Contacts of the helix formed by residues 38 - 47 (chain A) 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 THR 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 4.5 3.7 + - - +
37A PHE* 1.3 77.0 - - + +
39A GLN* 1.3 63.9 + - - +
41A LEU* 3.0 15.9 + - + +
42A VAL* 2.9 36.4 + - - +
349A LEU* 5.5 4.7 + - - +
352A VAL* 5.4 12.7 - - + +
353A ASN* 4.6 14.5 - - + +
356A CYS* 4.9 17.5 - - - -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 4.0 17.6 + - - +
37A PHE 3.3 0.2 - - - -
38A THR* 1.3 84.5 + - - +
40A ALA* 1.3 57.1 + - - +
42A VAL* 3.5 11.4 - - - +
43A ILE* 3.3 25.1 + - - +
349A LEU* 4.9 13.5 - - + -
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Residues in contact with ALA 40 (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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36A ARG 3.5 15.0 + - - +
37A PHE* 3.5 8.2 + - - +
38A THR 3.2 0.6 - - - -
39A GLN* 1.3 77.5 - - - +
41A LEU* 1.3 57.9 + - - +
43A ILE* 3.2 22.5 - - + +
44A ALA* 3.4 13.0 - - - +
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Residues in contact with LEU 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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37A PHE 3.2 12.9 + - - +
38A THR* 3.0 17.9 + - + +
40A ALA* 1.3 78.6 - - - +
42A VAL* 1.3 65.4 + - + +
44A ALA* 3.3 6.3 + - + +
45A TYR* 2.8 30.8 + - + +
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Residues in contact with VAL 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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38A THR* 2.9 20.0 + - - +
39A GLN* 3.5 18.6 - - - +
41A LEU* 1.3 78.4 - - + +
43A ILE* 1.3 63.3 + - + +
45A TYR* 3.4 13.5 - - + +
46A VAL* 2.9 36.4 + - + +
345A GLY* 4.7 10.5 - - - +
348A LEU* 5.5 2.7 - - + +
349A LEU* 4.3 36.3 - - + +
352A VAL* 5.2 8.3 - - + -
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Residues in contact with ILE 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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39A GLN 3.3 14.4 - - - +
40A ALA* 3.2 22.2 - - + +
42A VAL* 1.3 82.3 - - + +
44A ALA* 1.3 61.7 + - + +
45A TYR 3.2 0.2 - - - -
46A VAL* 4.0 6.3 - - + -
47A ILE* 3.2 51.5 + - + +
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Residues in contact with ALA 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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40A ALA 3.4 15.9 - - - +
41A LEU* 3.3 8.6 + - + +
43A ILE* 1.3 81.0 - - + +
45A TYR* 1.3 58.3 + - - +
48A GLY* 3.2 25.5 - - - +
49A TYR* 3.4 4.2 + - - +
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Residues in contact with TYR 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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41A LEU* 2.8 20.3 + - + +
42A VAL* 3.1 14.1 + - + +
44A ALA* 1.3 77.9 - - - +
46A VAL* 1.3 80.7 + - + +
49A TYR* 2.8 52.6 - + + +
50A VAL* 3.1 12.1 + - + +
341A ASN* 6.2 0.2 - - - -
345A GLY* 6.3 0.9 - - - -
335B ILE* 4.8 2.1 + - - +
336B ILE* 4.8 11.4 - - - +
339B LEU* 3.4 32.3 - - + +
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Residues in contact with VAL 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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42A VAL* 2.9 21.8 + - + +
43A ILE* 3.7 11.4 - - + +
45A TYR* 1.3 95.0 - - + +
47A ILE* 1.3 82.9 + - + +
50A VAL* 3.0 33.0 + - + +
51A CYS* 3.0 16.0 + - - -
341A ASN* 4.9 11.4 - - - +
342A ILE* 5.4 16.2 - - + -
345A GLY* 4.5 21.5 - - - -
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Residues in contact with ILE 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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43A ILE* 3.2 35.3 + - + +
44A ALA* 5.4 0.2 - - - -
46A VAL* 1.3 92.1 - - + +
48A GLY* 1.3 61.4 + - - +
51A CYS* 3.5 22.1 - - + +
52A VAL* 3.5 13.8 - - + +
342A ILE* 6.1 5.6 - - + -
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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