Contacts of the strand formed by residues 39 - 43 (chain D) in PDB entry 4G1U
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 MET 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU* 1.3 76.3 - - - +
40D VAL* 1.3 60.6 + - - +
187D LEU* 3.5 44.2 - - + +
190D LEU* 4.1 6.1 - - + -
191D ARG* 3.8 31.0 - - - +
194D THR* 4.1 9.8 - - + +
201D VAL* 3.6 34.8 - - + -
203D CYS* 4.2 6.1 - - - -
214D TYR* 3.3 25.4 - - + +
215D ALA* 3.3 6.7 - - + +
216D ASP* 2.8 44.0 + - - +
217D ARG 3.7 0.7 + - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.2 24.9 - - + -
38D GLU* 3.2 27.7 + - - +
39D MET* 1.3 74.4 - - - +
41D ALA* 1.3 65.8 + - - +
42D ILE* 4.7 1.6 - - + +
201D VAL 3.0 10.9 + - - +
202D CYS* 3.5 16.9 - - - -
203D CYS* 3.2 28.2 + - - -
215D ALA* 4.6 0.2 - - - -
217D ARG* 3.5 30.5 - - + +
219D MET* 3.9 26.9 - - - -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 1.3 79.6 - - - +
42D ILE* 1.3 58.1 + - - +
43D ILE* 3.6 1.1 + - + -
203D CYS* 3.5 5.6 - - - -
205D LEU* 3.5 28.9 - - + -
211D ALA* 4.2 1.3 - - + -
215D ALA* 3.7 21.5 - - + -
217D ARG 3.1 7.1 + - - -
218D ILE* 3.4 13.4 - - + +
219D MET* 2.7 33.5 + - - -
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.7 3.4 - - + -
34D ILE* 6.1 0.2 - - + -
40D VAL* 4.9 0.9 - - + -
41D ALA* 1.3 72.0 - - - +
43D ILE* 1.3 62.8 + - - +
50D LYS* 3.7 29.8 - - + +
53D LEU* 3.6 35.7 - - + -
54D LEU* 5.6 2.2 - - + +
57D LEU* 4.8 3.1 - - + -
202D CYS* 4.2 20.2 - - - -
203D CYS 3.0 10.0 + - - +
204D VAL* 3.5 22.2 - - + +
205D LEU 3.3 24.6 + - - +
219D MET* 3.5 32.5 - - + +
221D LEU* 4.4 3.6 - - + -
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Residues in contact with ILE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 4.6 2.7 - - - +
42D ILE* 1.3 74.9 - - - +
44D GLY* 1.3 61.3 + - - +
50D LYS* 3.4 13.7 - - - +
205D LEU* 3.4 25.4 - - + +
207D ASP 5.0 0.9 - - - +
208D LEU* 3.6 27.4 - - + -
211D ALA* 3.9 25.1 - - + -
218D ILE* 4.0 15.0 - - + -
219D MET 3.0 13.3 + - - +
220D LEU* 3.6 23.8 - - + -
221D LEU* 3.0 25.1 + - - +
235D VAL* 4.9 0.2 - - + -
236D LEU* 3.7 21.1 - - + -
245D TYR* 4.0 3.4 - - + +
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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