Contacts of the helix formed by residues 6 - 18 (chain F) in PDB entry 5A31
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 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F GLN* 1.3 88.1 - - + +
7F PRO* 1.3 74.7 - - - +
8F VAL* 3.2 2.5 - - - -
9F GLN* 3.3 35.6 + - + +
10F ALA* 3.1 19.6 + - - +
39F GLU* 4.2 14.4 - - - +
458H ALA* 6.2 0.4 - - - +
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Residues in contact with PRO 7 (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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5F GLN 4.4 3.1 - - - +
6F GLU* 1.3 87.8 - - - +
8F VAL* 1.3 56.3 + - + +
10F ALA* 3.3 6.7 + - + +
11F ALA* 2.8 36.5 + - - +
147H PHE* 4.7 10.0 - - + -
455H GLN* 3.5 55.4 - - + +
458H ALA* 5.1 7.0 - - + -
459H ALA* 4.1 21.8 - - + +
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Residues in contact with VAL 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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6F GLU 3.2 0.6 - - - -
7F PRO* 1.3 78.7 - - + +
9F GLN* 1.3 64.4 + - - +
11F ALA* 3.2 4.3 + - - +
12F ILE* 3.1 27.9 + - + +
27F LEU* 3.5 24.6 - - + +
31F LEU* 3.8 19.7 - - + -
147H PHE* 3.5 32.3 - - + -
459H ALA* 4.6 11.9 - - + -
462H LEU* 3.7 32.8 - - + -
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Residues in contact with GLN 9 (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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6F GLU* 3.3 33.6 + - + +
8F VAL* 1.3 81.7 - - - +
10F ALA* 1.3 62.3 + - + +
12F ILE* 3.2 15.6 + - - +
13F TRP* 3.1 39.6 + - + +
31F LEU* 4.4 16.2 - - + +
39F GLU* 3.7 33.8 + - - +
43F LEU* 4.3 9.9 - - + +
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Residues in contact with ALA 10 (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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5F GLN 4.9 4.7 - - - +
6F GLU 3.1 13.6 + - - +
7F PRO* 3.7 10.1 - - + +
9F GLN* 1.3 79.0 - - - +
11F ALA* 1.3 58.5 + - - +
13F TRP* 3.1 10.4 + - - +
14F GLN* 2.9 29.6 + - - +
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Residues in contact with ALA 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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7F PRO 2.8 20.9 + - - +
8F VAL 3.2 5.8 + - - +
10F ALA* 1.3 72.5 - - - +
12F ILE* 1.3 57.4 + - - +
14F GLN* 3.3 13.9 + - - +
15F ALA* 2.9 28.6 + - - +
27F LEU* 4.6 7.6 - - + -
116H PHE* 4.8 1.9 - - - -
145H ASN* 5.1 7.4 - - - +
147H PHE* 4.3 28.9 - - + -
148H LEU* 5.6 4.0 - - + +
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Residues in contact with ILE 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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8F VAL* 3.1 19.7 + - + +
9F GLN* 3.4 9.2 - - - +
11F ALA* 1.3 73.9 - - - +
13F TRP* 1.3 58.9 + - - +
15F ALA* 3.1 7.9 + - - +
16F LEU* 2.9 28.4 + - + +
24F ALA* 3.7 16.8 - - + +
27F LEU* 3.8 30.5 - - + +
28F ALA* 3.5 27.4 - - + +
31F LEU* 4.3 3.6 - - + -
43F LEU* 3.4 40.6 - - + -
47F CYS* 3.9 9.2 - - - -
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Residues in contact with TRP 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 GLN* 3.1 42.9 + - + +
10F ALA* 3.5 10.1 - - - +
12F ILE* 1.3 75.2 - - - +
14F GLN* 1.3 59.0 + - - +
16F LEU* 3.3 19.7 + - + +
17F ASN* 3.0 42.5 + - - +
42F PHE* 4.6 22.7 - + - -
43F LEU* 4.2 24.3 - - + +
46F THR* 4.5 10.8 - - + -
50F ARG* 3.7 28.3 - - - -
17H ASN* 4.8 14.4 - - - -
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Residues in contact with GLN 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 2.9 13.6 + - - +
11F ALA* 3.4 14.5 - - - +
13F TRP* 1.3 77.8 - - - +
15F ALA* 1.3 60.5 + - - +
17F ASN* 3.2 7.0 + - - +
18F HIS* 3.0 38.9 + - + +
112H ASP* 2.7 39.9 + - - +
115H CYS* 5.0 1.6 - - - -
116H PHE* 3.7 23.1 - - + -
145H ASN* 4.9 12.2 + - - +
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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 ALA 2.9 13.8 + - - +
12F ILE* 3.1 8.9 + - - +
14F GLN* 1.3 72.5 - - - +
16F LEU* 1.3 62.8 + - - +
18F HIS 3.4 1.2 + - - -
19F TYR 3.1 3.5 + - - -
20F ALA 2.9 33.2 + - - +
23F ASP* 4.7 4.3 - - + -
24F ALA* 3.8 25.4 - - + +
27F LEU* 6.1 1.1 - - + -
116H PHE* 3.4 24.4 - - + -
148H LEU* 4.9 4.0 - - + -
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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
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12F ILE 2.9 17.5 + - - +
13F TRP* 3.5 26.2 - - + +
15F ALA* 1.3 75.5 - - - +
17F ASN* 1.3 61.7 + - - +
19F TYR* 3.0 26.5 + - - -
21F TYR* 4.0 27.5 + - + -
24F ALA* 3.8 10.1 - - + -
43F LEU* 4.6 5.8 - - + -
46F THR* 3.7 27.6 - - + -
47F CYS* 3.5 35.4 - - - -
50F ARG* 3.8 24.8 + - + +
50H ARG* 5.0 0.5 + - - -
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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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13F TRP* 3.0 25.9 + - - +
14F GLN* 3.2 11.3 + - - +
16F LEU* 1.3 80.8 - - - +
18F HIS* 1.3 70.5 + - + +
19F TYR* 3.0 24.2 + - - -
50F ARG* 4.7 4.5 + - - -
13H TRP* 4.9 13.5 - - - -
50H ARG* 3.7 20.5 + - - +
73H TYR* 5.6 0.2 - - - -
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Residues in contact with HIS 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 GLN* 3.0 27.7 + - + +
15F ALA 3.4 0.8 + - - +
16F LEU 3.2 0.4 - - - -
17F ASN* 1.3 86.2 - - + +
19F TYR* 1.3 70.9 + - - +
20F ALA* 3.2 3.6 + - - -
70H GLN* 5.9 6.2 - - - +
73H TYR* 2.5 57.5 + + + -
112H ASP* 5.2 2.7 - - - -
113H SER* 3.2 33.7 - - - -
116H PHE* 3.5 32.9 - + + -
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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