Contacts of the strand formed by residues 207 - 213 (chain E) in PDB entry 3UNF
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 VAL 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E VAL* 4.7 2.2 - - + -
45E ALA 3.7 3.6 - - - +
47E LYS* 4.0 4.8 - - - +
189E LEU* 3.7 25.8 - - + -
192E LEU* 4.2 7.0 - - + -
202E LEU* 3.7 32.3 - - + -
203E THR 3.4 13.7 + - - +
204E THR 4.4 0.3 - - - +
205E LYS 3.6 1.6 - - - -
206E ASN* 1.3 95.2 - - - +
208E SER* 1.3 64.8 + - - +
209E ILE* 4.1 15.7 - - + -
222E ASP 3.2 22.2 - - - +
226E VAL* 3.8 14.8 - - + +
230E LEU* 4.9 3.4 - - + -
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Residues in contact with SER 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 3.5 4.2 - - - +
45E ALA* 2.8 41.1 + - - +
47E LYS* 4.1 15.4 - - - +
59E LYS* 5.1 3.9 + - - -
60E ILE* 3.7 21.2 + - - +
207E VAL* 1.3 73.4 - - - +
209E ILE* 1.3 64.8 + - - +
220E ILE* 4.0 9.9 - - - +
221E TYR 3.9 4.2 + - - -
222E ASP* 2.9 23.2 + - - -
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Residues in contact with ILE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.5 1.3 - - + -
43E LEU 3.3 9.6 - - - +
44E VAL* 4.4 10.5 - - + -
60E ILE* 3.7 4.3 - - - -
185E VAL* 4.1 17.9 - - + -
189E LEU* 4.4 10.1 - - + -
207E VAL* 4.1 9.0 - - + -
208E SER* 1.3 80.8 - - - +
210E GLY* 1.3 60.1 + - - +
211E ILE* 3.8 28.0 - - + -
219E THR 3.6 0.7 - - - +
220E ILE* 3.4 5.5 - - - +
221E TYR* 3.0 43.0 + - + +
226E VAL* 3.8 22.0 - - + +
229E PHE* 3.9 32.3 - - + -
230E LEU* 6.4 0.4 - - + -
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Residues in contact with GLY 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ALA 4.1 0.5 - - - +
42E VAL* 3.6 0.3 - - - -
43E LEU* 2.7 42.6 + - - +
60E ILE* 3.5 9.0 - - - +
209E ILE* 1.3 73.9 - - - +
211E ILE* 1.3 65.4 + - - +
218E PHE* 3.7 24.1 - - - -
219E THR 3.3 8.1 - - - -
220E ILE* 4.7 0.2 - - - -
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Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E HIS* 4.4 10.3 - - + +
41E ALA 3.7 3.6 - - - +
42E VAL* 4.0 11.4 - - + -
181E LEU* 3.7 31.4 - - + -
185E VAL* 4.0 21.5 - - + -
209E ILE* 3.8 12.8 - - + -
210E GLY* 1.3 79.6 - - - +
212E VAL* 1.3 64.8 + - - +
216E LEU* 4.6 9.6 - - + +
217E GLU 3.4 5.0 - - - +
218E PHE* 3.3 6.1 - - - -
219E THR* 3.1 30.4 + - - -
221E TYR* 3.5 31.6 - - + +
229E PHE* 4.0 13.9 - - + -
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Residues in contact with VAL 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E HIS* 3.7 3.0 - - - +
41E ALA* 2.8 37.5 + - + +
65E ASN 4.1 0.7 - - - +
66E HIS* 3.6 29.8 - - - +
132E ALA* 3.6 34.1 - - + +
133E GLY* 3.8 9.9 - - - +
134E TYR* 4.2 7.7 - - + +
211E ILE* 1.3 78.9 - - - +
213E GLY* 1.3 61.2 + - - +
216E LEU* 4.0 9.0 - - - +
218E PHE* 3.7 28.0 - - + +
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Residues in contact with GLY 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E THR 3.4 12.6 - - - -
40E HIS* 4.0 7.8 + - - -
134E TYR* 3.7 23.8 - - - +
212E VAL* 1.3 81.1 - - - +
214E LYS* 1.3 64.9 + - - +
215E ASP 3.3 2.7 - - - -
216E LEU* 3.0 19.9 + - - +
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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