Contacts of the helix formed by residues 15 - 23 (chain C) in PDB entry 4QZU
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 ASN 15 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ACT 5.2 6.3 - - - +
13C ASN 4.2 0.8 + - - -
14C GLU* 1.3 83.2 - - + +
16C PHE* 1.3 64.9 + - - +
17C GLU* 3.1 5.6 - - - +
18C GLY* 3.1 21.0 + - - -
19C TYR 3.2 11.5 + - - +
124C GLN* 3.0 23.6 + - - +
125C VAL 3.0 30.3 + - - +
126C CYS* 3.5 6.2 - - - +
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Residues in contact with PHE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ACT 6.0 2.7 - - + +
13C ASN* 3.4 31.1 - - - +
14C GLU 3.2 3.4 - - - -
15C ASN* 1.3 76.4 - - - +
17C GLU* 1.3 62.3 + - - +
19C TYR* 3.4 13.9 + + - +
20C MET* 3.0 55.8 + - + +
33C ALA* 3.8 24.5 - - + -
34C VAL* 4.2 8.9 - - + +
38C GLN* 3.5 23.6 - - - -
119C LEU* 4.6 0.4 - - + -
126C CYS* 3.6 19.1 - - - -
128C GLN* 3.8 10.5 - - - -
201C RTL 3.5 42.8 - - + -
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ACT 5.8 0.9 - - - +
15C ASN* 3.1 3.9 - - - +
16C PHE* 1.3 78.9 - - - +
18C GLY* 1.3 59.9 + - - +
20C MET* 3.4 8.9 + - - +
21C LYS* 2.9 36.4 + - + +
27C PHE* 6.0 0.2 - - - -
30C ARG* 3.1 52.5 + - - +
34C VAL* 4.1 19.0 - - + +
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASN* 3.1 24.1 + - - -
17C GLU* 1.3 80.8 - - - +
19C TYR* 1.3 58.3 + - - +
21C LYS* 3.4 6.4 + - - +
22C ALA* 2.9 30.1 + - - +
124C GLN* 3.4 20.9 - - - +
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASN* 3.2 5.1 + - - +
16C PHE* 3.8 21.1 - + - +
18C GLY* 1.3 76.8 - - - +
20C MET* 1.3 64.7 + - + +
22C ALA* 3.2 5.4 + - - +
23C LEU* 3.1 48.6 + - + +
77C LEU* 4.3 3.9 - - + +
97C GLN* 4.8 5.7 + - - -
104C ARG* 5.0 3.8 + - + +
105C GLY 4.9 1.6 + - - -
106C TRP* 5.9 0.2 - - - -
119C LEU* 3.7 43.8 - - + +
120C THR 3.7 26.7 - - - -
121C CYS* 4.0 10.8 - - + -
124C GLN* 4.0 11.0 - - + +
126C CYS* 3.6 26.7 - - + +
201C RTL 4.3 10.8 - - + -
202C ACT 3.9 23.0 + - - +
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Residues in contact with MET 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.0 64.1 + - + +
17C GLU* 3.8 8.5 - - - +
19C TYR* 1.3 78.8 - - + +
21C LYS* 1.3 63.5 + - - +
23C LEU* 3.1 8.7 + - - +
25C ILE* 3.1 45.4 + - + +
30C ARG* 3.6 45.3 - - + +
33C ALA* 3.8 13.7 - - - -
34C VAL* 4.0 6.7 - - + +
201C RTL 4.0 15.9 - - + -
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 2.9 26.8 + - + +
18C GLY* 3.8 6.1 - - - +
20C MET* 1.3 76.8 - - - +
22C ALA* 1.3 58.1 - - - +
24C ASP* 3.0 23.7 + - - +
30C ARG* 3.5 38.0 + - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLY 2.9 17.3 + - - +
19C TYR 3.5 5.8 - - - +
20C MET 3.2 0.2 - - - -
21C LYS* 1.3 76.8 - - - +
23C LEU* 1.3 56.4 + - - +
24C ASP* 3.2 1.6 - - - +
101C LYS* 3.1 26.7 + - - -
121C CYS* 3.6 34.7 - - + +
122C GLY* 5.5 1.1 - - - -
123C ASP* 5.7 0.7 - - - +
124C GLN* 3.9 11.7 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.1 48.1 + - + +
20C MET 3.1 9.5 + - - +
22C ALA* 1.3 75.3 - - - +
24C ASP* 1.3 67.2 + - - +
25C ILE* 4.1 22.2 - - + -
77C LEU* 4.1 11.0 - - + -
78C ASP* 3.3 14.0 - - + +
80C ARG* 2.9 21.2 + - - -
101C LYS* 4.3 3.4 - - + +
104C ARG* 3.5 39.9 - - + +
121C CYS* 3.6 24.7 - - + -
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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