Contacts of the helix formed by residues 37 - 46 (chain D) in PDB entry 7UUT
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 CYS 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ALA 4.1 0.4 + - - +
36D PRO* 1.3 75.6 - - - +
38D THR* 1.3 77.0 - - - +
39D SER* 3.1 24.7 + - - +
40D ASP* 3.2 19.7 + - - +
41D ILE* 3.6 12.6 + - - +
59D HIS* 3.4 28.9 - - + +
60D GLU* 3.1 16.6 - - + +
150D ASP* 3.6 11.2 - - - -
151D MET* 4.1 12.1 - - - -
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Residues in contact with THR 38 (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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37D CYS* 1.3 79.3 - - - +
39D SER* 1.3 63.0 + - - +
41D ILE* 3.1 16.2 + - + +
42D HIS* 3.1 43.3 + - + +
177D PRO* 6.0 1.6 - - - +
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Residues in contact with SER 39 (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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37D CYS* 3.1 18.3 - - - -
38D THR* 1.3 80.1 - - - +
40D ASP* 1.3 58.0 + - - +
42D HIS* 3.2 14.9 + - - +
43D THR* 2.9 29.7 + - - -
59D HIS* 4.0 12.7 - - - -
110D TRP* 4.6 16.8 - - - -
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Residues in contact with ASP 40 (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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36D PRO* 6.1 1.1 - - + -
37D CYS 3.2 16.8 + - - +
39D SER* 1.3 74.6 - - - +
41D ILE* 1.3 68.0 + - + +
43D THR* 3.2 7.5 + - - -
44D VAL* 3.0 30.1 + - - +
57D LEU* 3.9 18.5 - - + +
58D GLY* 2.8 35.9 + - - -
59D HIS* 3.7 14.8 + - - -
110D TRP* 4.9 1.7 - - - -
113D SER* 3.0 22.8 + - - +
120D PHE* 4.2 6.5 - - + -
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Residues in contact with ILE 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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36D PRO* 6.3 2.5 - - + -
37D CYS 3.8 14.1 - - - +
38D THR* 3.1 17.9 + - + +
40D ASP* 1.3 79.2 - - + +
42D HIS* 1.3 60.6 + - + +
45D PHE* 3.0 60.8 + - + +
46D GLU* 4.9 0.8 - - + +
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Residues in contact with HIS 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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38D THR* 3.1 34.8 + - + +
39D SER* 3.2 15.0 + - - +
41D ILE* 1.3 81.7 - - + +
43D THR* 1.3 62.7 + - - +
46D GLU* 3.1 56.8 + - - +
47D GLY 3.1 7.6 + - - -
48D ALA* 3.2 17.0 + - + -
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Residues in contact with THR 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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6D MET* 3.5 30.9 - - + +
39D SER 2.9 16.0 + - - -
40D ASP* 3.2 13.5 + - - +
42D HIS* 1.3 76.6 - - - +
44D VAL* 1.3 62.7 + - + +
47D GLY* 3.4 15.4 + - - -
48D ALA* 4.2 8.5 - - - +
49D ILE* 3.6 43.7 - - + +
50D GLY 4.3 1.1 - - - +
52D ARG* 5.0 0.7 - - + -
55D MET* 4.3 11.0 - - + -
57D LEU* 4.8 2.0 - - + -
110D TRP* 4.5 7.1 - - - -
113D SER 4.6 3.2 + - - +
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Residues in contact with VAL 44 (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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6D MET* 3.8 19.7 - - + -
8D SER 4.4 1.6 - - - +
9D ILE* 3.4 11.4 - - - +
10D GLY 2.8 36.3 + - - +
11D LYS 4.0 7.6 - - - +
12D VAL* 3.6 35.2 - - + -
40D ASP* 3.0 19.3 + - + +
41D ILE* 6.5 0.2 - - + -
43D THR* 1.3 77.8 - - - +
45D PHE* 1.3 82.0 + - + +
57D LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 45 (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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9D ILE* 4.7 6.4 - - - +
10D GLY* 3.7 32.3 - - - +
11D LYS* 5.5 0.2 - - - -
12D VAL* 5.1 12.6 - - + -
41D ILE* 3.0 46.9 + - + +
44D VAL* 1.3 95.8 - - + +
46D GLU* 1.3 64.8 + - + +
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Residues in contact with GLU 46 (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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9D ILE* 5.0 2.7 - - - -
41D ILE* 3.9 1.7 + - + +
42D HIS* 3.1 51.2 + - - +
45D PHE* 1.3 81.5 - - + +
47D GLY* 1.3 64.5 + - - +
48D ALA* 4.3 7.6 - - + +
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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