Contacts of the helix formed by residues 12 - 24 (chain A) in PDB entry 5UQ9
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.1 6.8 + - - +
11A LEU* 1.3 78.3 - - - +
13A VAL* 1.3 62.1 + - + +
14A MET* 3.0 9.6 - - + +
15A GLY 2.9 4.2 + - - +
16A GLN* 2.5 40.7 + - - +
74A LEU 5.8 3.1 - - - +
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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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12A ALA* 1.3 75.2 - - + +
14A MET* 1.3 64.0 + - + +
16A GLN* 4.3 13.4 + - - +
17A ASN* 2.2 41.7 + - - +
132A GLU* 3.0 37.4 - - + +
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Residues in contact with MET 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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12A ALA* 3.0 6.4 - - + +
13A VAL* 1.3 85.9 - - + +
15A GLY* 1.3 62.7 + - - +
17A ASN* 4.0 2.3 - - - +
18A LEU* 3.3 26.1 + - + +
74A LEU* 4.3 20.9 - - + -
128A VAL* 5.3 14.1 - - + +
131A GLY* 3.2 33.7 - - - +
132A GLU* 3.9 19.7 - - + +
135A ALA* 3.9 13.3 - - - +
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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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8A LEU* 3.7 7.5 - - - +
10A GLY 3.5 18.7 + - - -
12A ALA* 2.9 7.7 + - - +
14A MET* 1.3 76.2 - - - +
16A GLN* 1.3 65.3 + - - +
18A LEU* 3.2 3.1 + - - +
19A ILE* 3.0 28.6 + - - +
74A LEU* 3.6 20.7 - - - +
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Residues in contact with GLN 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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11A LEU* 3.6 27.1 + - + +
12A ALA 2.5 26.6 + - - +
13A VAL* 4.3 14.4 + - - +
15A GLY* 1.3 72.4 - - - +
17A ASN* 1.3 59.7 + - - +
19A ILE* 3.2 5.5 + - - +
20A LEU* 3.0 38.3 + - + +
38A LYS* 5.3 4.2 + - - +
42A PHE* 3.5 47.2 - - + +
46A GLU* 3.6 21.9 - - - +
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Residues in contact with ASN 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* 2.2 47.6 + - - +
14A MET 4.0 2.7 - - - +
16A GLN* 1.3 79.7 + - - +
18A LEU* 1.3 57.2 + - - +
20A LEU* 4.3 3.9 - - - +
21A ASN* 2.8 28.4 + - - +
132A GLU* 3.8 19.8 + - - +
133A GLU* 5.7 0.2 - - - -
135A ALA* 3.2 8.5 - - + +
136A ARG* 3.2 49.5 - - + +
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Residues in contact with LEU 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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8A LEU* 3.9 12.8 - - + -
14A MET* 3.3 12.2 + - + +
15A GLY 3.2 9.0 + - - +
17A ASN* 1.3 76.8 - - - +
19A ILE* 1.3 60.2 + - - +
21A ASN* 3.2 3.6 + - + +
22A MET* 2.9 37.4 + - + +
72A ILE* 5.5 5.6 - - + -
74A LEU* 3.7 26.2 - - + -
128A VAL* 4.3 22.4 - - + -
135A ALA* 3.3 22.9 - - + +
139A PRO* 3.9 22.2 - - + -
141A LEU* 5.3 3.8 - - + -
160A ILE* 4.1 19.1 - - + -
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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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8A LEU* 3.9 23.6 - - + -
11A LEU* 3.6 31.0 - - + -
15A GLY 3.0 17.9 + - - +
16A GLN 3.2 6.5 + - - +
18A LEU* 1.3 75.6 - - - +
20A LEU* 1.3 57.3 + - - +
22A MET* 3.2 9.7 + - - +
23A ASN* 2.7 29.1 + - - +
29A VAL* 3.7 28.9 - - + +
31A ALA* 3.6 17.0 - - + -
42A PHE* 3.9 22.2 - - + -
52A VAL* 4.1 15.3 - - + -
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Residues in contact with LEU 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 GLN* 3.0 28.1 + - + +
17A ASN* 4.1 8.3 - - - +
19A ILE* 1.3 72.8 - - - +
21A ASN* 1.3 56.9 + - - +
23A ASN* 4.0 7.0 - - + +
24A ASP* 2.7 43.8 + - - +
42A PHE* 4.2 13.2 - - + -
46A GLU* 3.4 33.9 - - + +
47A ALA* 4.1 17.9 - - + -
50A THR* 5.2 3.4 - - + -
52A VAL* 4.8 6.5 - - + -
136A ARG* 3.0 29.4 - - - +
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Residues in contact with ASN 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 ASN 2.8 20.7 + - - +
18A LEU* 3.3 8.7 - - + +
19A ILE 3.2 0.2 - - - -
20A LEU* 1.3 78.3 - - - +
22A MET* 1.3 58.2 + - - +
24A ASP* 3.4 2.2 + - - -
25A HIS* 2.5 55.4 + - - -
135A ALA 3.1 11.5 - - - +
136A ARG 3.0 32.6 + - - +
137A TYR 3.3 4.4 + - - -
138A GLY 3.5 8.1 + - - -
139A PRO* 3.6 8.1 - - - +
160A ILE* 3.4 22.5 + - + +
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Residues in contact with MET 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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6A ILE* 3.7 19.1 - - + -
8A LEU* 3.9 18.2 - - + -
18A LEU* 2.9 28.0 + - + +
19A ILE* 3.7 6.3 - - - -
21A ASN* 1.3 75.4 - - - +
23A ASN* 1.3 58.2 + - - +
25A HIS 3.3 3.1 + - - -
27A PHE* 3.1 38.4 + - + +
29A VAL* 3.6 36.6 - - + -
72A ILE* 4.2 14.8 - - + -
156A ILE* 4.2 16.8 - - + -
160A ILE* 3.6 33.9 - - + -
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Residues in contact with ASN 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 20.8 + - - +
20A LEU* 3.8 8.1 - - - +
21A ASN 3.2 0.2 - - - -
22A MET* 1.3 71.3 - - - +
24A ASP* 1.3 65.5 + - - +
25A HIS 3.0 9.8 + - - -
26A GLY* 3.3 11.4 + - - -
27A PHE 3.5 16.3 + - - +
28A VAL* 5.2 0.4 - - - +
29A VAL* 4.2 2.2 - - + +
50A THR* 2.2 32.6 + - - +
51A LYS* 3.5 14.6 - - - +
52A VAL* 3.3 36.1 - - + +
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Residues in contact with ASP 24 (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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20A LEU* 2.7 23.0 + - - +
21A ASN* 3.4 5.5 + - - +
22A MET 3.4 0.4 - - - -
23A ASN* 1.3 80.0 - - - +
25A HIS* 1.3 69.9 + - + +
26A GLY 3.7 0.7 - - - -
136A ARG* 2.5 45.5 + - - +
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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