Contacts of the helix formed by residues 16 - 22 (chain C) in PDB entry 1YKN
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 TYR 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA 5.0 0.2 - - - -
14C GLY 3.2 1.6 + - - -
15C PRO* 1.3 107.0 - - + +
17C VAL* 1.3 64.1 + - - +
18C HIS 3.1 2.9 - - - -
19C ILE* 3.0 30.9 + - + +
400D TRP* 3.7 14.2 + - + +
408D GLU* 3.4 44.0 - - + +
410D HIS* 3.3 29.6 - + + -
412D ASN* 3.2 41.1 + - + +
413D ASP* 3.5 25.0 + - + -
447D TYR* 5.9 1.3 - + - -
1550D DHB 6.4 0.2 - + - -
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Residues in contact with VAL 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 ALA* 4.1 20.9 - - + +
14C GLY 3.3 16.1 + - - +
15C PRO 3.3 2.3 - - - +
16C TYR* 1.3 78.5 - - - +
18C HIS* 1.3 79.4 + - + +
20C GLY* 3.1 4.3 + - - -
21C LEU* 3.0 50.8 + - + +
65C ASP 4.1 10.8 - - - +
67C PHE* 4.0 26.0 - - + -
132C ALA* 5.6 1.8 - - - -
400D TRP* 4.0 18.8 - - + +
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Residues in contact with HIS 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 PRO 4.7 3.7 + - - -
16C TYR 3.0 0.6 + - - -
17C VAL* 1.3 83.9 - - + +
19C ILE* 1.4 65.8 + - - +
22C ALA* 2.6 65.4 + - + +
23C LEU 3.4 0.3 + - - -
25C ALA* 4.3 6.4 + - + -
26C ALA* 3.5 17.5 - - + +
65C ASP* 4.0 21.8 - - + -
66C SER 3.5 18.8 + - - -
67C PHE* 4.9 2.7 - + + -
96C ALA* 3.6 10.2 - - + +
97C THR 3.5 19.6 + - - -
98C THR* 3.9 14.2 - - + +
410D HIS* 4.3 15.3 + - - +
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Residues in contact with ILE 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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16C TYR* 3.0 15.1 + - + +
18C HIS* 1.4 78.6 - - - +
20C GLY* 1.3 60.2 + - - +
23C LEU* 3.1 15.5 - - - +
26C ALA* 3.6 7.4 - - + +
28C ASN* 4.0 8.8 + - - +
400D TRP* 3.8 23.3 - - + -
401D GLN 4.3 17.3 - - - +
408D GLU* 4.7 8.1 - - + +
409D ARG* 3.5 39.5 - - + +
410D HIS* 3.7 23.3 - - + -
424D GLY 4.8 6.1 - - - +
425D GLY 4.7 2.0 - - - +
426D VAL* 3.0 26.7 - - + +
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Residues in contact with GLY 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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17C VAL 3.1 5.1 + - - -
19C ILE* 1.3 83.7 - - - +
21C LEU* 1.3 72.7 + - - +
23C LEU* 3.7 9.8 - - - +
31C ARG* 4.4 5.5 + - - -
398D GLU* 4.4 6.2 - - - +
399D MET 4.7 0.2 - - - -
400D TRP* 3.6 31.1 - - - -
426D VAL* 3.9 13.9 - - - +
427D GLY 5.8 0.2 - - - +
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Residues in contact with LEU 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 VAL* 3.0 33.2 + - + +
20C GLY* 1.3 88.9 - - - +
22C ALA* 1.3 61.6 + - - +
23C LEU* 3.9 3.8 - - - -
31C ARG* 5.7 0.4 - - - +
34C GLU* 5.5 3.3 - - - +
35C ILE 4.7 3.6 - - - +
36C TRP* 4.3 6.8 - - - -
67C PHE* 3.6 39.4 - - + -
94C ARG* 3.6 19.8 + - - +
398D GLU* 3.4 40.8 - - + +
400D TRP* 3.9 20.4 - - + -
464D GLY* 5.8 1.8 - - - -
473D LYS* 5.2 2.5 - - - +
475D ILE* 3.9 10.5 - - + -
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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 HIS* 2.6 43.2 + - + +
21C LEU* 1.3 74.7 - - - +
23C LEU* 1.3 59.7 - - - +
24C GLU* 3.4 2.7 - - - -
25C ALA* 3.2 5.7 + - + -
26C ALA 2.9 24.3 + - - -
36C TRP* 3.4 34.5 - - + -
67C PHE* 4.6 4.7 - - + -
96C ALA* 4.6 1.8 - - + -
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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