Contacts of the helix formed by residues 32 - 42 (chain D) in PDB entry 1TU3
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 GLY 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D ALA 3.0 5.7 - - - -
31D VAL* 1.3 79.8 - - - +
33D LYS* 1.3 58.2 + - - +
35D SER* 3.1 2.6 + - - -
36D LEU* 3.0 32.6 + - - +
133D ASN* 3.1 19.7 + - - -
4202D GNP 3.2 30.0 + - - -
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Residues in contact with LYS 33 (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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25D LEU* 3.6 24.4 - - + +
26D LEU* 3.4 34.8 - - - +
27D GLY* 3.2 29.2 + - - +
28D GLU 3.4 3.8 + - - -
31D VAL* 3.5 5.7 - - + +
32D GLY* 1.3 75.1 - - - +
34D SER* 1.3 64.6 + - - +
36D LEU* 3.3 17.4 - - - +
37D VAL* 3.3 18.5 - - - +
75D ASP* 3.8 4.5 - - - +
76D THR* 3.4 23.5 + - - -
78D GLY 4.1 0.9 - - - +
99D VAL* 4.1 10.5 - - + -
4202D GNP 3.0 38.2 + - - +
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Residues in contact with SER 34 (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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33D LYS* 1.3 70.1 - - - +
35D SER* 1.3 58.3 + - - +
37D VAL* 2.6 32.2 + - - +
38D LEU* 3.0 8.9 + - - +
49D GLN* 4.7 13.2 - - - -
50D GLU 5.5 0.7 - - - -
52D THR* 2.6 9.9 + - - -
75D ASP* 2.4 26.7 + - - -
4201D MG 2.1 29.6 - - - -
4202D GNP 2.8 21.1 + - - -
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Residues in contact with SER 35 (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 GLY 3.1 6.6 + - - -
34D SER* 1.3 73.8 - - - +
36D LEU* 1.3 52.9 + - - +
38D LEU* 3.1 10.4 + - - +
39D ARG* 2.8 36.7 + - - +
44D GLN 4.8 0.5 - - - +
45D PHE* 4.2 15.7 - - - -
49D GLN* 4.3 13.9 - - - +
164D ALA* 4.0 11.6 - - - +
4202D GNP 2.7 49.1 + - - -
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Residues in contact with LEU 36 (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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25D LEU* 4.7 7.6 - - + -
32D GLY 3.0 15.5 + - - +
33D LYS* 3.3 8.5 - - - +
34D SER 3.0 0.2 - - - -
35D SER* 1.3 76.3 + - - +
37D VAL* 1.3 60.5 + - - +
39D ARG* 4.1 2.5 - - - +
40D PHE* 3.4 21.8 + - - +
97D ILE* 5.4 2.7 - - + -
99D VAL* 3.8 30.1 - - + -
131D SER* 3.9 15.3 - - - +
133D ASN* 3.1 32.5 - - - +
162D THR* 4.0 9.2 - - + +
164D ALA* 4.0 16.1 - - + +
170D VAL* 4.3 15.6 - - + +
173D ILE* 6.0 5.2 - - + -
174D PHE* 4.0 12.8 - - + -
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Residues in contact with VAL 37 (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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25D LEU* 3.6 30.3 - - + -
33D LYS 3.3 17.3 - - - +
34D SER* 2.6 16.8 + - - +
36D LEU* 1.3 71.8 - - - +
38D LEU* 1.3 54.8 + - + +
40D PHE* 3.3 3.3 + - - +
41D VAL* 2.6 59.3 + - + +
58D LEU* 3.8 18.4 - - + -
73D ILE* 4.1 16.2 - - + +
75D ASP* 4.0 17.9 - - + -
174D PHE* 5.0 2.9 - - + -
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Residues in contact with LEU 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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34D SER 3.0 10.9 + - - +
35D SER* 3.5 9.9 - - - +
37D VAL* 1.3 76.0 - - + +
39D ARG* 1.3 60.9 + - - +
41D VAL* 4.5 1.8 - - - +
42D LYS* 2.6 38.1 + - + +
43D GLY 2.8 6.0 + - - -
44D GLN* 3.3 37.2 - - + +
45D PHE* 5.1 10.5 - - - -
49D GLN* 3.0 42.4 - - - +
58D LEU* 4.7 12.6 - - + -
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Residues in contact with ARG 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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35D SER 2.8 20.0 + - - +
36D LEU* 4.1 5.8 - - - +
38D LEU* 1.3 71.7 - - - +
40D PHE* 1.3 65.0 + - - +
43D GLY* 3.0 41.5 + - - +
44D GLN 3.4 13.2 + - - +
45D PHE* 4.2 13.9 - - + +
164D ALA* 2.9 20.7 + - - +
165D LYS 2.4 27.5 + - - -
166D THR 4.6 1.2 + - - -
167D SER* 3.5 21.9 - - - -
170D VAL* 3.5 29.6 - - + -
171D ASN* 5.4 4.3 + - - +
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Residues in contact with PHE 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 LEU 3.4 16.4 + - - +
37D VAL 3.3 2.4 + - - +
38D LEU 3.2 0.4 - - - -
39D ARG* 1.3 83.4 - - - +
41D VAL* 1.3 65.7 + - + +
42D LYS 4.5 1.2 - - - -
60D GLN* 3.6 38.5 + - + -
62D VAL* 5.7 4.9 - - + -
73D ILE* 3.6 22.7 - - + -
170D VAL* 4.1 6.3 - - + -
171D ASN* 4.1 30.4 + - - +
174D PHE* 3.4 65.1 - + + -
175D MET* 4.4 15.0 - - + -
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Residues in contact with VAL 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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37D VAL* 2.6 48.4 + - + +
38D LEU 4.1 0.2 - - - +
40D PHE* 1.3 74.7 - - + +
42D LYS* 1.3 85.8 + - + +
58D LEU* 3.9 19.1 - - + -
59D THR 3.8 2.0 - - - +
60D GLN* 3.2 43.9 + - + +
73D ILE* 3.8 21.8 - - + -
836I ARG* 3.8 15.9 - - - +
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Residues in contact with LYS 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 LEU* 2.6 19.1 + - + +
39D ARG 3.9 0.9 - - - -
40D PHE 4.5 0.7 - - - -
41D VAL* 1.3 103.4 + - + +
43D GLY* 1.3 57.4 + - - +
44D GLN* 3.3 44.2 - - + +
58D LEU* 5.3 3.4 - - + -
60D GLN* 5.3 2.2 - - - +
836I ARG* 3.4 29.7 - - - +
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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