Contacts of the strand formed by residues 40 - 46 (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 HIS 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E LYS* 3.2 5.2 - - - +
37E SER* 2.8 41.7 + - - +
39E THR* 1.3 107.5 + - - +
41E ALA* 1.3 62.3 + - - +
42E VAL* 4.3 0.4 - - + -
139E PRO* 3.5 4.6 - - - +
179E CYS 6.0 0.2 - - - -
181E LEU* 3.7 53.7 - - + +
184E LEU* 3.9 6.6 - - + +
211E ILE* 4.4 5.6 - - + +
212E VAL 3.7 5.2 + - - +
213E GLY* 4.0 9.5 + - - -
214E LYS* 5.5 0.2 - - - +
215E ASP* 3.1 46.3 + - + -
216E LEU* 4.5 4.4 - - + +
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Residues in contact with ALA 41 (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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35E LEU 3.6 4.5 - - - -
36E LYS* 4.1 2.0 - - + -
40E HIS* 1.3 73.2 - - - +
42E VAL* 1.3 63.7 + - - +
132E ALA* 3.9 15.5 - - + +
133E GLY 4.0 12.8 - - - +
139E PRO* 4.0 6.7 - - + +
140E HIS 3.8 22.9 - - - +
141E ILE* 4.1 5.6 - - + -
210E GLY 4.1 0.5 - - - +
211E ILE* 3.7 2.6 - - - +
212E VAL* 2.8 39.9 + - + +
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Residues in contact with VAL 42 (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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33E VAL 3.9 0.2 - - - +
34E GLY* 3.4 3.3 - - - -
35E LEU* 2.8 53.7 + - + +
40E HIS 4.3 0.2 - - - -
41E ALA* 1.3 78.6 - - - +
43E LEU* 1.3 66.6 + - - +
44E VAL* 3.9 22.7 - - + -
141E ILE* 4.2 1.0 - - - +
181E LEU* 3.9 13.9 - - + -
184E LEU* 3.9 20.0 - - + -
185E VAL* 3.9 35.0 - - + -
209E ILE* 4.5 3.1 - - + -
210E GLY 3.6 5.2 - - - +
211E ILE* 4.0 7.0 - - + -
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Residues in contact with LEU 43 (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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33E VAL 3.5 2.5 - - - +
34E GLY* 3.8 21.3 - - - -
41E ALA 4.3 0.2 + - - -
42E VAL* 1.3 72.3 - - - +
44E VAL* 1.3 64.6 + - - +
60E ILE* 4.1 13.7 - - + -
68E GLY 3.7 26.7 - - - +
69E ILE 3.7 22.7 - - - +
70E SER* 3.7 18.8 - - - +
130E LEU* 3.7 17.0 - - + +
132E ALA* 3.6 21.5 - - + +
141E ILE* 4.7 2.2 - - + -
209E ILE* 3.3 5.2 - - - +
210E GLY 2.7 41.2 + - - +
218E PHE* 4.3 9.2 - - + -
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Residues in contact with VAL 44 (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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32E THR* 3.5 1.4 - - - -
33E VAL* 2.6 45.1 + - + +
35E LEU* 5.5 0.2 - - + -
42E VAL* 3.9 17.7 - - + -
43E LEU* 1.3 78.8 - - - +
45E ALA* 1.3 59.1 + - - +
185E VAL* 4.3 5.2 - - + +
188E GLY* 4.1 31.9 - - - +
189E LEU* 3.8 23.3 - - + +
192E LEU* 3.6 25.2 - - + +
207E VAL* 4.7 0.9 - - + -
208E SER 3.5 7.4 - - - +
209E ILE* 4.4 12.6 - - + -
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Residues in contact with ALA 45 (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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31E ALA 4.0 3.8 - - - -
32E THR* 3.7 19.5 - - - +
44E VAL* 1.3 74.8 - - - +
46E LEU* 1.3 61.2 + - - +
47E LYS 3.7 0.4 + - - -
59E LYS* 3.7 27.4 - - + -
60E ILE* 3.9 16.8 - - + +
70E SER* 4.5 1.1 - - - -
192E LEU* 4.0 7.1 - - - +
207E VAL* 3.7 3.6 - - - -
208E SER* 2.8 35.0 + - - +
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Residues in contact with LEU 46 (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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30E SER* 2.9 39.3 + - - -
31E ALA* 3.1 23.0 + - + +
45E ALA* 1.3 71.8 - - - +
47E LYS* 1.3 70.6 + - - +
48E ARG* 5.6 7.2 - - + +
59E LYS* 3.6 7.8 - - - -
161E ARG* 6.0 2.5 - - - +
192E LEU* 3.8 23.5 - - + +
195E THR* 4.7 8.3 - - - +
196E LEU* 3.8 39.9 - - + -
202E LEU* 4.2 3.6 - - + -
206E ASN* 3.4 28.5 - - - +
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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