Contacts of the strand formed by residues 210 - 216 (chain A) in PDB entry 4DF3
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 GLU 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A MET* 5.5 1.3 - - - -
208A GLY 4.8 6.5 - - - +
209A LEU* 1.3 79.3 - - - +
211A ILE* 1.3 64.4 - - - +
212A LYS* 3.3 1.2 + - - -
229A ALA* 3.2 3.7 - - - +
230A VAL* 2.9 40.0 + - + +
27B ARG* 4.4 15.6 + - - -
43B ARG* 4.1 23.6 + - - +
54B GLU* 4.9 3.9 - - - +
56B ASN* 3.5 24.6 + - - +
58B TYR* 5.8 4.2 - - - -
59B ARG* 4.7 13.9 + - - +
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 4.0 26.2 - - + -
204A LEU* 4.3 21.8 - - + -
205A MET* 4.3 13.8 - - + +
209A LEU 4.8 0.9 - - - +
210A GLU* 1.3 73.1 - - - +
212A LYS* 1.3 60.2 + - - +
213A ASP 3.8 9.0 - - - +
214A VAL* 3.8 29.6 - - + -
227A ILE* 3.9 16.4 - - + -
228A TYR 3.7 3.4 - - - +
229A ALA* 3.8 16.4 - - + -
59B ARG* 3.0 17.0 + - - -
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.8 18.6 - - + +
72A GLU* 2.8 35.9 + - - +
210A GLU 3.3 4.3 + - - +
211A ILE* 1.3 74.5 - - - +
213A ASP* 1.3 60.4 + - - +
228A TYR* 2.7 37.2 + - + +
229A ALA* 4.6 1.6 - - - -
230A VAL* 4.4 13.6 - - + +
58B TYR* 3.3 27.1 + - - +
59B ARG* 3.9 26.7 + - - +
220B PHE 4.5 9.9 + - - -
221B ASP* 5.5 4.9 + - - +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY 3.8 3.6 - - - +
70A LEU* 3.5 15.2 - - + -
71A ILE* 2.9 47.9 + - + +
211A ILE* 3.7 2.8 - - - +
212A LYS* 1.3 81.6 - - - +
214A VAL* 1.3 83.1 + - - +
215A VAL* 4.0 4.0 - - - +
226A MET 4.5 0.4 - - - -
228A TYR* 2.8 40.3 + - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 4.1 19.3 - - + +
197A TYR* 3.1 28.0 - - - +
201A ILE* 5.0 4.3 - - + -
211A ILE* 3.8 19.1 - - + -
213A ASP* 1.3 86.1 + - - +
215A VAL* 1.3 70.3 + - - +
225A ALA* 3.9 17.9 - - + -
226A MET 3.3 11.7 - - - +
227A ILE* 4.2 15.7 - - + -
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.6 42.0 - - + +
68A LYS* 3.6 24.5 - - + +
69A GLY 3.9 4.3 - - - +
70A LEU* 3.8 18.1 - - + +
189A VAL* 4.7 0.7 - - - -
213A ASP* 4.0 12.3 - - - +
214A VAL* 1.3 81.2 - - - +
216A HIS* 1.3 65.0 + - - +
217A LEU* 3.8 4.5 - - + +
225A ALA* 3.2 4.5 - - - -
226A MET* 2.8 37.1 + - + +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 2.9 32.3 + - - +
184A ALA* 2.9 26.6 + - + -
185A ARG 3.4 22.0 - - - -
186A SER* 3.3 25.7 + - - +
189A VAL* 3.9 27.8 - - + +
190A THR* 6.1 0.9 - - + -
215A VAL* 1.3 75.5 - - - +
217A LEU* 1.3 57.5 + - - +
218A ASP* 3.1 39.9 + - + +
222A ARG 3.3 21.2 + - - -
224A HIS 3.6 15.0 + - - -
225A ALA* 4.0 4.0 - - - +
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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