Contacts of the helix formed by residues 10 - 23 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.3 4.6 - - - -
9A ALA* 1.3 75.6 - - - +
11A THR* 1.3 59.9 + - - -
12A MET 3.5 1.3 - - - -
13A GLY 4.0 3.1 - - - +
14A SER* 2.4 33.9 + - - -
31A ASP* 4.1 3.0 + - - -
39A ARG* 5.1 13.5 - - - -
43A PHE* 5.9 0.2 - - - -
87A ALA 5.6 0.4 + - - -
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Residues in contact with THR 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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10A GLY* 1.3 72.1 - - - +
12A MET* 1.3 65.2 - - - +
14A SER* 3.8 3.0 + - - -
15A GLY* 3.1 19.2 + - - -
39A ARG* 5.1 7.2 + - - +
43A PHE* 4.0 31.8 - - + -
141A ASN* 4.8 20.0 - - - +
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Residues in contact with MET 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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11A THR* 1.3 78.4 - - - +
13A GLY* 1.3 60.5 + - - +
15A GLY* 3.1 1.9 + - - -
16A ILE* 2.8 38.9 + - + +
87A ALA* 4.7 5.2 - - + +
115A ASN* 3.8 26.7 - - - +
139A PHE* 3.3 48.9 - - + +
140A PHE 4.0 5.2 - - - +
141A ASN* 4.2 31.9 - - - +
143A ALA* 4.4 11.1 - - + +
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Residues in contact with GLY 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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6A VAL* 3.4 20.3 - - - +
8A GLY 3.0 26.5 - - - -
10A GLY 3.6 4.4 + - - -
11A THR 3.4 0.6 - - - -
12A MET* 1.3 78.5 - - - +
14A SER* 1.3 57.7 + - - +
16A ILE* 3.3 1.8 + - - +
17A ALA* 2.9 23.7 + - - +
29A LEU* 4.4 0.7 - - - -
87A ALA* 4.1 15.5 + - - +
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Residues in contact with SER 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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8A GLY 3.9 2.2 + - - -
9A ALA* 3.0 12.0 + - - -
10A GLY 2.4 31.4 + - - -
13A GLY* 1.3 73.1 - - - +
15A GLY* 1.3 61.0 + - - +
17A ALA* 4.0 3.8 - - - -
18A GLN* 2.9 29.3 + - - +
29A LEU* 4.6 4.0 - - - -
40A GLY* 3.6 11.0 - - - -
43A PHE* 3.8 14.3 - - - -
44A ILE* 3.5 34.8 - - - +
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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 THR 3.1 13.1 + - - -
12A MET 3.1 6.7 + - - -
14A SER* 1.3 76.5 - - - +
16A ILE* 1.3 55.6 + - - +
18A GLN* 3.2 4.1 + - - +
19A ALA* 2.9 29.5 + - - +
43A PHE* 4.7 7.5 - - - -
143A ALA* 3.5 11.0 - - - -
144A PRO* 3.6 24.8 - - - +
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Residues in contact with ILE 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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6A VAL* 4.0 10.3 - - + -
12A MET* 2.8 26.0 + - + +
13A GLY* 3.6 4.5 - - - +
15A GLY* 1.3 76.4 - - - +
17A ALA* 1.3 62.9 + - - +
19A ALA* 3.4 5.6 + - - +
20A PHE* 3.2 31.1 + - + -
85A ILE* 3.9 37.5 - - + -
87A ALA* 4.5 5.6 - - + -
115A ASN* 4.1 19.7 - - + -
139A PHE* 3.6 44.4 - - + -
143A ALA* 3.9 7.2 - - + -
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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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6A VAL* 4.2 6.0 - - + +
13A GLY 2.9 16.2 + - - +
14A SER* 3.5 10.3 - - - +
15A GLY 3.2 0.2 - - - -
16A ILE* 1.3 74.8 - - - +
18A GLN* 1.3 65.2 + - - +
20A PHE* 3.2 4.9 + - - +
21A ALA* 3.0 24.5 + - - +
27A VAL* 3.7 28.1 - - + +
29A LEU* 4.1 16.6 - - + -
44A ILE* 4.3 7.9 - - + -
69A ILE* 4.7 4.7 - - + -
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Residues in contact with GLN 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 SER 2.9 16.8 + - - +
15A GLY 3.5 3.8 - - - +
17A ALA* 1.3 76.1 - - - +
19A ALA* 1.3 65.1 + - - +
20A PHE 3.1 0.2 + - - -
21A ALA* 3.2 6.1 + - - +
22A ALA* 2.8 30.2 + - + +
44A ILE* 3.5 26.7 - - + +
47A ASN* 3.2 36.4 + - - +
48A LEU* 3.8 28.1 - - + +
51A LEU* 4.5 10.1 - - - +
65A ILE* 4.9 2.2 - - + +
69A ILE* 4.7 1.3 - - - -
144A PRO* 3.5 28.7 - - + +
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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 2.9 14.0 + - - +
16A ILE* 3.5 13.0 - - - +
17A ALA 3.3 0.2 - - - -
18A GLN* 1.3 79.5 - - - +
20A PHE* 1.3 60.4 - - + +
22A ALA* 3.9 4.9 + - - +
23A LYS* 3.6 23.2 + - - +
139A PHE* 5.2 2.0 - - + -
143A ALA 4.2 17.3 - - - +
144A PRO* 4.2 9.0 - - + +
172A ILE* 4.2 13.7 - - + +
174A LYS* 4.2 14.8 - - - +
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Residues in contact with PHE 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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4A VAL* 3.7 31.4 - - + -
6A VAL* 5.3 0.4 - - + -
16A ILE* 3.2 29.6 + - + -
17A ALA* 3.2 4.2 + - - +
19A ALA* 1.3 76.1 - - + +
21A ALA* 1.3 67.5 + - - +
23A LYS 3.1 9.9 + - - -
24A GLY 3.4 0.2 + - - -
25A PHE* 3.1 35.7 + + + -
27A VAL* 3.6 19.5 - - + -
83A LEU* 4.1 10.5 - - + -
85A ILE* 3.5 31.4 - - + -
137A MET* 4.3 7.2 - - + -
139A PHE* 4.3 3.4 - + - -
168A THR* 4.0 14.4 - - - -
172A ILE* 3.7 43.1 - - + -
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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 3.0 16.9 + - - +
18A GLN 3.8 1.6 - - - +
20A PHE* 1.3 77.7 - - - +
22A ALA* 1.3 63.1 + - - +
24A GLY 2.9 12.8 + - - -
25A PHE 3.7 11.4 - - - -
27A VAL* 3.8 3.1 - - + +
65A ILE* 3.7 17.7 - - + +
68A ARG* 3.0 21.4 + - + +
69A ILE* 3.5 34.1 - - + -
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Residues in contact with ALA 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 GLN* 2.8 23.1 + - + +
19A ALA* 4.1 5.4 - - - +
21A ALA* 1.3 76.0 - - - +
23A LYS* 1.3 69.3 + - - +
24A GLY 3.4 0.9 + - - -
48A LEU* 5.6 1.8 - - + -
61A THR* 6.0 0.5 - - - +
65A ILE* 3.5 30.9 - - + +
68A ARG* 4.4 5.4 + - - -
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Residues in contact with LYS 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 ALA 3.6 10.2 + - - +
20A PHE 3.1 8.3 + - - +
21A ALA 3.1 1.6 - - - -
22A ALA* 1.3 87.2 + - - +
24A GLY* 1.3 59.3 + - - +
25A PHE* 3.6 11.4 - - + -
171A ALA 3.4 23.7 - - - +
172A ILE* 3.7 33.7 + - + +
173A GLY* 4.5 6.7 - - - +
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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