Contacts of the helix formed by residues 34 - 47 (chain B) in PDB entry 3I5D
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 LEU 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN* 1.3 63.9 + - - +
36B ARG* 3.4 3.4 - - - +
37B PHE* 3.1 22.2 - - + +
38B THR* 3.1 30.0 + - - +
356B CYS* 5.2 14.8 - - + -
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Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 1.3 74.6 - - - +
36B ARG* 1.3 61.1 + - - +
37B PHE 3.0 4.7 - - - -
38B THR* 3.1 22.4 + - - -
39B GLN* 3.2 12.8 + - - +
353B ASN* 4.0 25.3 + - + +
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.4 2.1 - - - +
35B ASN* 1.3 76.2 - - - +
37B PHE* 1.3 58.5 + - - +
39B GLN* 4.0 7.5 - - - +
40B ALA* 3.4 20.3 + - - +
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.1 28.6 + - + +
35B ASN 3.0 0.4 - - - -
36B ARG* 1.3 77.6 - - - +
38B THR* 1.3 74.5 + - + +
39B GLN 3.2 0.9 - - - -
40B ALA* 3.3 8.8 + - + +
41B LEU* 3.1 36.2 + - + +
356B CYS* 5.4 4.3 - - - -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU 3.1 12.9 + - - +
35B ASN* 3.1 5.7 + - - -
37B PHE* 1.3 80.5 - - + +
39B GLN* 1.3 60.8 + - - +
41B LEU* 3.0 15.3 + - + +
42B VAL* 2.9 32.9 + - - +
349B LEU* 4.5 1.0 + - - -
352B VAL* 3.9 22.6 - - + +
353B ASN* 2.8 27.8 + - - +
356B CYS* 3.3 35.4 - - + -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 3.2 14.8 + - - +
36B ARG* 4.1 8.1 - - - +
38B THR* 1.3 83.5 + - - +
40B ALA* 1.3 58.7 + - - +
42B VAL* 3.5 10.9 - - - +
43B ILE* 3.4 22.2 + - - +
349B LEU* 4.8 8.5 - - + -
353B ASN* 5.5 0.9 - - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG 3.4 15.4 + - - +
37B PHE* 3.3 8.6 + - + +
38B THR 3.2 0.4 - - - -
39B GLN* 1.3 77.0 - - - +
41B LEU* 1.3 60.8 + - - +
43B ILE* 4.1 6.5 - - - +
44B ALA* 3.4 22.3 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.1 28.4 + - + +
38B THR* 3.0 19.5 + - + +
40B ALA* 1.3 78.1 - - - +
42B VAL* 1.3 63.2 + - + +
43B ILE 3.3 0.2 - - - -
44B ALA* 3.3 6.6 + - + +
45B TYR* 2.8 30.8 + - + +
352B VAL* 6.4 1.3 - - + -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR 2.9 16.0 + - - +
39B GLN* 3.5 13.7 - - - +
41B LEU* 1.3 78.4 - - + +
43B ILE* 1.3 65.7 + - + +
45B TYR* 3.4 13.8 - - + +
46B VAL* 2.9 35.5 + - + +
345B GLY 4.1 12.6 - - - +
348B LEU* 4.3 7.2 - - + +
349B LEU* 3.5 42.0 - - + +
352B VAL* 4.2 13.0 - - + -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN 3.4 16.1 + - - +
40B ALA* 4.1 7.2 - - - +
41B LEU 3.3 0.4 - - - -
42B VAL* 1.3 83.4 - - + +
44B ALA* 1.3 56.6 + - - +
46B VAL* 3.6 6.8 - - - +
47B ILE* 3.2 42.1 + - + +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA 3.4 17.1 + - - +
41B LEU* 3.3 8.0 + - + +
42B VAL 3.3 0.4 - - - -
43B ILE* 1.3 78.6 - - - +
45B TYR* 1.3 57.2 - - - +
47B ILE* 5.4 0.2 - - - -
48B GLY* 3.2 26.4 - - - +
49B TYR* 3.4 3.8 + - - +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 2.8 19.8 + - + +
42B VAL* 3.1 14.8 + - + +
44B ALA* 1.3 78.3 - - - +
46B VAL* 1.3 81.9 + - + +
49B TYR* 2.8 52.1 - + + +
50B VAL* 3.1 11.2 + - + +
335C ILE* 3.8 16.9 + - + +
336C ILE* 4.2 6.4 + - - -
339C LEU* 2.6 42.6 - - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 2.9 21.4 + - + +
43B ILE* 3.6 9.6 - - - +
45B TYR* 1.3 95.4 - - + +
47B ILE* 1.3 84.7 + - + +
50B VAL* 3.0 33.2 + - + +
51B CYS* 3.0 15.4 + - - -
341B ASN* 4.5 13.9 - - - +
342B ILE* 5.5 13.2 - - + -
345B GLY* 3.8 29.2 - - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 3.2 19.8 + - + +
44B ALA* 5.4 0.2 - - - -
46B VAL* 1.3 86.2 - - + +
48B GLY* 1.3 61.1 + - - +
51B CYS* 3.5 14.6 - - + +
52B VAL* 3.5 19.9 - - + +
342B ILE* 5.8 11.0 - - + -
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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