Contacts of the helix formed by residues 11 - 21 (chain F) in PDB entry 4Q44
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 CYS 11 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ASP* 1.3 81.7 - - - +
12F PHE* 1.3 54.4 + - - +
13F PHE 3.5 1.6 - - - -
14F ALA* 3.0 13.3 + - + -
15F ALA* 2.6 43.9 + - - -
18F MET* 5.6 4.0 - - - -
43F THR* 4.7 0.9 - - - +
44F ALA 4.0 8.3 - - - +
45F ASN* 4.8 6.5 - - - -
46F TYR* 4.7 14.1 - - - -
49F ARG* 3.3 27.1 - - - +
401F 1FZ 2.5 32.2 + - - -
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Residues in contact with PHE 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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9F MET* 3.8 33.2 - - + -
10F ASP 3.1 7.3 - - - -
11F CYS* 1.3 73.7 - - - +
13F PHE* 1.3 82.0 + + - +
15F ALA* 3.0 6.3 + - + +
16F VAL* 2.9 30.1 + - + +
79F TYR* 3.2 43.5 - - + -
82F ALA* 3.8 22.0 - - + -
83F SER* 4.3 5.8 - - - -
86F ILE* 5.9 1.3 - - + -
102F LEU* 3.8 19.5 - - + -
103F ASP* 3.7 30.5 - - + +
136F LEU* 5.4 1.8 - - + -
401F 1FZ 3.3 15.6 + + - +
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Residues in contact with PHE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F CYS 3.5 0.2 - - - -
12F PHE* 1.3 102.1 - + - +
14F ALA* 1.3 58.9 + - - +
16F VAL* 3.2 4.5 + - - +
17F GLU* 2.9 31.7 + - - +
31F ILE* 3.7 33.4 - - + -
42F SER* 4.4 6.1 - - - -
43F THR* 3.6 10.3 - - + -
76F PHE* 6.2 1.3 - + - -
79F TYR* 3.5 44.8 - + + -
102F LEU* 4.5 9.9 - - + -
401F 1FZ 3.2 48.8 + + - -
841G RDG 4.5 12.8 - + - -
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Residues in contact with ALA 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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11F CYS* 3.0 10.0 + - + +
13F PHE* 1.3 79.2 - - - +
15F ALA* 1.3 56.8 + - - +
17F GLU* 3.8 1.0 - - - +
18F MET* 2.9 36.8 + - - +
29F ILE* 4.2 9.4 - - + -
31F ILE* 3.6 16.2 - - + +
43F THR* 4.0 5.2 - - + +
44F ALA* 4.1 5.8 - - - -
45F ASN* 3.8 36.6 - - + +
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Residues in contact with ALA 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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9F MET* 6.2 0.2 - - + -
10F ASP 3.3 24.0 - - - +
11F CYS* 2.6 16.9 + - - +
12F PHE* 3.0 11.0 + - + +
14F ALA* 1.3 70.1 - - - +
16F VAL* 1.3 60.3 + - - +
18F MET* 3.4 7.9 + - - +
19F ARG* 2.9 29.5 + - - +
25F ARG* 5.7 0.3 + - - -
136F LEU* 3.5 23.3 - - + +
137F THR* 5.5 2.9 - - - +
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Residues in contact with VAL 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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12F PHE* 2.9 33.6 + - + +
13F PHE 3.5 6.3 - - - +
15F ALA* 1.3 75.9 - - - +
17F GLU* 1.3 58.6 + - - +
19F ARG* 3.1 27.9 + - - +
20F ASP* 2.9 28.6 + - - +
75F ARG* 3.6 20.0 - - - +
78F ALA* 4.1 7.2 - - + -
79F TYR* 3.8 28.0 - - + -
82F ALA* 4.5 7.6 - - + -
136F LEU* 4.0 14.4 - - + -
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Residues in contact with GLU 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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13F PHE 2.9 21.7 + - - +
14F ALA* 3.8 7.0 - - - +
16F VAL* 1.3 75.4 - - - +
18F MET* 1.3 57.2 + - - +
20F ASP* 4.2 1.0 - - - +
21F ASN* 3.1 21.0 + - - +
24F LEU* 3.4 15.0 - - - +
29F ILE* 4.4 2.9 - - + -
31F ILE* 3.8 9.2 - - + -
72F LEU* 3.6 36.1 - - + +
74F GLY* 4.2 2.0 + - - -
75F ARG* 3.1 42.1 + - - +
79F TYR* 2.5 27.7 + - - +
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Residues in contact with MET 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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11F CYS* 5.6 1.8 - - - -
14F ALA 2.9 22.0 + - - +
15F ALA* 3.8 7.0 - - - +
17F GLU* 1.3 74.7 - - - +
19F ARG* 1.3 65.3 + - - +
20F ASP 3.3 0.2 - - - -
21F ASN 3.4 19.7 - - - +
22F PRO* 3.5 8.5 - - - +
24F LEU* 3.4 21.1 - - + +
25F ARG* 3.6 52.5 + - + +
29F ILE* 3.7 10.1 - - + -
45F ASN* 3.5 38.4 - - + -
47F PRO* 5.9 1.1 - - + -
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Residues in contact with ARG 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 ALA 2.9 18.1 + - - +
16F VAL* 3.1 29.9 + - - +
18F MET* 1.3 80.7 - - - +
20F ASP* 1.3 78.1 + - - +
22F PRO* 4.2 8.8 - - - +
25F ARG* 4.5 12.4 + - - +
78F ALA* 5.0 9.1 + - - +
81F GLU* 6.2 2.0 - - - +
82F ALA* 5.2 2.6 - - - +
133F GLU 5.4 0.6 + - - -
134F LEU* 2.8 46.4 + - - +
135F GLN* 3.9 24.8 + - + +
136F LEU* 3.3 26.6 - - + +
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Residues in contact with ASP 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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16F VAL* 2.9 21.4 + - - +
17F GLU* 4.2 2.5 - - - +
19F ARG* 1.3 100.4 + - - +
21F ASN* 1.3 59.7 + - + +
22F PRO* 3.4 7.8 - - - +
75F ARG* 2.3 42.2 + - - +
78F ALA* 4.9 1.0 - - - +
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Residues in contact with ASN 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 GLU 3.1 8.1 + - - +
18F MET 3.4 7.5 - - - +
20F ASP* 1.3 78.5 - - + +
22F PRO* 1.3 62.7 - - - +
23F ALA* 2.9 26.0 + - - +
24F LEU* 3.0 45.4 + - + +
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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