Contacts of the helix formed by residues 12 - 25 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D GLY 3.2 6.6 + - - +
11D LEU* 1.3 76.8 - - - +
13D VAL* 1.3 61.1 + - + +
14D MET* 3.1 8.5 - - + +
15D GLY 3.0 4.0 + - - +
16D GLN* 2.6 41.6 + - - +
74D LEU 5.6 4.5 - - - +
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Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 1.3 76.6 - - + +
14D MET* 1.3 60.1 + - - +
16D GLN* 4.5 10.5 - - - +
17D ASN* 3.2 41.0 + - - +
132D GLU* 4.2 28.0 - - + +
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Residues in contact with MET 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.1 6.1 - - + +
13D VAL* 1.3 78.1 - - - +
15D GLY* 1.3 65.1 + - - +
17D ASN* 3.4 3.3 + - - +
18D LEU* 3.2 26.8 + - + +
74D LEU* 4.0 20.9 - - + -
128D VAL* 4.0 28.0 - - + +
131D GLY* 3.1 35.7 - - - +
132D GLU* 4.2 10.3 - - + -
135D ALA* 3.9 19.8 - - + +
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Residues in contact with GLY 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.7 9.4 - - - +
10D GLY 3.4 21.7 + - - -
11D LEU* 5.1 0.2 - - - -
12D ALA* 3.0 6.9 + - - +
14D MET* 1.3 79.5 - - - +
16D GLN* 1.3 63.0 + - - +
18D LEU 3.5 0.7 + - - -
19D ILE* 3.1 30.0 + - - +
74D LEU* 3.6 18.6 - - - +
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.6 28.3 + - + +
12D ALA 2.6 26.4 + - - +
13D VAL* 4.4 9.3 - - - +
15D GLY* 1.3 72.2 - - - +
17D ASN* 1.3 64.1 + - - +
19D ILE* 3.1 6.3 + - - +
20D LEU* 2.9 34.6 + - + +
38D LYS 5.7 0.6 + - - -
41D ASP* 5.1 4.8 + - - -
42D PHE* 3.5 43.7 - - + +
46D GLU* 3.8 26.8 + - + +
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D VAL* 3.2 31.8 + - - +
14D MET 4.0 2.2 - - - +
16D GLN* 1.3 81.2 - - - +
18D LEU* 1.3 58.7 + - - +
20D LEU* 4.5 5.0 - - - +
21D ASN* 2.8 24.6 + - - +
132D GLU* 2.9 26.1 + - - +
133D GLU* 4.9 0.8 - - - +
135D ALA* 2.9 19.6 - - + +
136D ARG* 3.5 37.7 - - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.7 17.9 - - + -
14D MET* 3.2 16.6 + - + +
15D GLY 3.9 0.2 - - - +
16D GLN 3.2 0.2 - - - -
17D ASN* 1.3 74.4 - - - +
19D ILE* 1.3 61.4 + - - +
21D ASN* 3.6 3.0 - - + +
22D MET* 3.0 37.6 + - + +
72D ILE* 5.3 8.5 - - + -
74D LEU* 3.6 26.0 - - + -
128D VAL* 4.5 21.1 - - + -
135D ALA* 3.4 21.1 - - + +
139D PRO* 3.9 24.0 - - + -
141D LEU* 5.4 3.6 - - + -
160D ILE* 4.3 18.2 - - + -
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.8 29.8 - - + -
11D LEU* 3.7 27.6 - - + -
15D GLY 3.1 14.1 + - - +
16D GLN 3.1 8.3 + - - +
18D LEU* 1.3 76.2 - - - +
20D LEU* 1.3 57.5 + - - +
22D MET* 3.3 8.8 + - - +
23D ASN* 2.9 26.0 + - - +
29D VAL* 3.7 20.7 - - + +
31D ALA* 3.8 17.5 - - + -
42D PHE* 3.9 13.7 - - + -
52D VAL* 3.7 26.5 - - + -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLN* 2.9 23.0 + - + +
17D ASN* 4.8 4.5 - - - +
19D ILE* 1.3 73.5 - - - +
21D ASN* 1.3 60.5 + - - +
23D ASN* 3.6 4.7 - - + +
24D ASP* 2.9 36.1 + - - +
42D PHE* 3.8 18.8 - - + -
46D GLU* 3.6 37.2 - - + +
47D ALA* 4.2 9.0 - - + -
50D THR* 4.8 8.5 - - + -
52D VAL* 4.7 7.6 - - + -
136D ARG* 3.4 36.8 - - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASN 2.8 21.7 + - - +
18D LEU* 3.6 7.2 - - + +
19D ILE 3.3 0.2 - - - -
20D LEU* 1.3 75.0 - - - +
22D MET* 1.3 57.6 + - - +
24D ASP* 3.5 1.9 + - - +
25D HIS* 2.7 55.6 + - - -
135D ALA 3.5 10.0 + - - +
136D ARG* 3.1 36.5 + - - +
137D TYR* 3.3 6.8 - - - +
138D GLY 3.4 13.5 - - - +
139D PRO* 3.7 4.2 - - - +
160D ILE* 3.4 21.8 + - + +
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Residues in contact with MET 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.6 26.7 - - + -
8D LEU* 4.3 16.4 - - + -
18D LEU* 3.0 26.3 + - + +
19D ILE* 3.8 5.6 - - - +
21D ASN* 1.3 73.5 - - - +
23D ASN* 1.3 65.4 + - - +
25D HIS 3.3 5.7 + - - -
27D PHE* 3.1 32.6 + - + +
29D VAL* 3.6 37.0 - - + -
72D ILE* 4.5 8.7 - - + -
156D ILE* 3.8 15.9 - - + -
160D ILE* 3.6 33.7 - - + -
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE 2.9 17.8 + - - +
20D LEU* 3.6 9.6 - - + +
21D ASN 3.2 0.4 - - - -
22D MET* 1.3 72.6 - - - +
24D ASP* 1.3 64.5 + - - +
25D HIS 3.0 4.7 - - - -
26D GLY* 3.0 19.6 + - - -
27D PHE 3.6 11.8 + - - +
29D VAL* 4.4 0.4 - - + +
50D THR* 3.7 25.6 - - + +
51D LYS* 2.9 34.5 + - - +
52D VAL* 3.2 20.7 + - + +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 2.9 16.6 + - - +
21D ASN* 3.5 5.8 + - - +
23D ASN* 1.3 81.9 + - - +
25D HIS* 1.3 65.0 + - + +
26D GLY 3.4 1.6 + - - -
50D THR* 5.7 2.6 - - - +
136D ARG* 2.4 42.1 + - - +
137D TYR* 5.5 0.9 - - - -
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Residues in contact with HIS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASN* 2.7 41.6 + - - +
22D MET 3.3 6.1 + - - +
23D ASN 3.0 1.2 - - - -
24D ASP* 1.3 85.7 - - + +
26D GLY* 1.3 60.3 + - - +
27D PHE* 3.5 25.4 - - + -
137D TYR* 5.2 6.5 - - - -
159D GLY* 3.1 33.5 + - - -
160D ILE* 3.9 8.2 - - + -
163D LYS* 5.2 0.8 + - - -
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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