Contacts of the helix formed by residues 5 - 18 (chain D) in PDB entry 4DHI
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 PRO 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLY 3.8 3.1 - - - +
4D LEU* 1.3 89.1 - - + +
6D ARG* 1.3 66.2 + - - +
7D ARG* 4.2 9.4 - - + +
8D ILE* 3.1 30.1 + - + +
9D ILE* 3.2 9.7 + - - +
33D ARG* 3.7 26.7 - - - +
60D GLU 5.7 1.3 - - - +
62D TYR 5.2 7.9 - - - +
63D PRO* 6.5 0.7 - - + -
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Residues in contact with ARG 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 LEU 3.6 1.4 + - - -
5D PRO* 1.3 71.1 - - - +
7D ARG* 1.3 62.3 + - - +
9D ILE* 3.4 15.0 + - + +
10D LYS* 3.0 27.7 + - + +
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Residues in contact with ARG 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TRP* 3.8 23.6 - - - -
131B THR* 3.9 19.5 + - - +
134B ASP* 4.4 10.2 + - - +
135B PHE* 4.3 7.7 - - - -
168B TYR* 4.5 11.6 + - - +
5D PRO* 3.1 8.6 - - + +
6D ARG* 1.3 78.0 - - - +
8D ILE* 1.3 59.2 + - + +
10D LYS* 3.5 2.3 + - - +
11D GLU* 2.8 48.5 + - - +
62D TYR* 3.3 28.0 + - + -
63D PRO* 3.5 35.6 - - + +
97D PRO 2.9 20.4 + - - -
99D LEU 2.7 29.7 + - - -
100D GLN* 3.9 3.2 - - - +
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Residues in contact with ILE 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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4D LEU* 4.3 22.9 - - + -
5D PRO* 3.1 27.1 + - + +
7D ARG* 1.3 74.6 - - + +
9D ILE* 1.3 66.2 + - - +
11D GLU* 3.3 6.0 + - + +
12D THR* 2.8 40.1 + - - +
32D ALA 4.4 7.0 - - - +
33D ARG* 3.5 35.7 - - + +
35D PHE* 5.0 0.2 - - + -
58D LEU* 3.7 31.9 - - + -
62D TYR* 4.0 23.3 - - + +
101D ILE* 6.1 0.2 - - + -
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Residues in contact with ILE 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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4D LEU* 3.6 41.5 - - + +
5D PRO 3.2 8.4 + - - +
6D ARG* 3.4 16.1 + - + +
8D ILE* 1.3 78.4 - - - +
10D LYS* 1.3 57.6 + - - +
12D THR* 3.4 5.8 + - - -
13D GLN* 3.0 53.1 + - + +
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Residues in contact with LYS 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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130B TRP* 3.4 62.6 - - + +
134B ASP* 5.2 3.0 + - - +
6D ARG* 3.0 18.8 + - + +
7D ARG 3.8 3.8 - - - +
9D ILE* 1.3 75.1 - - - +
11D GLU* 1.3 66.7 + - - +
13D GLN* 3.3 13.4 + - + +
14D ARG* 3.0 29.1 + - + +
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Residues in contact with GLU 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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130B TRP* 3.4 23.6 - - + -
7D ARG* 2.8 40.3 + - - +
8D ILE* 3.9 5.6 - - + +
10D LYS* 1.3 77.3 - - - +
12D THR* 1.3 58.6 + - - +
14D ARG* 3.4 4.2 + - - +
15D LEU* 2.9 34.7 + - + +
58D LEU* 6.1 0.2 - - - -
62D TYR* 2.5 31.2 + - - -
100D GLN* 3.4 14.4 - - - +
101D ILE* 2.9 44.8 + - + +
102D ARG 4.6 0.3 + - - -
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Residues in contact with THR 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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4D LEU* 5.6 2.0 - - - +
8D ILE* 2.8 27.0 + - - +
9D ILE* 3.7 6.9 - - - -
11D GLU* 1.3 76.1 - - - +
13D GLN* 1.3 63.5 + - + +
15D LEU* 3.3 5.7 + - - +
16D LEU* 3.0 38.0 + - + +
27D PRO* 3.8 33.9 - - + -
32D ALA 4.9 1.2 + - - -
35D PHE* 3.5 25.0 - - + -
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Residues in contact with GLN 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 ILE* 3.0 40.8 + - + +
10D LYS* 3.3 11.6 + - - +
12D THR* 1.3 77.2 - - + +
14D ARG* 1.3 56.0 + - - +
16D LEU* 3.3 6.5 + - - +
17D ALA* 2.9 31.7 + - - +
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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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130B TRP* 4.0 24.4 - - + +
10D LYS* 3.0 22.2 + - + +
11D GLU* 3.8 5.8 - - - +
13D GLN* 1.3 74.0 - - - +
15D LEU* 1.3 61.3 + - - +
17D ALA* 4.5 4.9 - - + +
18D GLU* 2.8 53.9 + - - +
100D GLN* 3.9 23.0 + - - +
102D ARG* 3.3 51.2 + - - +
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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 GLU* 2.9 21.4 + - + +
12D THR* 3.7 4.7 - - - +
14D ARG* 1.3 76.7 - - - +
16D LEU* 1.3 65.7 + - + +
18D GLU 5.1 0.4 - - - +
19D PRO* 3.4 26.3 - - + +
20D VAL* 4.6 10.5 - - + +
25D ALA* 4.8 18.5 - - + +
35D PHE* 4.2 20.0 - - + -
101D ILE* 3.8 38.6 - - + -
102D ARG* 3.8 26.5 - - + +
105D LEU* 4.1 20.9 - - + -
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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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12D THR* 3.0 29.7 + - + +
13D GLN* 3.9 4.7 - - - +
15D LEU* 1.3 81.1 - - + +
17D ALA* 1.3 61.2 + - - +
19D PRO* 3.9 10.7 - - - +
25D ALA 3.5 24.7 - - - +
26D GLU* 4.3 11.0 - - + -
27D PRO* 4.1 27.6 - - + -
35D PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 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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13D GLN 2.9 18.6 + - - +
14D ARG* 4.1 5.8 - - - +
16D LEU* 1.3 78.1 - - - +
18D GLU* 1.3 67.3 + - + +
19D PRO* 3.7 5.2 - - - +
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Residues in contact with GLU 18 (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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14D ARG* 2.8 41.7 + - - +
15D LEU 3.6 3.3 - - - +
17D ALA* 1.3 84.3 - - + +
19D PRO* 1.3 61.6 - - - +
102D ARG* 2.7 42.5 + - - +
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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