Contacts of the helix formed by residues 5 - 18 (chain F) in PDB entry 4DHZ
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 6.2 2.0 - - + -
3F GLY 4.6 2.0 - - - +
4F LEU* 1.4 92.0 - - + +
6F ARG* 1.3 65.8 + - + +
7F ARG* 3.2 8.3 + - + +
8F ILE* 3.3 29.3 + - + +
9F ILE* 3.5 9.0 + - - +
33F ARG* 4.0 19.1 - - - +
60F GLU 5.7 1.3 - - - +
62F TYR 5.2 5.6 - - - +
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Residues in contact with ARG 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 2.9 53.0 + - - +
137A ASP* 3.9 8.5 - - - +
138A PHE* 3.6 41.9 - - - +
141A GLU* 3.3 27.5 + - - -
168A TYR* 4.7 9.5 - - + +
4F LEU 3.9 1.0 + - - -
5F PRO* 1.3 72.5 - - + +
7F ARG* 1.3 59.9 + - - +
8F ILE 3.3 0.2 - - - -
9F ILE* 3.9 13.2 - - + -
10F LYS* 3.0 58.1 + - - +
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Residues in contact with ARG 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TRP* 3.9 15.5 - - - -
131A THR* 3.9 18.7 + - - +
134A ASP* 5.1 2.2 - - - -
135A PHE* 4.1 7.5 - - - -
168A TYR* 3.4 30.3 + - + +
5F PRO* 3.2 5.0 - - + +
6F ARG* 1.3 81.8 - - - +
8F ILE* 1.3 61.7 + - + +
10F LYS* 5.1 2.0 - - - -
11F GLU* 2.9 45.2 + - - +
62F TYR* 3.2 28.0 + - + -
63F PRO* 3.5 38.0 - - + +
97F PRO 2.9 21.6 + - - -
99F LEU 2.8 24.9 + - - -
100F GLN* 3.5 9.7 - - - +
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Residues in contact with ILE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 4.0 26.7 - - + -
5F PRO* 3.3 29.8 + - + +
6F ARG 3.3 0.2 - - - -
7F ARG* 1.3 78.9 - - + +
9F ILE* 1.3 67.4 + - - +
11F GLU* 3.0 4.9 + - - +
12F THR* 2.8 37.4 + - - +
32F ALA* 4.3 15.3 - - + +
33F ARG* 4.2 20.6 - - + +
35F PHE* 5.4 0.2 - - + -
58F LEU* 3.7 26.9 - - + -
62F TYR* 3.7 28.9 - - + +
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Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 3.9 41.5 - - + +
5F PRO 3.5 8.3 + - - +
6F ARG* 3.4 14.2 + - + +
8F ILE* 1.3 80.7 - - - +
10F LYS* 1.3 67.4 + - + +
12F THR* 3.4 5.7 + - - -
13F GLN* 3.2 20.4 + - + +
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Residues in contact with LYS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TRP* 4.2 18.2 - - + -
134A ASP* 3.2 33.5 + - + +
6F ARG* 3.0 48.3 + - + +
7F ARG* 5.7 0.2 - - - -
9F ILE* 1.3 81.6 - - + +
11F GLU* 1.3 59.0 + - - +
13F GLN* 3.3 7.7 + - - +
14F ARG* 3.0 34.8 + - + +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TRP* 3.4 21.9 - - + -
7F ARG* 2.9 32.1 + - - +
8F ILE* 3.0 6.3 + - - +
10F LYS* 1.3 75.1 - - - +
12F THR* 1.3 60.1 + - - +
14F ARG* 4.0 2.2 - - - +
15F LEU* 3.1 31.7 + - + +
35F PHE* 6.1 0.7 - - - -
58F LEU* 5.9 0.2 - - - -
62F TYR* 2.7 26.0 + - - -
100F GLN* 3.2 11.0 - - + +
101F ILE* 2.6 53.5 + - + +
102F ARG* 4.5 0.6 + - - +
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Residues in contact with THR 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 2.8 26.4 + - - +
9F ILE* 3.6 5.8 - - - -
11F GLU* 1.3 73.9 - - - +
13F GLN* 1.3 67.8 + - - +
15F LEU* 2.9 16.6 + - - -
16F LEU* 3.0 31.0 + - + +
27F PRO* 3.8 27.3 - - + +
32F ALA* 4.8 2.4 + - - +
35F PHE* 3.8 19.9 - - + -
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Residues in contact with GLN 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 3.2 12.4 + - + +
10F LYS* 3.3 11.2 + - - +
12F THR* 1.3 78.6 - - - +
14F ARG* 1.3 67.7 - - + +
16F LEU* 3.4 5.8 + - - +
17F ALA* 3.2 34.7 + - - +
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Residues in contact with ARG 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 5.8 2.4 + - - -
130A TRP* 3.6 61.8 - - + +
10F LYS* 3.0 18.9 + - + +
11F GLU* 4.1 4.3 - - - +
13F GLN* 1.3 83.9 - - + +
15F LEU* 1.3 58.0 + - - +
17F ALA* 5.2 1.3 - - - -
18F GLU* 3.2 34.5 + - - +
102F ARG* 3.5 16.8 + - - +
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLU* 3.1 22.6 + - + +
12F THR* 2.9 6.0 + - - +
14F ARG* 1.3 72.0 - - - +
16F LEU* 1.3 60.6 + - + +
18F GLU* 2.7 21.2 - - - +
19F PRO* 4.4 4.0 - - - +
20F VAL* 5.5 5.3 - - + +
25F ALA* 4.1 34.3 - - + +
35F PHE* 4.4 19.5 - - + -
101F ILE* 4.2 24.7 - - + -
102F ARG* 3.7 48.9 - - + +
105F LEU* 4.8 4.7 - - + -
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F THR* 3.0 34.1 + - + +
13F GLN* 4.0 5.8 - - - +
15F LEU* 1.3 85.5 - - + +
17F ALA* 1.3 63.7 + - - +
18F GLU 3.3 6.5 + - - +
19F PRO* 5.1 3.5 - - - +
25F ALA 4.4 10.1 - - - +
26F GLU* 4.9 2.2 - - + -
27F PRO* 3.8 29.8 - - + -
35F PHE* 5.4 0.4 - - + -
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 3.2 31.3 + - - +
14F ARG* 4.8 1.8 - - - +
16F LEU* 1.3 77.2 - - - +
18F GLU* 1.3 57.4 + - - +
19F PRO* 4.3 4.2 - - - +
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ARG 3.2 10.3 + - - +
15F LEU* 2.7 26.5 - - - +
16F LEU 3.6 2.8 - - - -
17F ALA* 1.3 77.5 - - - +
19F PRO* 1.3 89.5 - - + +
20F VAL* 4.7 1.0 - - - +
102F ARG* 2.7 53.6 + - - +
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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