues in contact with LEU 217 (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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47F CYS* 4.9 5.4 - - + -
48F LEU 3.2 21.5 - - - +
49F ALA* 3.6 19.3 - - + -
67F ILE* 4.2 1.5 - - - +
195F ILE* 4.0 28.7 - - + -
198F SER* 5.2 3.8 - - - -
199F LEU* 4.4 10.5 - - + -
215F ILE* 5.0 1.3 - - + -
216F GLU* 1.3 78.5 - - - +
218F ALA* 1.3 67.0 - - - +
228F MET* 3.9 4.4 - - - +
229F PHE* 2.9 65.9 + - + +
234F LEU* 3.7 25.1 - - + +
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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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46F VAL 4.0 0.2 - - - +
47F CYS* 3.4 2.9 - - - +
48F LEU* 2.8 37.6 + - + +
67F ILE* 4.1 13.9 - - + -
217F LEU* 1.3 77.5 - - - +
219F THR* 1.3 63.9 + - - +
226F PHE* 3.9 29.8 - - + -
227F HIS 3.1 16.8 - - - +
228F MET* 4.0 5.8 - - - -
229F PHE* 4.1 2.5 - - - -
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Residues in contact with THR 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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46F VAL 3.3 6.5 - - - -
47F CYS* 4.1 10.5 - - + -
191F LEU* 4.1 19.7 - - + -
195F ILE* 3.9 22.4 - - + -
217F LEU* 4.6 0.9 - - + -
218F ALA* 1.3 80.4 - - - +
220F VAL* 1.3 67.4 + - - +
221F GLN* 4.0 16.0 + - - +
226F PHE* 4.4 0.5 - - - -
227F HIS* 2.9 39.2 + - - +
229F PHE* 3.5 27.1 - - + -
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Residues in contact with VAL 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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45F GLY* 3.1 3.0 - - - -
46F VAL* 2.9 39.8 + - + +
48F LEU* 5.4 4.9 - - + -
73F HIS* 3.9 22.0 - - + +
75F GLY* 4.6 1.8 - - - +
144F GLY 4.0 18.8 - - - +
145F GLY* 5.2 0.2 - - - -
146F VAL* 3.6 24.4 - - + +
219F THR* 1.3 79.6 - - - +
221F GLN* 1.3 64.4 + - - +
224F GLN 4.2 6.7 - - - +
225F ASN 4.7 0.4 - - - -
226F PHE* 3.7 42.0 - - + +
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Residues in contact with GLN 221 (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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44F GLU 3.4 9.1 - - - +
146F VAL* 4.1 5.5 - - - +
191F LEU* 3.9 27.2 - - + +
219F THR* 4.0 13.3 + - - +
220F VAL* 1.3 80.9 - - - +
222F PRO* 1.3 75.5 - - + +
223F GLY 3.1 5.2 - - - +
224F GLN* 2.6 60.2 + - - +
225F ASN 5.0 0.2 + - - -
227F HIS* 6.2 0.2 - - - -
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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