Contacts of the helix formed by residues 15 - 23 (chain C) in PDB entry 5EJK
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 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C HIS* 5.8 0.2 - - - -
13C HIS 3.7 2.9 + - - -
14C ILE* 1.3 83.3 - - - +
16C PRO* 1.3 76.5 - - - +
17C ARG* 3.5 2.4 + - - -
18C ALA 3.5 2.1 + - - -
19C LEU* 3.3 17.7 + - - +
34C VAL* 4.5 2.5 - - - -
200C GLU 4.6 7.7 + - - -
201C ARG* 5.2 4.5 - - - +
202C GLY 5.1 7.2 - - - -
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Residues in contact with PRO 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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15C GLY* 1.3 79.9 - - - +
17C ARG* 1.3 62.8 + - - +
19C LEU* 4.6 3.1 - - + +
20C SER* 2.9 33.0 + - - -
27C MSE 4.7 15.3 - - + -
30C ALA* 3.6 26.9 - - + +
31C ARG* 4.3 11.0 - - + +
34C VAL* 3.8 27.3 - - + -
202C GLY* 4.1 16.2 - - - +
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 1.3 79.6 - - - +
18C ALA* 1.3 60.3 + - - +
20C SER* 2.4 23.2 + - - -
21C LYS* 3.0 26.7 + - - +
27C MSE 4.8 8.9 - - + -
200C GLU* 3.3 24.5 - - - +
201C ARG* 2.6 38.5 + - - +
202C GLY* 3.2 27.7 - - - +
203C GLU* 4.3 5.8 - - - +
204C ASN* 3.1 54.0 + - - +
205C THR 3.6 0.6 - - - +
206C LYS 3.1 23.6 + - - -
208C PRO* 4.6 3.8 - - - +
211C LYS* 3.5 17.0 - - - +
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Residues in contact with ALA 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 ILE* 3.2 22.4 - - + -
15C GLY 3.5 0.8 + - - -
16C PRO 3.3 0.4 - - - -
17C ARG* 1.3 80.4 - - - +
19C LEU* 1.3 58.8 + - - +
21C LYS* 3.9 1.8 - - - +
22C ALA* 2.9 32.8 + - - +
199C PHE* 4.5 8.4 - - + -
200C GLU* 3.1 49.5 - - - +
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Residues in contact with LEU 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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5C ALA* 3.9 18.2 - - + +
8C LEU* 3.5 37.5 - - + -
9C HIS* 3.9 22.0 - - + +
14C ILE* 3.3 35.9 - - + +
15C GLY 3.3 15.0 + - - +
16C PRO* 4.0 5.6 - - + +
18C ALA* 1.3 75.0 - - - +
20C SER* 1.3 65.7 + - - +
22C ALA* 4.6 2.9 - - - +
23C SER* 2.8 31.9 + - - -
25C ILE* 5.2 0.9 - - - -
30C ALA* 4.9 6.1 - - + +
33C VAL* 4.4 15.7 - - + -
34C VAL* 5.2 3.1 - - + -
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Residues in contact with SER 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 PRO 2.9 15.6 + - - -
17C ARG* 2.4 27.5 + - - -
19C LEU* 1.3 76.4 - - - +
21C LYS* 1.3 60.0 + - - +
24C ASN* 3.0 10.2 + - - -
25C ILE* 2.9 50.1 + - - +
26C SER 4.4 2.2 - - - -
27C MSE 4.4 11.3 - - - -
30C ALA* 4.2 10.5 - - - +
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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 ARG* 3.0 23.3 + - - +
18C ALA* 3.9 3.6 - - - +
20C SER* 1.3 84.2 + - - +
22C ALA* 1.3 65.1 + - - +
24C ASN* 3.4 17.4 - - - +
200C GLU* 4.5 18.2 - - - +
204C ASN 3.8 7.7 + - - -
205C THR* 2.5 47.0 + - - +
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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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4C GLU* 5.0 1.9 - - - +
8C LEU* 4.1 23.1 - - + -
18C ALA 2.9 21.8 + - - +
19C LEU 4.2 0.9 - - - +
21C LYS* 1.3 75.9 - - - +
23C SER* 1.3 58.6 + - - +
24C ASN* 3.8 6.1 + - - +
199C PHE* 5.2 13.7 - - + -
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Residues in contact with SER 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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1C PRO* 3.3 34.1 - - - +
4C GLU* 4.0 19.6 - - - +
5C ALA* 3.6 13.2 - - - +
8C LEU* 5.1 3.4 - - - -
19C LEU 2.8 22.7 + - - -
22C ALA* 1.3 76.9 - - - +
24C ASN* 1.3 72.9 + - - +
25C ILE* 3.1 20.4 - - - +
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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