Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 6XOX
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 2.9 17.7 + - - +
37A TYR* 3.3 9.5 - - - +
38A ARG 3.1 3.4 - - - +
39A ALA* 1.3 80.3 - - - +
41A HIS* 1.3 67.7 + - - +
42A ARG* 2.9 29.4 + - - +
211A LYS* 5.9 0.4 - - - +
218A ASN* 3.3 28.5 + - + +
219A PHE 4.5 0.9 - - - +
220A HIS* 3.6 34.3 - - + -
242A THR* 5.1 0.5 - - - +
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Residues in contact with HIS 41 (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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38A ARG 4.6 9.8 + - - -
39A ALA* 4.7 2.9 + - - -
40A THR* 1.3 80.5 - - - +
42A ARG* 1.3 63.9 + - - +
43A LEU* 3.6 3.5 + - - +
217A VAL* 3.8 19.2 - - + +
218A ASN 2.9 10.6 + - - +
219A PHE* 3.3 37.4 - + + -
220A HIS* 3.0 26.4 + - - +
242A THR* 3.9 23.8 - - + +
379A CYS* 4.3 9.5 - - + +
380A ARG* 6.0 1.1 - - - -
383A ILE* 4.3 27.1 - - + +
258R SER* 5.7 9.4 + - - -
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Residues in contact with ARG 42 (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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37A TYR* 3.0 62.9 + - - -
38A ARG* 4.6 4.9 - - - +
40A THR* 2.9 29.4 + - - -
41A HIS* 1.3 73.1 - - - +
43A LEU* 1.3 55.0 + - - +
220A HIS* 3.5 28.0 - - + +
240A ASP* 3.4 24.0 + - - +
241A VAL* 3.5 19.1 - - + -
242A THR* 2.4 48.4 + - - +
99B TRP* 4.3 17.9 - - + -
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Residues in contact with LEU 43 (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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41A HIS 4.0 3.1 - - - +
42A ARG* 1.3 77.2 - - - +
44A LEU* 1.3 61.1 + - - +
45A LEU 4.0 0.2 + - - -
212A PHE* 4.8 5.6 - - + -
219A PHE* 3.6 29.4 - - + -
220A HIS 2.8 27.5 + - - +
221A MET* 3.4 24.8 - - + -
222A PHE* 3.3 16.3 + - - +
241A VAL* 3.6 3.6 - - - -
242A THR* 4.2 2.9 - - - +
243A ALA* 3.1 17.5 - - + +
245A ILE* 3.7 22.7 - - + -
375A VAL* 3.8 22.2 - - + -
379A CYS* 3.9 11.4 - - - -
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Residues in contact with LEU 44 (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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43A LEU* 1.3 72.3 - - - +
45A LEU* 1.3 67.6 + - - +
46A LEU* 3.3 10.6 + - + -
222A PHE* 3.4 18.4 - - + +
224A VAL* 3.7 14.6 - - + -
234A TRP* 5.4 0.7 - - + -
235A ILE* 4.4 15.3 - - + -
238A PHE* 3.6 49.4 - - + -
241A VAL* 3.9 9.6 - - + +
243A ALA 2.9 13.2 + - - +
244A ILE* 3.5 28.1 - - + +
245A ILE* 2.8 29.0 + - - +
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Residues in contact with LEU 45 (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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43A LEU 4.0 2.2 + - - -
44A LEU* 1.3 70.4 - - - +
46A LEU* 1.3 62.0 + - - +
47A GLY* 5.0 2.7 - - - +
52A GLY 4.3 17.5 - - - +
53A LYS* 4.5 14.1 - - + -
56A ILE* 5.0 0.2 - - + -
221A MET* 3.7 38.5 - - + +
222A PHE 3.2 17.9 + - - +
223A ASP* 3.5 31.4 - - + +
224A VAL* 4.1 11.8 - - - +
245A ILE* 3.5 19.5 - - + +
247A VAL* 4.6 16.6 - - + -
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Residues in contact with LEU 46 (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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44A LEU* 3.3 7.4 + - + -
45A LEU* 1.3 75.2 - - - +
47A GLY* 1.3 66.2 + - - +
224A VAL* 3.8 24.7 - - + -
231A ARG* 4.1 18.6 - - - +
234A TRP* 4.3 6.1 - - + -
235A ILE* 3.7 21.8 - - + -
244A ILE* 4.2 16.4 - - + -
245A ILE 2.9 6.9 + - - -
246A PHE* 3.3 9.8 - - + -
247A VAL* 2.9 24.2 + - - -
272A LEU* 4.5 19.1 - - + -
276A ILE* 3.7 29.4 - - + -
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Residues in contact with GLY 47 (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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45A LEU* 4.2 5.1 + - - +
46A LEU* 1.3 81.7 - - - +
48A ALA* 1.3 62.9 + - - +
231A ARG* 4.1 13.4 + - - -
246A PHE* 5.3 2.5 - - - -
247A VAL* 3.3 21.3 - - - -
272A LEU* 5.3 3.6 - - - -
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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