Contacts of the helix formed by residues 10 - 22 (chain D) in PDB entry 6ACQ
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 GLY 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLY* 3.4 4.0 - - - -
9D ALA* 1.3 75.6 - - - +
11D THR* 1.3 62.2 + - - -
12D MET 3.4 2.5 - - - -
13D GLY 4.3 1.9 - - - +
14D SER* 1.9 35.2 + - - +
31D ASP* 4.8 0.4 + - - -
39D ARG* 5.1 11.4 - - - -
43D PHE* 5.9 0.2 - - - -
87D ALA 5.7 1.8 + - - -
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Residues in contact with THR 11 (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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10D GLY* 1.3 72.2 - - - +
12D MET* 1.3 61.7 + - - +
14D SER* 4.0 1.7 - - - -
15D GLY* 3.1 24.4 + - - -
39D ARG* 5.2 7.5 + - - +
43D PHE* 4.3 30.4 - - + -
141D ASN* 4.2 27.1 - - - +
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Residues in contact with MET 12 (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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10D GLY 3.4 0.2 - - - -
11D THR* 1.3 80.5 - - - +
13D GLY* 1.3 60.2 + - - +
15D GLY* 3.3 2.4 + - - -
16D ILE* 3.0 36.2 + - + +
87D ALA* 4.6 8.7 - - + +
115D ASN* 3.8 31.0 - - - +
139D PHE* 3.9 26.9 - - + +
141D ASN* 3.7 40.4 - - - +
143D ALA* 4.2 12.6 - - + -
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Residues in contact with GLY 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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6D VAL* 3.5 15.5 - - - +
8D GLY 3.2 23.3 - - - -
10D GLY* 3.9 4.0 + - - +
11D THR 3.6 0.2 - - - -
12D MET* 1.3 78.3 - - - +
14D SER* 1.3 62.9 + - - +
16D ILE* 3.2 3.5 + - - +
17D ALA* 3.0 21.0 + - - +
29D LEU* 5.5 0.4 - - - -
87D ALA* 3.7 19.8 + - - +
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Residues in contact with SER 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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8D GLY 4.0 1.6 + - - -
9D ALA* 3.0 17.0 + - - +
10D GLY 1.9 31.1 + - - -
11D THR 4.0 2.5 - - - -
13D GLY* 1.3 76.1 - - - +
15D GLY* 1.3 56.9 + - - +
17D ALA* 3.4 4.4 + - - +
18D GLN* 3.0 25.0 + - - +
29D LEU* 4.7 5.4 - - - -
40D GLY* 4.0 21.4 - - - -
43D PHE* 4.3 15.3 - - - +
44D ILE* 3.5 19.2 - - - +
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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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11D THR 3.1 16.7 + - - -
12D MET 3.3 3.3 + - - -
14D SER* 1.3 75.4 - - - +
16D ILE* 1.3 57.5 + - - +
18D GLN* 3.6 3.8 + - - -
19D ALA* 3.0 28.4 + - - +
43D PHE* 5.3 4.4 - - - -
47D ASN* 6.0 0.9 - - - -
143D ALA* 3.5 10.3 - - - +
144D PRO* 3.5 26.5 - - - +
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Residues in contact with ILE 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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6D VAL* 4.1 9.9 - - + -
12D MET* 3.0 27.4 + - + +
13D GLY* 3.6 8.7 - - - +
14D SER 3.2 0.4 - - - -
15D GLY* 1.3 74.4 - - - +
17D ALA* 1.3 66.4 + - - +
19D ALA* 3.2 5.5 + - - +
20D PHE* 3.0 48.0 + - + -
85D ILE* 4.0 18.8 - - + -
87D ALA* 4.7 4.3 - - + -
115D ASN* 4.2 22.0 - - + +
139D PHE* 3.6 40.2 - - + -
143D ALA* 3.9 8.7 - - + -
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Residues in contact with ALA 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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6D VAL* 4.2 9.4 - - + +
13D GLY 3.0 13.0 + - - +
14D SER 3.6 8.1 - - - +
15D GLY 3.3 0.2 - - - -
16D ILE* 1.3 76.8 - - - +
18D GLN* 1.3 63.0 + - - +
20D PHE* 3.1 5.3 + - - +
21D ALA* 2.9 24.1 + - - +
27D VAL* 3.9 24.5 - - + +
29D LEU* 3.7 26.0 - - + -
44D ILE* 4.5 3.1 - - + -
69D ILE* 4.5 6.1 - - + -
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Residues in contact with GLN 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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14D SER 3.0 14.7 + - - +
15D GLY* 3.7 6.2 - - - +
17D ALA* 1.3 79.1 - - - +
19D ALA* 1.3 57.5 + - - +
21D ALA* 3.8 0.5 - - - +
22D ALA* 2.8 38.2 + - + +
44D ILE* 3.7 24.4 - - + +
47D ASN* 3.4 35.8 + - - +
48D LEU* 4.1 25.3 - - + +
51D LEU* 4.5 13.1 - - - +
65D ILE* 4.9 1.5 - - + +
69D ILE* 4.3 10.8 - - - -
144D PRO* 3.8 26.7 - - + +
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Residues in contact with ALA 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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15D GLY 3.0 19.2 + - - +
16D ILE* 3.5 8.1 - - - +
18D GLN* 1.3 76.8 - - - +
20D PHE* 1.3 62.6 + - + +
22D ALA* 3.8 13.2 - - - +
23D LYS* 3.9 6.6 + - - +
139D PHE* 5.5 2.0 - - + -
143D ALA* 4.2 7.2 - - + +
144D PRO* 3.9 23.6 - - + +
172D ILE* 4.3 21.3 - - + +
174D LYS* 4.4 11.9 - - - +
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Residues in contact with PHE 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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4D VAL* 4.0 17.9 - - + -
6D VAL* 5.2 1.8 - - + -
16D ILE* 3.0 31.7 + - + -
17D ALA* 3.1 9.2 + - - +
19D ALA* 1.3 75.7 - - + +
21D ALA* 1.3 68.2 + - - +
23D LYS* 3.0 11.4 + - - +
24D GLY 3.5 5.9 + - - -
25D PHE* 3.6 35.8 + + + -
27D VAL* 3.9 13.5 - - + -
83D LEU* 4.1 13.5 - - + -
85D ILE* 3.5 31.0 - - + -
137D MET* 4.7 7.0 - - + -
139D PHE* 4.4 4.5 - + - -
168D THR* 4.0 14.4 - - - -
172D ILE* 3.6 41.3 - - + -
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Residues in contact with ALA 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 ALA 2.9 10.6 + - - +
18D GLN 3.8 1.8 - - - +
20D PHE* 1.3 71.6 - - - +
22D ALA* 1.3 53.4 + - - +
23D LYS 2.7 1.6 + - - -
24D GLY* 2.6 28.4 + - - -
25D PHE 3.8 12.8 - - - -
27D VAL* 3.6 4.1 - - + +
65D ILE* 3.8 14.1 - - + +
68D ARG* 3.5 17.2 + - + +
69D ILE* 3.3 41.7 - - + -
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Residues in contact with ALA 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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18D GLN* 2.8 27.1 + - + +
19D ALA* 3.8 11.7 - - - +
21D ALA* 1.3 70.6 - - - +
23D LYS* 1.3 62.5 + - + +
24D GLY 3.5 0.2 - - - -
48D LEU* 6.1 0.2 - - + -
61D THR* 6.1 0.3 - - - +
65D ILE* 3.7 28.1 - - + +
68D ARG* 5.3 1.1 + - - -
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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