Contacts of the helix formed by residues 9 - 21 (chain A) in PDB entry 5E67
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 ASN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS 4.3 0.4 + - - -
8A LEU* 1.3 75.7 - - - +
10A PRO* 1.3 77.9 - - - +
11A TRP* 2.8 38.0 + - - +
12A ALA* 3.1 25.7 + - + +
13A VAL* 3.2 11.1 + - - +
61A PHE* 4.3 2.0 - - - -
168A ASP* 5.3 0.4 + - - -
170A PHE* 3.4 41.9 - - + +
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Residues in contact with PRO 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 LEU 4.4 2.5 - - - +
9A ASN* 1.3 95.6 - - - +
11A TRP* 1.3 63.3 + - + +
13A VAL 3.2 1.2 + - - -
14A VAL* 3.1 27.0 + - - +
61A PHE* 3.8 20.1 - - + -
93A PHE* 3.4 22.2 - - + -
97A TYR* 4.2 28.9 - - + +
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Residues in contact with TRP 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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9A ASN* 2.8 16.3 + - - +
10A PRO* 1.3 76.2 - - + +
12A ALA* 1.3 61.7 + - - +
14A VAL* 3.4 16.0 + - + +
15A GLY 2.9 23.4 + - - -
96A LYS 4.7 3.6 - - - -
97A TYR* 3.7 48.3 - + + -
98A SER 4.0 17.7 - - - -
167A PRO* 3.5 39.7 + - + -
168A ASP* 3.4 31.8 + - + +
170A PHE* 3.8 13.5 - - + -
171A TRP* 3.2 19.6 - + + +
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Residues in contact with ALA 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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8A LEU* 5.6 1.3 - - + -
9A ASN* 3.1 26.0 + - + +
11A TRP* 1.3 77.1 - - - +
13A VAL* 1.3 59.3 + - + +
15A GLY 3.3 0.2 + - - -
16A PHE* 2.9 27.3 + - - +
170A PHE* 3.3 26.0 + - + +
173A ALA* 5.2 1.6 - - + -
174A GLY* 3.3 16.8 - - - +
257A LYS 5.7 0.2 - - - +
259A ILE* 4.4 21.8 - - + +
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Residues in contact with VAL 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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8A LEU* 3.8 35.4 - - + -
9A ASN 3.2 12.4 + - - +
10A PRO 3.2 8.5 + - - +
12A ALA* 1.3 74.8 - - - +
14A VAL* 1.3 64.5 + - - +
16A PHE* 3.0 8.0 + - - +
17A ILE* 2.9 34.6 + - + +
58A LEU* 4.0 13.0 - - + -
61A PHE* 4.0 13.9 - - + -
62A PHE* 3.9 31.4 - - + -
93A PHE* 4.0 12.1 - - + -
259A ILE* 5.4 1.1 - - + -
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Residues in contact with VAL 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 PRO 3.1 14.9 + - - +
11A TRP* 3.7 12.1 - - + +
13A VAL* 1.3 78.3 - - - +
15A GLY* 1.3 53.0 + - - +
17A ILE 3.2 0.7 + - - -
18A ASP* 2.7 34.1 + - - +
93A PHE* 3.7 11.4 - - + -
94A PHE* 4.3 9.2 - - + -
97A TYR* 3.2 34.5 - - + +
98A SER 3.7 22.2 - - - +
99A LEU* 3.7 22.6 - - + +
171A TRP* 3.8 13.7 - - + -
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Residues in contact with GLY 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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11A TRP 2.9 11.3 + - - -
12A ALA 3.7 2.0 - - - -
14A VAL* 1.3 77.8 - - - +
16A PHE* 1.3 61.4 + - - +
18A ASP* 3.3 4.2 + - - +
19A ALA 3.2 14.9 + - - -
171A TRP* 3.4 40.5 - - - -
175A PHE* 3.3 18.1 - - - -
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Residues in contact with PHE 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 ALA 2.9 14.0 + - - +
13A VAL* 3.0 9.6 + - - +
15A GLY* 1.3 75.1 - - - +
17A ILE* 1.3 63.6 + - + +
19A ALA* 2.9 6.7 + - - +
20A GLU* 2.8 63.6 + - + +
45A VAL* 3.9 22.7 - - + -
47A VAL* 4.5 6.1 - - + -
51A ASP* 6.2 0.4 - - - -
54A LEU* 3.6 28.3 - - + -
55A LEU* 6.1 0.2 - - + -
58A LEU* 4.5 12.8 - - + -
174A GLY 3.3 19.3 - - - +
177A SER* 4.0 14.4 - - - -
178A GLY* 3.9 15.5 - - - -
259A ILE* 4.2 13.9 - - + -
403A MXE 4.2 6.3 - - - -
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Residues in contact with ILE 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 VAL* 2.9 27.1 + - + +
14A VAL 3.9 2.7 - - - +
16A PHE* 1.3 83.4 - - + +
18A ASP* 1.3 68.1 + - - +
19A ALA 3.1 1.1 - - - -
20A GLU 3.5 0.2 + - - -
21A GLY* 3.0 35.3 + - - +
23A PHE* 3.8 31.6 - - + -
43A PHE* 3.8 10.8 - - + -
45A VAL* 3.6 31.6 - - + -
58A LEU* 5.6 4.5 - - + -
62A PHE* 6.3 0.2 - - + -
94A PHE* 4.1 19.7 - - + -
99A LEU* 4.0 10.2 - - + +
103A ALA* 4.6 5.4 - - - +
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Residues in contact with ASP 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 VAL 2.7 12.9 + - - +
15A GLY 3.4 9.6 - - - +
17A ILE* 1.3 74.0 - - - +
19A ALA* 1.3 56.9 + - - +
99A LEU* 3.4 23.4 - - - +
100A ILE 2.8 24.1 + - - -
101A THR* 2.8 56.1 + - + +
103A ALA* 3.9 6.3 - - - +
171A TRP* 2.9 27.5 + - + -
175A PHE* 3.9 7.7 - - + -
179A ASP* 4.6 0.9 - - - +
206A GLN* 4.8 3.6 + - - -
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Residues in contact with ALA 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 GLY 3.2 5.4 + - - +
16A PHE 2.9 11.0 + - - +
17A ILE 4.1 0.2 - - - -
18A ASP* 1.3 78.0 - - - +
20A GLU* 1.3 55.6 + - - +
175A PHE* 3.6 25.1 - - + +
178A GLY* 3.7 12.3 - - - -
179A ASP* 3.4 29.1 - - - +
401A MG 2.2 29.3 - - - -
15B T 3.4 4.0 + - - -
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Residues in contact with GLU 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 PHE* 2.8 41.2 + - + +
17A ILE* 5.0 0.2 - - - -
19A ALA* 1.3 76.1 - - - +
21A GLY* 1.3 69.6 + - - +
22A SER 3.5 0.7 + - - -
44A SER 4.4 2.3 - - - +
45A VAL* 4.7 8.7 - - + +
46A THR 3.8 12.7 + - - +
47A VAL* 3.8 9.5 - - - +
178A GLY* 4.0 6.7 - - - -
402A MG 2.4 25.5 - - - -
403A MXE 3.2 28.1 + - - -
14B A 3.7 22.5 + - - +
15B T 2.9 24.3 + - - +
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Residues in contact with GLY 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 ILE* 3.0 49.6 + - - +
20A GLU* 1.3 83.8 - - - +
22A SER* 1.3 59.8 + - - -
23A PHE* 4.3 3.3 - - - -
43A PHE* 5.1 1.6 - - - -
44A SER 3.9 5.6 - - - -
45A VAL* 4.6 1.3 - - - -
103A ALA* 5.9 3.1 - - - +
15B T 4.7 2.6 + - - -
16B G 5.7 0.3 + - - -
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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