Contacts of the helix formed by residues 10 - 22 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F GLY* 3.2 5.7 + - - -
9F ALA* 1.3 79.5 - - - +
11F THR* 1.3 64.7 + - - -
12F MET 3.4 2.0 - - - -
13F GLY 4.1 2.0 - - - +
14F SER* 2.9 26.9 + - - -
31F ASP* 4.4 1.0 + - - -
39F ARG* 4.4 16.2 - - - -
43F PHE* 5.4 0.7 - - - -
87F ALA 5.4 3.0 + - - -
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Residues in contact with THR 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F GLY* 1.3 71.3 - - - +
12F MET* 1.3 66.5 + - + +
15F GLY* 3.2 17.5 + - - -
39F ARG* 4.7 11.2 + - - +
43F PHE* 3.5 33.7 - - + -
141F ASN* 4.0 28.3 - - - +
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Residues in contact with MET 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F THR* 1.3 80.1 - - + +
13F GLY* 1.3 61.9 + - - +
15F GLY* 3.1 2.1 + - - -
16F ILE* 2.8 37.5 + - + +
87F ALA* 4.6 3.6 - - + +
115F ASN* 3.8 26.0 - - - +
139F PHE* 3.4 45.3 - - + +
140F PHE 4.1 0.9 - - - +
141F ASN* 3.8 40.4 - - - +
142F PRO* 5.4 0.2 - - - -
143F ALA* 4.1 16.8 - - + +
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Residues in contact with GLY 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 3.2 18.1 - - - +
8F GLY 3.3 22.7 - - - -
10F GLY 3.7 4.0 + - - +
11F THR 3.5 0.4 - - - -
12F MET* 1.3 80.3 - - - +
14F SER* 1.3 57.9 + - - +
16F ILE* 3.3 3.5 + - - +
17F ALA* 3.0 22.3 + - - +
29F LEU* 4.5 0.2 - - - -
87F ALA* 3.7 22.0 + - - +
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Residues in contact with SER 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLY 3.9 1.0 + - - -
9F ALA 3.9 11.0 - - - -
10F GLY 2.9 18.0 + - - -
13F GLY* 1.3 75.7 - - - +
15F GLY* 1.3 59.3 + - - +
17F ALA* 3.8 6.5 - - - -
18F GLN* 3.0 21.1 + - - +
29F LEU* 4.3 6.7 - - - -
40F GLY* 3.8 12.0 + - - -
43F PHE* 2.9 30.5 - - - +
44F ILE* 3.2 29.1 - - - +
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F THR 3.2 10.2 + - - -
12F MET 3.1 6.3 + - - -
14F SER* 1.3 82.3 + - - +
16F ILE* 1.3 56.7 + - - +
18F GLN* 3.4 2.1 + - - -
19F ALA* 3.1 22.3 + - - +
43F PHE* 4.6 7.0 - - - -
143F ALA* 3.7 9.2 - - - -
144F PRO* 3.4 32.2 - - - +
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 4.0 9.4 - - + -
12F MET* 2.8 26.0 + - + +
13F GLY* 3.6 8.7 - - - +
14F SER 3.3 0.2 - - - -
15F GLY* 1.3 75.2 - - - +
17F ALA* 1.3 64.9 + - - +
19F ALA* 3.1 12.6 + - - +
20F PHE* 3.1 26.2 + - + -
85F ILE* 3.9 33.9 - - + -
87F ALA* 4.4 1.6 - - + -
115F ASN* 4.0 25.6 - - + +
139F PHE* 3.7 39.3 - - + -
143F ALA* 3.9 9.9 - - + -
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 4.1 5.4 - - + +
13F GLY 3.0 16.2 + - - +
14F SER* 3.6 10.5 - - - +
16F ILE* 1.3 76.6 - - - +
18F GLN* 1.3 59.5 + - - +
19F ALA 3.2 0.2 + - - -
20F PHE* 3.4 2.5 + - - +
21F ALA* 2.9 31.6 + - - +
27F VAL* 3.8 28.0 - - + +
29F LEU* 4.2 15.0 - - + -
44F ILE* 4.3 7.9 - - + -
69F ILE* 4.5 5.6 - - + -
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Residues in contact with GLN 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER 3.0 17.1 + - - +
15F GLY* 3.7 4.6 - - - +
16F ILE 3.3 0.2 - - - -
17F ALA* 1.3 77.3 - - - +
19F ALA* 1.3 57.8 + - - +
21F ALA* 4.0 0.6 - - - +
22F ALA* 3.0 33.3 + - + +
44F ILE* 3.7 28.4 - - + +
47F ASN* 3.1 38.6 + - - +
48F LEU* 3.4 26.3 - - + +
51F LEU* 4.4 10.3 - - - +
65F ILE* 4.7 2.6 - - + +
69F ILE* 4.4 10.3 - - - -
144F PRO* 3.7 24.2 - - + +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLY 3.1 17.1 + - - +
16F ILE* 3.1 7.6 + - - +
17F ALA 3.1 0.6 - - - -
18F GLN* 1.3 79.3 - - - +
20F PHE* 1.3 62.4 + - + +
22F ALA* 3.8 4.1 + - - +
23F LYS* 3.7 23.2 + - - +
139F PHE* 5.3 2.0 - - + -
143F ALA* 4.0 19.3 - - + +
144F PRO* 4.0 11.2 - - + +
172F ILE* 4.5 12.4 - - + +
174F LYS* 4.6 12.1 - - - +
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Residues in contact with PHE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 3.8 22.2 - - + -
6F VAL* 5.4 0.4 - - + -
16F ILE* 3.1 29.0 + - + +
17F ALA* 3.8 6.3 - - - +
19F ALA* 1.3 77.7 - - + +
21F ALA* 1.3 65.3 + - - +
23F LYS 3.1 10.2 + - - -
24F GLY 3.3 0.7 + - - -
25F PHE* 3.2 37.8 + + + +
27F VAL* 3.8 14.8 - - + -
83F LEU* 4.1 9.6 - - + -
85F ILE* 3.6 30.3 - - + -
137F MET* 4.2 8.5 - - + -
139F PHE* 4.2 4.9 - + - -
168F THR* 3.7 24.7 - - + -
172F ILE* 3.7 36.3 - - + -
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ALA 2.9 20.4 + - - +
18F GLN 4.0 0.9 - - - +
20F PHE* 1.3 74.3 - - - +
22F ALA* 1.3 62.9 + - - +
23F LYS 3.1 0.9 + - - -
24F GLY 3.1 1.7 + - - -
25F PHE 3.6 13.9 - - - +
27F VAL* 3.8 5.1 - - + +
65F ILE* 3.8 16.3 - - + +
68F ARG* 3.0 29.6 + - + -
69F ILE* 3.6 31.6 - - + -
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLN* 3.0 23.3 + - + +
19F ALA* 4.1 5.8 - - - +
20F PHE 3.3 0.2 - - - -
21F ALA* 1.3 76.0 - - - +
23F LYS* 1.3 69.1 + - + +
24F GLY 3.4 0.2 - - - -
48F LEU* 5.7 1.8 - - + -
65F ILE* 3.7 30.8 - - + +
68F ARG* 4.3 5.7 + - - -
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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