Contacts of the helix formed by residues 4 - 15 (chain D) in PDB entry 1QSW
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 GLU 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D VAL 3.9 1.4 + - - -
3D PHE* 1.3 76.9 - - - +
5D ARG* 1.3 68.2 + - - +
6D CYS 3.5 1.6 - - - +
7D GLU* 3.1 25.9 + - + +
8D LEU 3.0 18.2 + - - -
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Residues in contact with ARG 5 (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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3D PHE 3.9 1.6 + - - -
4D GLU* 1.3 74.3 - - - +
6D CYS* 1.3 69.1 + - - +
8D LEU* 3.2 1.0 + - - -
9D ALA* 2.9 22.9 + - - +
29D MET* 3.0 17.4 - - + +
38D TYR* 4.0 27.5 - - + +
123D GLN 2.9 29.7 + - - -
124D TYR* 3.3 29.8 + - - +
126D GLN* 2.7 38.8 + - - +
127D GLY* 5.1 0.6 - - - -
128D CYS* 3.5 8.9 - - - -
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Residues in contact with CYS 6 (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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4D GLU* 3.5 2.0 - - - +
5D ARG* 1.3 94.0 - - - +
7D GLU* 1.3 59.6 + - - +
9D ALA* 3.8 0.7 - - - +
10D ARG* 2.9 52.1 + - - +
127D GLY 4.1 4.0 - - - -
128D CYS* 2.0 58.5 - - + +
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Residues in contact with GLU 7 (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 LYS* 3.2 24.4 + - - -
2D VAL 4.6 1.2 - - - +
3D PHE* 3.7 20.7 - - + -
4D GLU* 3.1 39.2 + - + +
6D CYS* 1.3 75.6 - - - +
8D LEU* 1.3 62.1 + - - +
10D ARG* 3.5 16.9 + - - +
11D THR* 2.7 30.9 + - - +
14D ARG* 4.7 1.3 + - - +
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Residues in contact with LEU 8 (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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3D PHE* 3.7 19.3 - - + -
4D GLU 3.0 13.7 + - - +
5D ARG 3.6 6.5 - - - +
7D GLU* 1.3 76.2 - - - +
9D ALA* 1.3 64.5 + - - +
11D THR* 3.6 1.4 - - - -
12D LEU* 2.8 33.0 + - + +
29D MET* 3.6 19.1 - - + -
32D ALA* 4.1 9.0 - - + -
38D TYR* 3.4 35.9 - - + -
56D ILE* 3.7 23.3 - - + -
57D PHE* 6.0 1.1 - - + -
89D ILE* 3.7 29.6 - - + -
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Residues in contact with ALA 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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5D ARG 2.9 16.5 + - - +
6D CYS 3.3 4.9 + - - +
8D LEU* 1.3 75.8 - - - +
10D ARG* 1.3 57.5 + - - +
12D LEU* 3.2 3.8 + - - +
13D LYS* 3.0 27.5 + - - +
25D LEU* 3.7 6.0 - - + +
29D MET* 3.6 22.3 - - + -
125D VAL* 4.2 15.3 - - + -
128D CYS* 4.0 21.1 - - + -
130D VAL* 3.9 8.3 - - + -
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Residues in contact with ARG 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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6D CYS* 2.9 35.4 + - - +
7D GLU* 4.0 16.2 - - - +
9D ALA* 1.3 73.2 - - - +
11D THR* 1.3 66.6 + - - +
13D LYS* 3.8 2.2 - - - +
14D ARG* 3.0 46.0 + - - +
128D CYS* 3.1 32.5 + - - +
129D GLY* 5.3 3.4 - - - +
130D VAL* 3.8 13.2 - - + -
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Residues in contact with THR 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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3D PHE* 4.0 13.3 - - + -
7D GLU* 2.7 26.3 + - - +
8D LEU* 3.1 7.2 + - - -
10D ARG* 1.3 78.1 - - - +
12D LEU* 1.3 64.2 + - - +
14D ARG* 3.2 27.5 + - - +
15D LEU* 3.0 35.7 + - + +
89D ILE* 3.7 33.4 - - + -
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Residues in contact with LEU 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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8D LEU* 2.8 27.7 + - + +
9D ALA 3.6 0.7 - - - +
11D THR* 1.3 78.6 - - - +
13D LYS* 1.3 61.8 + - - +
15D LEU* 3.0 13.5 + - - +
16D GLY 3.3 0.2 + - - -
17D MET* 3.1 31.1 + - + +
25D LEU* 3.5 16.8 - - + -
28D TRP* 4.1 27.6 - - + +
29D MET* 3.9 27.4 - - + +
57D PHE* 3.9 26.9 - - + -
89D ILE* 4.1 11.4 - - + -
93D VAL* 4.0 18.8 - - + -
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Residues in contact with LYS 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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9D ALA 3.0 15.7 + - - +
10D ARG* 3.8 5.6 - - - +
12D LEU* 1.3 76.7 - - - +
14D ARG* 1.3 63.9 + - + +
16D GLY* 3.0 15.2 + - - -
17D MET 4.8 1.8 - - - +
18D ASP* 2.5 42.6 + - + +
25D LEU* 3.9 13.1 - - + +
130D VAL* 3.2 41.8 + - + +
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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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7D GLU* 4.7 1.2 + - - +
10D ARG* 3.0 47.5 + - - +
11D THR* 3.5 33.6 + - - +
13D LYS* 1.3 76.9 - - + +
15D LEU* 1.3 66.4 + - + +
16D GLY 3.3 1.0 + - - -
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Residues in contact with LEU 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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11D THR* 3.0 37.0 + - + +
12D LEU* 3.6 6.3 - - - +
13D LYS 3.0 2.2 - - - -
14D ARG* 1.3 84.8 - - + +
16D GLY* 1.3 58.4 + - - +
17D MET* 3.4 2.4 + - - -
89D ILE* 4.2 4.3 - - + -
90D ALA* 4.1 29.4 - - + +
93D VAL* 3.8 36.1 - - + +
97D LYS* 2.9 23.6 + - - -
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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