Contacts of the helix formed by residues 8 - 23 (chain A) in PDB entry 5DPW
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 SER 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS 5.2 0.7 - - - -
5A GLN 5.6 0.2 - - - -
6A ARG 4.0 1.6 + - - -
7A LYS* 1.3 78.3 - - - +
9A LEU* 1.3 65.5 + - - +
10A ALA* 4.1 5.0 + - - +
11A ILE* 3.1 30.4 + - - +
12A ARG* 3.0 18.6 + - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 1.3 73.9 - - - +
10A ALA* 1.3 59.0 + - - +
12A ARG* 3.1 27.2 + - - +
13A GLN* 2.8 58.4 + - - +
101A GLU* 3.8 26.7 - - + +
102A ASP* 3.5 26.2 - - + -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.4 5.5 + - - +
9A LEU* 1.3 78.3 - - - +
11A ILE* 1.3 59.3 + - + +
13A GLN* 3.3 17.1 + - - +
14A GLU* 2.8 29.2 + - - +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.8 28.5 - - + -
8A SER* 3.1 26.8 + - - +
9A LEU 3.2 0.6 - - - -
10A ALA* 1.3 75.8 - - + +
12A ARG* 1.3 61.5 + - - +
14A GLU* 3.1 23.3 + - - +
15A GLU* 2.9 31.4 + - + +
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.8 21.3 - - + -
4A LYS* 3.6 33.5 + - - +
7A LYS* 3.0 36.6 + - + -
8A SER* 3.0 7.5 + - - +
9A LEU* 3.4 40.4 - - - +
11A ILE* 1.3 76.0 - - - +
13A GLN* 1.3 57.1 + - - +
15A GLU* 3.3 8.4 + - - +
16A VAL* 2.8 31.1 + - - +
100A ASP* 3.9 2.6 + - - -
101A GLU* 4.2 10.1 + - - -
102A ASP* 2.7 53.7 + - + +
104A PHE* 3.5 9.0 - - + -
106A TYR* 3.4 15.3 + - - -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 2.8 47.3 + - + +
10A ALA* 3.4 17.8 - - - +
11A ILE 3.2 0.2 - - - -
12A ARG* 1.3 74.2 - - - +
14A GLU* 1.3 54.9 + - - +
16A VAL* 3.2 4.9 + - + +
17A ALA* 2.8 37.2 + - - +
101A GLU 4.3 9.3 + - - -
102A ASP* 4.0 18.6 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 2.8 13.3 + - - +
11A ILE* 3.3 30.1 - - - +
13A GLN* 1.3 74.3 - - - +
15A GLU* 1.3 59.6 + - - +
17A ALA* 3.1 6.9 + - - +
18A GLY* 2.8 27.7 + - - -
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.5 21.1 - - - -
7A LYS* 4.6 10.2 - - - +
11A ILE* 2.9 14.4 + - + +
12A ARG* 3.5 11.4 - - - +
14A GLU* 1.3 78.7 - - - +
16A VAL* 1.3 63.7 + - - +
18A GLY 3.3 0.2 + - - -
19A ILE* 2.9 37.3 + - + +
47A LYS* 2.3 47.1 + - - +
104A PHE* 4.2 4.3 - - + -
4B ASP* 5.1 2.0 - - - -
6B TRP* 3.3 16.7 - - + +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG 2.8 16.7 + - - +
13A GLN* 3.4 7.9 - - + +
15A GLU* 1.3 73.3 - - - +
17A ALA* 1.3 62.9 + - + +
19A ILE* 4.1 3.6 - - - +
20A ARG* 2.8 39.5 + - + +
28A PRO* 3.8 19.9 - - + +
102A ASP 3.1 20.4 - - - +
103A GLY* 3.7 30.1 - - - -
104A PHE* 3.7 21.3 - - + +
6B TRP* 5.5 1.1 - - - -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN 2.8 21.1 + - - +
14A GLU* 3.4 7.6 - - - +
16A VAL* 1.3 76.0 - - + +
18A GLY* 1.3 61.0 + - - +
20A ARG* 3.7 3.9 - - - +
21A ALA* 2.8 32.7 + - - +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU 2.8 17.7 + - - -
15A GLU 3.8 0.9 - - - -
17A ALA* 1.3 72.9 - - - +
19A ILE* 1.3 65.0 + - - +
21A ALA* 3.4 7.4 + - - +
22A LYS* 2.8 29.6 + - - +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU* 2.9 27.2 + - + +
16A VAL 4.1 2.5 - - - +
18A GLY* 1.3 81.5 - - - +
20A ARG* 1.3 57.2 + - + +
21A ALA 3.1 0.9 - - - -
22A LYS* 3.4 19.7 - - + +
23A PHE* 2.7 36.5 + - + +
28A PRO* 5.2 4.5 - - + -
49A LEU* 3.7 32.8 - - + -
6B TRP* 3.4 46.7 - - + +
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 2.8 27.4 + - + +
17A ALA* 3.9 4.5 - - - +
19A ILE* 1.3 73.9 - - + +
21A ALA* 1.3 62.0 + - - +
23A PHE 4.1 2.5 - - - -
24A PRO* 2.8 62.0 + - - +
25A ASN 3.7 2.4 - - - -
26A LYS 3.2 31.1 + - - +
27A ILE* 3.4 27.5 - - - +
28A PRO* 4.4 18.2 - - + +
52A GLN* 4.3 6.9 - - - +
95A TYR* 4.3 22.3 + - - +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 2.8 17.3 + - - +
18A GLY* 3.4 8.3 - - - +
20A ARG* 1.3 79.5 - - - +
22A LYS* 1.3 63.3 + - - +
24A PRO* 3.7 9.1 - - - +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY 2.8 17.4 + - - +
19A ILE* 3.4 21.5 - - + +
21A ALA* 1.3 79.3 - - - +
23A PHE* 1.3 93.3 + - + +
24A PRO* 3.5 5.4 - - - +
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 2.7 20.2 + - + +
20A ARG* 3.4 6.8 + - - +
22A LYS* 1.3 109.2 - - + +
24A PRO* 1.3 61.2 - - - +
25A ASN* 3.0 11.5 + - + +
26A LYS* 3.2 32.7 + - + +
49A LEU* 3.4 33.5 - - + +
8B ASN* 4.5 13.7 - - + -
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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