Contacts of the strand formed by residues 207 - 212 (chain B) in PDB entry 3EYF
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B TRP* 3.4 6.8 - - - -
167B ASN* 2.8 40.6 + - - +
205B THR* 4.6 16.4 - - - +
206B TYR* 1.3 79.7 - - - +
208B CYS* 1.3 74.0 - - - +
209B ASN* 3.8 15.8 + - - +
220B ASP* 4.0 9.4 - - + -
221B LYS 3.1 18.6 - - - +
222B LYS* 3.7 24.9 - - + +
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Residues in contact with CYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.9 7.6 - - - -
152B CYS* 2.0 52.9 - - + -
164B VAL* 4.3 7.6 - - + -
165B SER 3.3 6.1 - - - +
166B TRP* 3.7 21.7 - - + -
207B ILE* 1.3 76.5 - - - +
209B ASN* 1.3 60.4 + - - +
210B VAL* 4.4 4.7 - - - -
219B VAL 3.9 0.3 - - - +
220B ASP* 3.4 0.7 - - - -
221B LYS* 2.8 46.9 + - - -
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Residues in contact with ASN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 3.5 1.7 + - - +
164B VAL* 3.4 6.1 - - - +
165B SER* 2.6 62.3 + - - +
167B ASN 3.7 1.4 + - - -
168B SER* 3.0 37.3 + - - +
207B ILE* 3.8 16.5 + - - +
208B CYS* 1.3 73.0 - - - +
210B VAL* 1.3 60.8 + - - +
211B ASN 4.1 0.2 + - - -
220B ASP* 2.9 29.7 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PRO* 4.2 11.9 - - + -
133B VAL* 4.1 27.1 - - + -
154B VAL* 3.9 28.9 - - + -
162B VAL* 3.7 25.4 - - + -
163B THR 3.6 4.3 - - - +
164B VAL* 4.6 8.5 - - + -
208B CYS* 4.4 9.6 - - - -
209B ASN* 1.3 78.3 - - - +
211B ASN* 1.3 65.8 + - - +
212B HIS 4.1 0.2 - - - -
218B LYS* 3.2 6.2 - - - +
219B VAL 2.6 45.4 + - - +
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Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO 4.4 0.2 - - - +
162B VAL* 3.6 3.7 - - - -
163B THR* 3.0 48.1 + - - +
209B ASN 4.1 0.2 + - - -
210B VAL* 1.3 75.0 - - - +
212B HIS* 1.3 63.9 + - - +
213B LYS* 3.3 40.9 + - + +
216B ASN* 5.8 0.3 - - - -
217B THR 3.7 6.5 + - - +
218B LYS* 3.8 29.7 - - + +
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Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LYS 3.2 25.0 + - - -
130B GLY* 3.8 2.2 - - - -
131B PRO* 3.7 20.6 - - + -
157B TYR* 3.7 11.3 - + + -
158B PHE 3.4 16.6 - - - -
159B PRO* 2.5 32.4 + - + -
161B PRO 3.5 14.4 - - - -
162B VAL* 4.1 7.6 - - + -
210B VAL* 4.1 0.8 - - - +
211B ASN* 1.3 74.3 - - - +
213B LYS* 1.3 62.0 + - - +
214B PRO* 3.7 8.5 - - + +
215B SER* 2.6 32.9 + - - +
216B ASN 3.2 2.6 + - - -
217B THR 2.7 34.9 + - - +
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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