Contacts of the strand formed by residues 217 - 223 (chain B) in PDB entry 3F12
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 THR 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY* 3.5 7.9 - - - -
131B PRO* 3.9 28.1 - - + +
210B VAL* 4.2 1.7 - - - +
211B ASN* 3.6 2.6 - - - -
212B HIS* 2.7 36.1 + - - +
215B SER* 2.8 21.5 + - - -
216B ASN* 1.3 77.2 - - - +
218B LYS* 1.3 56.2 + - - +
219B VAL* 4.1 19.8 + - + +
13D GLN* 4.2 0.7 - - - +
127D SER* 3.1 28.4 + - - +
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL 3.5 8.7 - - - +
211B ASN* 3.4 16.4 - - + +
217B THR* 1.3 75.7 - - - +
219B VAL* 1.3 70.5 + - - +
220B ASP* 4.7 11.2 - - - +
13D GLN* 3.2 22.0 + - - +
14D PRO 5.1 2.6 + - - -
15D GLY 4.8 4.0 + - - -
16D ARG* 2.8 69.9 - - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PRO 4.9 5.8 - - - +
133B VAL* 3.6 36.1 - - + +
208B CYS 3.8 0.9 - - - +
210B VAL* 2.7 44.6 + - + +
217B THR* 4.1 19.0 - - + -
218B LYS* 1.3 84.2 - - - +
220B ASP* 1.3 79.1 + - - +
221B LYS* 4.3 5.8 + - + -
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 5.5 1.0 + - - -
207B ILE* 4.0 15.6 - - + +
208B CYS 3.5 4.0 - - - -
209B ASN* 3.8 30.3 + - - +
210B VAL 4.4 0.9 + - - +
218B LYS* 4.7 12.2 - - - +
219B VAL* 1.3 88.0 + - - +
221B LYS* 1.3 71.2 + - - +
222B LYS 4.3 0.2 - - - -
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Residues in contact with LYS 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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124A GLU* 2.7 34.9 + - - -
133B VAL* 3.3 40.2 - - + +
135B PRO* 4.7 14.8 - - + +
152B CYS* 4.4 2.8 - - - -
207B ILE* 3.7 3.9 - - - -
208B CYS* 3.4 30.5 + - - -
219B VAL* 4.3 8.3 + - + -
220B ASP* 1.3 81.5 - - - +
222B LYS* 1.3 72.6 + - - +
223B VAL* 3.7 4.2 - - - +
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Residues in contact with LYS 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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135B PRO* 4.3 8.3 - - - +
205B THR* 4.7 17.2 + - + +
206B TYR 3.9 6.7 - - - +
207B ILE* 3.6 26.7 - - + +
221B LYS* 1.3 87.3 - - - +
223B VAL* 1.3 74.0 + - - +
224B GLU* 3.2 37.3 + - + +
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Residues in contact with VAL 223 (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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135B PRO* 4.2 17.7 - - + -
136B LEU 3.9 23.1 - - - +
137B ALA* 4.8 0.4 - - - -
150B LEU* 4.1 24.0 - - + +
151B GLY 4.2 5.4 - - - +
152B CYS* 4.8 2.9 - - - -
166B TRP* 3.5 29.6 - - + -
205B THR* 5.8 0.5 - - - -
206B TYR* 2.9 36.1 + - + +
221B LYS 3.7 6.5 - - - +
222B LYS* 1.3 82.4 - - - +
224B GLU* 1.3 68.4 + - - +
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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