Contacts of the helix formed by residues 31 - 41 (chain C) in PDB entry 3IUX
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 LYS 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C PRO* 1.3 75.0 - - - +
32C PRO* 1.3 74.5 - - + +
33C LEU 3.4 2.2 - - - +
34C LEU 3.2 3.5 + - - -
35C LEU* 2.8 26.2 + - - +
105C ARG* 3.1 38.3 + - - +
106C ASN* 2.9 27.5 + - + +
107C LEU 3.8 16.7 + - - +
108C VAL* 3.9 26.2 - - + -
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Residues in contact with PRO 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 1.3 92.3 - - + +
33C LEU* 1.3 64.1 + - + +
35C LEU* 3.4 9.2 + - + +
36C LYS* 2.9 27.9 + - - +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 3.4 0.8 - - - +
32C PRO* 1.3 82.1 - - + +
34C LEU* 1.3 59.1 + - - +
36C LYS* 3.2 15.0 + - + +
37C LEU* 2.9 23.2 + - - +
81C LEU* 4.0 21.3 - - + +
84C ASP* 4.4 20.0 - - + -
85C LEU* 3.7 31.6 - - + +
106C ASN* 5.2 2.2 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 4.1 3.6 - - + -
31C LYS 3.2 7.1 + - - +
33C LEU* 1.3 77.0 - - - +
35C LEU* 1.3 60.1 + - - +
37C LEU* 3.2 13.6 + - + -
38C LEU* 2.9 56.7 + - + +
53C VAL* 4.2 15.0 - - + -
57C LEU* 5.0 10.1 - - + -
85C LEU* 3.8 21.7 - - + +
86C PHE* 5.9 1.8 - - + -
103C ILE* 4.5 6.7 - - + +
106C ASN* 3.6 42.4 + - + +
107C LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 3.7 22.9 - - + +
31C LYS 2.8 20.9 + - - +
32C PRO* 3.7 9.6 - - + +
34C LEU* 1.3 72.4 - - - +
36C LYS* 1.3 63.0 + - - +
38C LEU* 3.3 3.0 + - + +
39C LYS* 2.9 45.4 + - + +
45C LYS 3.5 24.0 - - - +
46C ASP* 3.9 28.7 - - + +
48C TYR* 4.0 13.7 - - + +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PRO 2.9 14.9 + - - +
33C LEU* 3.5 16.4 - - + +
35C LEU* 1.3 76.9 - - - +
37C LEU* 1.3 63.4 + - - +
39C LYS* 3.4 5.8 + - - +
40C SER* 3.0 24.5 + - - -
81C LEU* 4.0 26.2 - - + -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU 2.9 11.0 + - - +
34C LEU* 3.2 9.6 + - + +
36C LYS* 1.3 76.3 - - - +
38C LEU* 1.3 79.6 + - + +
40C SER* 2.8 22.4 + - - -
41C VAL* 3.6 5.4 + - + +
56C TYR 4.8 0.4 - - - +
57C LEU* 3.9 16.2 - - + -
60C TYR* 3.5 54.6 - - + -
81C LEU* 3.6 17.4 - - + +
82C LEU* 4.0 22.7 - - + +
85C LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 3.5 33.2 - - + -
34C LEU* 2.9 32.4 + - + +
35C LEU* 3.8 3.6 - - - +
37C LEU* 1.3 86.6 - - + +
39C LYS* 1.3 61.5 + - - +
41C VAL* 3.2 14.9 + - - +
42C GLY 3.3 0.7 + - - -
43C ALA* 2.9 35.4 + - + +
48C TYR* 4.1 16.2 - - + +
53C VAL* 3.9 28.0 - - + +
56C TYR* 3.7 23.3 - - + -
57C LEU* 4.1 5.6 - - + +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 5.5 0.5 - - - +
35C LEU* 2.9 36.9 + - + +
36C LYS* 3.9 5.4 - - - +
38C LEU* 1.3 76.3 - - - +
40C SER* 1.3 61.0 + - - +
41C VAL 3.3 0.9 + - - -
42C GLY* 3.5 9.9 + - - -
43C ALA 3.4 20.5 - - - +
44C GLN* 4.7 3.5 + - - -
45C LYS* 3.4 29.0 - - - +
46C ASP* 2.8 23.1 + - - -
48C TYR* 4.4 5.6 - - - +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.5 15.2 - - - +
36C LYS* 3.0 15.7 + - - -
37C LEU* 2.8 19.0 + - - -
39C LYS* 1.3 79.5 - - - +
41C VAL* 1.3 55.3 + - - +
42C GLY 3.5 0.9 - - - -
60C TYR* 3.6 22.5 - - - -
81C LEU* 5.8 1.6 - - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 3.0 35.0 + - - +
62A MET* 3.4 14.3 - - + +
63A THR* 4.3 3.6 - - - +
37C LEU* 3.9 9.2 - - + +
38C LEU* 3.5 12.3 - - - +
39C LYS 3.2 0.2 - - - -
40C SER* 1.3 80.7 + - - +
42C GLY* 1.3 59.0 + - - +
56C TYR* 3.5 34.6 - - + +
59C GLN* 3.9 32.8 - - + +
60C TYR* 3.9 10.3 - - + +
63C THR* 3.9 17.3 - - + -
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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