Contacts of the helix formed by residues 12 - 19 (chain C) in PDB entry 1Y8Q
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 SER 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C GLY 4.1 0.6 + - - -
11C ILE* 1.3 77.7 - - - +
13C GLU* 1.3 63.8 + - - +
14C GLU* 3.6 8.7 + - - +
15C GLU* 2.9 39.7 + - - +
16C ALA* 3.0 22.0 + - - +
35C ARG* 4.8 0.8 - - - +
105C MET* 4.7 2.4 - - - +
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Residues in contact with GLU 13 (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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12C SER* 1.3 72.6 - - - +
14C GLU* 1.3 65.6 + - - +
16C ALA* 3.1 8.0 + - - +
17C ALA* 2.9 25.5 + - - +
308D LYS* 4.5 29.2 + - + +
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Residues in contact with GLU 14 (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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12C SER* 3.2 8.2 + - - +
13C GLU* 1.3 80.1 - - - +
15C GLU* 1.3 60.1 + - - +
17C ALA* 3.3 8.0 + - - +
18C GLN* 3.2 26.4 + - - +
104C PRO* 6.1 0.9 - - - +
105C MET* 3.4 28.4 - - + +
54D VAL* 4.8 1.2 - - - +
65D LYS* 3.8 37.5 + - - +
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Residues in contact with GLU 15 (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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11C ILE* 3.7 7.7 - - + -
12C SER* 2.9 48.2 + - - +
14C GLU* 1.3 77.1 - - - +
16C ALA* 1.3 60.5 + - - +
18C GLN* 3.4 8.3 - - - +
19C TYR* 3.0 46.0 + - + -
35C ARG* 3.0 41.7 + - - +
105C MET* 3.7 37.5 - - + +
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Residues in contact with ALA 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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11C ILE* 3.6 18.6 - - + +
12C SER 3.0 14.5 + - - +
13C GLU* 3.1 11.2 + - - +
15C GLU* 1.3 77.3 - - - +
17C ALA* 1.3 57.7 + - - +
20C ASP* 3.1 28.6 + - - +
23C ILE* 4.1 6.2 - - - +
307D LEU* 3.8 24.7 - - + +
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Residues in contact with ALA 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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13C GLU 2.9 16.0 + - - +
14C GLU* 3.6 7.9 - - - +
15C GLU 3.2 0.4 - - - -
16C ALA* 1.3 78.7 - - - +
18C GLN* 1.3 60.7 + - - +
20C ASP* 3.6 12.2 - - - +
54D VAL* 4.0 23.2 - - + +
55D SER* 3.5 20.6 + - - -
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Residues in contact with GLN 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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14C GLU* 3.2 16.0 + - - +
15C GLU* 3.4 13.5 - - - +
17C ALA* 1.3 78.3 - - - +
19C TYR* 1.3 86.0 + - + +
20C ASP 3.3 1.5 + - - -
103C ASN* 3.7 18.4 + - - +
104C PRO* 5.6 2.6 - - - +
105C MET* 3.4 39.4 - - - +
54D VAL* 3.6 24.6 - - + +
55D SER* 4.1 6.8 - - - +
57D LEU* 4.5 18.6 - - + +
58D ASN* 3.2 27.4 + - - +
65D LYS* 6.3 0.6 - - - +
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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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11C ILE* 5.0 3.6 - - + -
15C GLU* 3.0 46.7 + - + +
18C GLN* 1.3 94.0 - - + +
20C ASP* 1.3 65.5 + - - +
21C ARG 3.3 2.9 - - - -
22C GLN* 3.0 29.7 + - + +
23C ILE* 2.9 38.9 + - + +
31C GLN* 3.8 19.3 - - + -
35C ARG* 5.6 5.2 - - + -
57C LEU 3.7 20.9 - - - -
58C ALA 3.7 5.8 - - - -
59C GLY* 3.3 15.5 - - - -
103C ASN* 3.1 21.2 + - - -
105C MET* 4.0 12.8 - - - +
106C VAL* 4.9 0.2 - - - +
58D ASN* 4.4 4.3 - - + -
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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