Contacts of the helix formed by residues 8 - 17 (chain B) 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 THR 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLN* 3.3 9.4 - - - +
7B GLU* 1.3 92.5 - - + +
9B PHE* 1.3 66.6 + - - +
10B LEU* 4.0 5.1 + - - +
11B CYS* 3.3 21.8 + - - +
12B TYR* 3.0 27.5 + - - -
44C GLN* 5.1 4.3 + - - -
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Residues in contact with PHE 9 (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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58A GLY* 3.3 23.1 - - - -
61A ILE* 3.4 33.9 - - + -
62A MET* 3.9 11.4 - - + -
67A TYR* 3.7 34.3 - + + -
72A GLN* 2.9 38.3 + - - +
75A VAL* 3.8 5.6 - - + -
93A VAL* 3.7 27.1 - - + -
8B THR* 1.3 71.1 - - - +
10B LEU* 1.3 78.0 + - + +
12B TYR* 3.1 5.5 + - - +
13B TRP* 2.9 46.1 + + + +
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Residues in contact with LEU 10 (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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58A GLY* 4.0 17.3 - - - +
59A GLN* 4.6 7.6 - - - +
62A MET* 3.8 22.2 - - + -
8B THR* 3.3 5.4 + - - +
9B PHE* 1.3 104.4 - - + +
11B CYS* 1.3 57.6 + - - +
13B TRP* 3.3 11.8 + - + +
14B ARG* 2.8 28.8 + - - +
41C VAL 3.9 1.6 - - - +
42C GLY* 2.8 44.4 - - - +
44C GLN* 3.8 19.8 - - + +
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Residues in contact with CYS 11 (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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1B CYS* 2.0 58.6 - - + -
2B ASN 3.7 7.2 - - - -
6B PRO* 3.8 22.0 - - + -
7B GLU 4.9 0.4 - - - +
8B THR* 3.1 26.0 + - - +
10B LEU* 1.3 75.0 - - - +
12B TYR* 1.3 66.5 + - - +
14B ARG* 3.2 1.2 + - - -
15B CYS* 2.9 31.5 + - - -
44C GLN* 4.5 5.9 + - - +
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Residues in contact with TYR 12 (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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72A GLN 3.9 5.8 - - - -
73A HIS* 3.6 54.2 - + + -
93A VAL* 3.4 25.1 - - + +
94A LYS* 3.9 29.4 + - + -
96A HIS* 4.9 1.6 + - - -
6B PRO* 3.1 55.3 + - + +
7B GLU* 4.4 6.3 - - - -
8B THR 3.0 28.0 + - - -
9B PHE 3.4 5.8 - - - +
11B CYS* 1.3 76.2 - - - +
13B TRP* 1.3 56.4 + - - +
15B CYS* 3.2 5.3 + - + +
16B LEU 3.0 24.3 + - - -
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Residues in contact with TRP 13 (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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54A LEU* 2.8 38.4 + - + +
55A PHE* 5.5 1.8 - - - -
57A LEU* 3.8 36.8 - - + -
58A GLY* 3.3 19.3 - - - -
61A ILE* 4.1 15.0 - - + -
86A PHE* 5.6 0.4 - + - -
91A PHE* 4.3 11.2 - + - -
93A VAL* 3.8 22.0 - - + -
99A ILE* 4.3 11.4 - - + -
9B PHE* 2.9 38.4 + + + +
10B LEU* 3.6 14.8 - - + +
11B CYS 3.2 0.2 - - - -
12B TYR* 1.3 75.4 - - - +
14B ARG* 1.3 62.5 + - - +
16B LEU* 3.3 36.8 - - + +
17B GLN* 3.1 40.4 + - - +
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Residues in contact with ARG 14 (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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1B CYS* 3.6 38.1 + - - +
10B LEU 2.8 17.3 + - - +
11B CYS* 3.2 5.1 + - - +
13B TRP* 1.3 78.5 - - - +
15B CYS* 1.3 61.5 + - - +
17B GLN* 3.0 26.8 + - - +
18B HIA 3.6 33.4 + - + +
44C GLN* 3.9 37.6 + - + +
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Residues in contact with CYS 15 (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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96A HIS* 3.7 17.8 + - + +
1B CYS* 3.6 12.8 - - - -
3B CYS* 2.0 62.8 - - + +
6B PRO* 4.3 5.6 - - + -
11B CYS* 2.9 26.9 + - - +
12B TYR* 3.6 7.4 - - + +
14B ARG* 1.3 75.6 - - - +
16B LEU* 1.3 62.5 + - - +
17B GLN 3.2 0.7 + - - -
18B HIA 3.2 19.1 + - - +
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Residues in contact with LEU 16 (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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54A LEU* 3.9 21.5 - - + -
93A VAL* 4.1 7.0 - - + +
96A HIS* 3.5 51.6 + - + +
99A ILE* 4.1 15.3 - - + -
100A TYR* 3.4 32.0 - - + -
12B TYR 3.0 13.0 + - - +
13B TRP* 3.3 45.5 - - + +
15B CYS* 1.3 77.2 - - - +
17B GLN* 1.3 59.2 + - + +
18B HIA 3.6 5.2 + - - +
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Residues in contact with GLN 17 (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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51A LYS* 4.7 13.0 - - - +
54A LEU* 3.4 31.0 + - + +
55A PHE* 5.0 2.1 + - - +
100A TYR* 3.4 21.8 + - - +
13B TRP* 3.1 44.5 + - - +
14B ARG* 3.0 14.7 + - + +
16B LEU* 1.3 77.8 - - + +
18B HIA 1.5 57.7 + - + -
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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