Contacts of the helix formed by residues 10 - 24 (chain F) in PDB entry 4DHX
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 ALA 10 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F ASP* 1.3 77.6 + - - +
11F GLN* 1.3 57.9 - - - +
13F ARG* 3.4 26.4 + - - +
14F ALA* 3.0 29.3 + - - +
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Residues in contact with GLN 11 (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 ASP* 2.9 14.8 + - - +
10F ALA* 1.3 79.3 - - - +
12F MET* 1.3 57.3 + - - +
14F ALA* 3.9 5.0 - - - +
15F ALA* 3.2 26.1 + - + +
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Residues in contact with MET 12 (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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1200D GLN* 4.0 17.0 - - - +
1203D ARG* 3.7 29.4 - - + -
1204D VAL* 3.8 31.2 - - + -
1207D CYS* 3.6 21.5 - - - -
9F ASP* 3.4 20.1 + - + +
10F ALA 3.2 0.4 - - - -
11F GLN* 1.3 77.4 - - - +
13F ARG* 1.3 65.3 + - - +
15F ALA* 3.3 6.4 + - + +
16F ILE* 3.0 40.5 + - + +
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Residues in contact with ARG 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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1206D ARG* 6.2 0.8 - - - +
1207D CYS* 3.8 22.2 - - + +
1210D ASP* 3.4 40.2 + - - -
1211D VAL* 3.9 13.1 - - + +
9F ASP* 3.2 32.1 + - - +
10F ALA* 3.4 24.7 + - - +
12F MET* 1.3 78.1 - - - +
14F ALA* 1.3 58.9 + - - +
16F ILE* 3.4 3.6 + - - +
17F ASN* 2.9 39.7 + - - +
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Residues in contact with ALA 14 (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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10F ALA 3.0 17.3 + - - +
11F GLN* 3.9 8.1 - - + +
12F MET 3.2 0.2 - - - -
13F ARG* 1.3 75.6 - - - +
15F ALA* 1.3 59.0 + - - +
17F ASN* 3.4 7.9 + - - +
18F GLN* 2.8 30.2 + - - +
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Residues in contact with ALA 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 GLN 3.2 16.4 + - - +
12F MET* 3.7 8.1 - - + +
14F ALA* 1.3 78.6 - - - +
16F ILE* 1.3 62.4 + - + +
18F GLN* 3.3 8.6 + - - +
19F LYS* 3.1 22.9 + - - +
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Residues in contact with ILE 16 (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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1204D VAL* 4.9 4.5 - - + +
1207D CYS* 3.9 32.8 - - + +
1208D CYS* 4.4 5.8 - - - -
1211D VAL* 3.9 15.7 - - + -
12F MET* 3.0 27.4 + - + +
13F ARG* 3.7 5.6 - - - +
15F ALA* 1.3 74.8 - - + +
17F ASN* 1.3 65.6 + - - +
19F LYS* 3.2 6.6 + - - +
20F LEU* 3.0 35.3 + - + +
91F ILE* 5.0 0.9 - - + -
95F LEU* 3.5 39.2 - - + +
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Residues in contact with ASN 17 (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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31B GLU* 3.9 21.9 + - + +
1211D VAL* 3.4 28.8 - - - +
1214D HIS* 4.0 10.9 - - - +
1215D LEU* 3.5 15.2 - - - +
13F ARG* 2.9 30.2 + - - +
14F ALA* 3.7 7.0 - - - +
16F ILE* 1.3 75.8 - - - +
18F GLN* 1.3 62.8 + - - +
20F LEU* 3.3 8.1 + - - +
21F ILE* 3.0 34.8 + - + +
26F ARG* 4.5 3.5 + - - -
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Residues in contact with GLN 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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35B ALA* 3.2 44.6 + - - +
38B ILE* 3.6 34.2 - - + +
39B GLU* 4.1 3.8 - - - +
14F ALA 2.8 18.5 + - - +
15F ALA* 3.4 10.1 - - - +
16F ILE 3.2 0.2 - - - -
17F ASN* 1.3 76.8 - - - +
19F LYS* 1.3 62.7 + - - +
21F ILE* 3.3 7.0 + - - +
22F GLU* 3.1 56.1 + - - +
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Residues in contact with LYS 19 (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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15F ALA 3.1 15.9 + - - +
16F ILE* 3.2 5.8 + - - +
18F GLN* 1.3 74.0 - - - +
20F LEU* 1.3 64.3 + - - +
22F GLU* 3.9 16.2 - - - +
23F THR* 2.8 48.0 + - + +
94F PHE* 4.5 12.8 - - + -
95F LEU* 5.0 7.4 - - + -
98F HIS* 4.2 27.8 + - + +
99F ALA* 4.3 21.6 - - - +
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Residues in contact with LEU 20 (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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1211D VAL* 3.7 30.5 - - + -
1215D LEU* 3.9 16.8 - - + -
16F ILE* 3.0 27.3 + - + +
17F ASN* 3.7 7.2 - - - +
19F LYS* 1.3 76.0 - - - +
21F ILE* 1.3 61.4 + - - +
23F THR* 4.0 2.7 - - - -
24F GLY 3.5 0.5 + - - -
25F GLU* 3.2 26.3 + - + -
26F ARG* 2.8 36.0 + - + +
29F LEU* 4.4 6.3 - - + -
91F ILE* 4.6 12.8 - - + -
94F PHE* 3.6 31.6 - - + -
95F LEU* 4.5 4.3 - - + -
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Residues in contact with ILE 21 (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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31B GLU* 4.7 10.3 - - + +
32B LEU* 3.9 22.2 - - + +
35B ALA* 3.8 33.0 - - + -
36B LYS* 5.7 10.3 - - + +
39B GLU* 5.7 2.5 - - - +
17F ASN* 3.0 24.2 + - + +
18F GLN* 3.7 4.7 - - - +
20F LEU* 1.3 75.8 - - - +
22F GLU* 1.3 68.4 + - + +
24F GLY* 3.1 14.9 + - - -
26F ARG* 3.8 41.9 - - + +
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Residues in contact with GLU 22 (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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36B LYS* 6.3 0.4 - - - +
38B ILE* 5.6 0.2 - - - +
39B GLU* 3.6 43.8 - - - +
18F GLN* 3.1 40.7 + - - +
19F LYS* 3.8 24.3 - - - +
21F ILE* 1.3 81.3 - - + +
23F THR* 1.3 68.4 + - + +
24F GLY 3.3 0.2 - - - -
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Residues in contact with THR 23 (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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19F LYS* 2.8 44.0 + - + +
22F GLU* 1.3 83.4 - - + +
24F GLY* 1.3 57.5 + - - +
25F GLU* 3.2 10.1 + - - +
28F ARG* 3.4 17.4 + - - -
94F PHE* 3.2 26.9 - - + -
98F HIS* 5.0 6.1 - - + -
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Residues in contact with GLY 24 (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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20F LEU 3.5 0.4 + - - -
21F ILE 3.1 15.4 + - - -
22F GLU 3.3 0.8 - - - -
23F THR* 1.3 77.5 + - - +
25F GLU* 1.3 64.6 + - - +
26F ARG 3.1 2.9 - - - -
27F GLU* 3.1 21.8 + - - +
28F ARG* 3.1 24.4 + - - +
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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