Contacts of the helix formed by residues 11 - 20 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 1.3 73.0 - - - +
12A PHE* 1.3 55.5 + - - +
13A PHE 3.5 1.3 - - - -
14A ALA* 3.1 9.6 + - + -
15A ALA* 2.5 38.2 + - + +
18A MET* 5.3 4.3 - - + -
43A THR* 4.5 1.1 - - - -
44A ALA 4.0 8.7 - - - +
45A ASN* 4.5 5.4 - - - -
46A TYR* 3.5 33.7 - - - -
49A ARG* 3.2 30.7 - - - +
401A 1FZ 2.5 31.9 + - - -
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Residues in contact with PHE 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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9A MET* 3.6 29.6 - - + -
10A ASP 3.2 6.8 + - - -
11A CYS* 1.3 72.8 - - - +
13A PHE* 1.3 83.8 + + - +
15A ALA* 3.1 3.8 + - - +
16A VAL* 2.9 36.0 + - + +
79A TYR* 3.5 40.4 - + + -
82A ALA* 4.2 17.3 - - + -
83A SER 4.4 4.0 - - - -
86A ILE* 5.5 1.3 - - + -
102A LEU* 3.8 27.1 - - + -
103A ASP* 3.6 28.5 - - + +
136A LEU* 5.4 5.8 - - + -
401A 1FZ 3.1 20.2 + + + +
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Residues in contact with PHE 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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11A CYS 3.2 0.2 + - - -
12A PHE* 1.3 100.3 - + - +
14A ALA* 1.3 60.1 + - - +
16A VAL* 3.1 5.0 + - - +
17A GLU* 2.9 31.2 + - - +
31A ILE* 3.7 29.6 - - + -
42A SER* 4.0 13.2 - - - -
43A THR* 3.6 9.2 - - + -
76A PHE* 6.0 1.8 - + - -
79A TYR* 3.4 48.0 - + + +
102A LEU* 4.4 11.9 - - + -
401A 1FZ 3.0 45.2 + + - -
841B RDG 4.8 11.4 - - - -
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Residues in contact with ALA 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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11A CYS* 3.1 7.7 + - + +
13A PHE* 1.3 79.4 - - - +
15A ALA* 1.3 56.4 + - - +
17A GLU* 3.8 0.8 - - - -
18A MET* 2.9 37.3 + - - +
29A ILE* 3.9 16.1 - - + +
31A ILE* 3.6 15.7 - - + +
43A THR* 4.0 4.8 - - + +
44A ALA* 4.1 7.6 - - - +
45A ASN* 3.9 31.0 - - + +
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Residues in contact with ALA 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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10A ASP 3.3 17.7 - - - +
11A CYS* 2.5 23.7 + - + +
12A PHE* 3.3 6.3 - - - +
14A ALA* 1.3 70.9 - - - +
16A VAL* 1.3 60.3 + - - +
18A MET* 3.8 13.9 - - + +
19A ARG* 2.9 30.0 + - - +
136A LEU* 3.6 21.7 - - + +
137A THR* 5.5 4.9 - - + -
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Residues in contact with VAL 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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12A PHE* 2.9 34.2 + - + +
13A PHE 3.1 6.0 + - - +
15A ALA* 1.3 77.2 - - - +
17A GLU* 1.3 57.5 + - - +
19A ARG* 3.1 19.9 + - - +
20A ASP* 2.9 43.8 + - - +
75A ARG* 3.8 9.6 - - - +
78A ALA* 4.1 12.6 - - + +
79A TYR* 3.8 28.5 - - + -
82A ALA* 4.9 3.1 - - + -
136A LEU* 4.3 15.7 - - + -
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Residues in contact with GLU 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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13A PHE 2.9 19.3 + - - +
14A ALA* 3.9 6.1 - - - +
16A VAL* 1.3 75.9 - - - +
18A MET* 1.3 57.4 + - - +
20A ASP* 3.5 4.8 + - - +
21A ASN* 3.1 30.3 + - - +
24A LEU* 3.7 6.9 - - + +
29A ILE* 4.5 0.9 - - + -
31A ILE* 3.8 10.3 - - + -
72A LEU* 3.5 35.6 - - + +
74A GLY* 4.5 0.9 - - - -
75A ARG* 3.2 43.8 + - - +
79A TYR* 2.6 27.6 + - - +
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Residues in contact with MET 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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11A CYS* 5.3 4.7 - - + -
14A ALA* 2.9 32.1 + - + +
15A ALA* 3.8 11.9 - - + +
17A GLU* 1.3 75.2 - - - +
19A ARG* 1.3 65.5 + - - +
21A ASN 3.2 24.5 - - - -
22A PRO* 3.4 8.1 - - - +
24A LEU* 4.0 1.1 - - + -
25A ARG* 3.5 45.0 - - + +
29A ILE* 3.6 13.9 - - + -
45A ASN* 3.7 33.2 - - + -
47A PRO* 5.8 0.2 - - - -
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Residues in contact with ARG 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 ALA 2.9 20.5 + - - +
16A VAL* 3.1 16.7 + - - +
18A MET* 1.3 78.2 - - - +
20A ASP* 1.3 94.3 + - - +
21A ASN 3.2 0.6 + - - -
22A PRO* 4.2 9.0 - - - +
78A ALA* 4.8 2.6 + - - +
81A GLU* 3.9 22.2 + - - -
82A ALA* 5.3 4.2 - - - +
134A LEU* 3.2 34.0 + - - +
135A GLN* 3.9 32.4 + - + +
136A LEU* 3.3 20.3 - - + +
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Residues in contact with ASP 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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16A VAL 2.9 12.5 + - - +
17A GLU* 4.2 3.8 - - - +
19A ARG* 1.3 119.0 + - - +
21A ASN* 1.3 61.0 + - + +
22A PRO* 4.0 4.0 - - - +
75A ARG* 2.3 38.7 + - - +
78A ALA* 4.8 0.3 - - - +
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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