Contacts of the helix formed by residues 8 - 17 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLN* 3.3 9.2 - - - +
6D PRO* 4.5 0.4 - - - +
7D GLU* 1.3 92.5 - - + +
9D PHE* 1.3 67.4 + - - +
10D LEU* 3.9 6.4 + - - +
11D CYS* 3.2 22.3 + - - +
12D TYR* 2.9 27.3 + - - -
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Residues in contact with PHE 9 (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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58C GLY* 3.6 22.9 - - - -
61C ILE* 3.5 29.6 - - + -
62C MET* 3.5 24.0 - - + -
67C TYR* 3.8 29.8 - + + -
72C GLN* 2.9 41.0 + - - +
75C VAL* 4.0 5.2 - - + -
93C VAL* 3.8 25.1 - - + -
8D THR* 1.3 70.9 - - - +
10D LEU* 1.3 64.0 + - + +
12D TYR* 3.1 4.9 + - - +
13D TRP* 2.8 59.4 + + + +
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Residues in contact with LEU 10 (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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39A LYS 5.3 0.4 - - - +
40A SER 3.5 25.6 - - - +
41A VAL* 3.8 22.9 - - - +
42A GLY* 4.1 11.0 - - - +
58C GLY 5.2 2.2 - - - +
59C GLN* 4.2 10.8 - - - +
62C MET* 4.3 25.5 - - + -
8D THR* 3.2 5.5 + - - +
9D PHE* 1.3 93.1 - - + +
11D CYS* 1.3 56.9 + - - +
13D TRP* 3.3 14.9 + - + +
14D ARG* 2.9 27.7 + - - +
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Residues in contact with CYS 11 (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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1D CYS* 2.1 62.3 - - + -
2D ASN 3.8 4.0 - - - -
6D PRO* 3.7 22.9 - - + -
7D GLU 4.9 0.4 - - - +
8D THR* 3.1 24.6 + - - +
10D LEU* 1.3 74.7 - - - +
12D TYR* 1.3 66.3 + - - +
14D ARG* 3.1 2.3 + - - -
15D CYS* 3.0 29.3 + - - -
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Residues in contact with TYR 12 (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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72C GLN 3.9 4.3 - - - -
73C HIS* 3.5 54.3 - + + -
93C VAL* 3.4 24.4 - - + +
94C LYS* 3.8 28.7 + - + -
96C HIS* 5.0 1.4 + - - -
6D PRO* 3.0 55.4 + - + +
7D GLU 4.3 8.1 - - - -
8D THR 2.9 27.5 + - - -
9D PHE* 3.5 6.1 - - - +
11D CYS* 1.3 75.2 - - - +
13D TRP* 1.3 59.3 + - - +
15D CYS* 3.2 6.2 + - + +
16D LEU 3.0 24.1 + - - -
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Residues in contact with TRP 13 (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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54C LEU* 2.8 40.3 + - + -
55C PHE* 5.4 2.5 - - - -
57C LEU* 3.7 30.1 - - + -
58C GLY* 3.5 20.8 - - - -
61C ILE* 4.0 16.2 - - + -
91C PHE* 4.6 9.0 - + - -
93C VAL* 3.9 21.1 - - + -
99C ILE* 4.5 8.7 - - + -
9D PHE* 2.8 44.0 + + + +
10D LEU* 3.6 13.9 - - + +
11D CYS 3.1 0.2 - - - -
12D TYR* 1.3 73.5 - - - +
14D ARG* 1.3 62.2 + - - +
16D LEU* 3.3 37.7 - - + +
17D GLN* 3.1 38.5 + - - +
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Residues in contact with ARG 14 (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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3A ACT 3.5 29.7 + - - -
42A GLY 3.7 21.4 + - - +
44A GLN* 3.1 44.8 - - - +
1D CYS* 4.1 12.1 - - - -
10D LEU 2.9 17.4 + - - +
11D CYS* 3.5 6.3 - - - +
13D TRP* 1.3 75.5 - - - +
15D CYS* 1.3 63.1 + - - +
17D GLN* 3.0 24.6 + - - +
18D HIA 3.8 31.4 + - + +
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Residues in contact with CYS 15 (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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96C HIS* 3.7 17.8 + - + +
1D CYS* 3.6 13.5 - - - -
3D CYS* 2.0 62.6 - - + +
6D PRO* 4.3 5.4 - - + -
11D CYS* 3.0 22.4 + - - +
12D TYR* 3.2 8.5 + - + +
14D ARG* 1.3 76.3 - - - +
16D LEU* 1.3 63.0 + - - +
17D GLN 3.0 1.4 + - - -
18D HIA 3.2 20.3 + - - +
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Residues in contact with LEU 16 (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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54C LEU* 4.0 16.2 - - + -
93C VAL* 4.1 7.2 - - + +
96C HIS* 3.5 49.7 + - + +
99C ILE* 4.1 16.2 - - + -
100C TYR* 3.4 31.3 - - + -
12D TYR 3.0 12.1 + - - +
13D TRP* 3.3 52.7 - - + +
15D CYS* 1.3 76.2 - - - +
17D GLN* 1.3 60.8 + - + +
18D HIA 3.8 4.3 + - - +
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Residues in contact with GLN 17 (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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51C LYS* 4.8 14.4 - - - +
54C LEU* 3.4 31.6 - - + +
55C PHE* 5.1 1.4 + - - +
100C TYR* 3.4 21.7 + - - +
13D TRP* 3.1 44.4 + - - +
14D ARG* 3.0 12.5 + - - +
15D CYS 3.0 1.2 - - - -
16D LEU* 1.3 79.6 - - + +
18D HIA 1.5 56.8 + - - +
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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