Contacts of the strand formed by residues 17 - 23 (chain C) in PDB entry 1K5J
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 LEU 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C SER* 1.3 80.0 + - - +
18C ILE* 1.3 72.4 + - - +
116C GLN* 3.6 3.1 - - - -
117C HIS* 2.7 50.4 + - + +
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Residues in contact with ILE 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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17C LEU* 1.3 82.8 - - - +
19C TRP* 1.3 60.2 + - - +
115C GLY 3.6 7.2 - - - +
116C GLN* 4.6 7.6 - - + +
65D ILE* 3.6 33.4 - - + +
67D THR* 3.8 32.5 - - + +
74D LYS* 6.1 0.7 - - + -
76D VAL* 3.9 26.6 - - + +
96D LEU* 4.1 24.2 - - + -
100D VAL* 5.5 1.8 - - + -
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Residues in contact with TRP 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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17C LEU 4.1 5.8 - - - +
18C ILE* 1.3 75.1 - - - +
20C GLY* 1.3 71.1 + - - +
21C CYS* 3.9 19.7 - - + -
30C PHE* 4.0 30.7 - + - -
32C PHE* 4.1 20.6 - + + -
45C LEU* 3.8 28.3 - - + -
47C LEU* 4.0 6.3 - - + -
102C PHE* 3.6 26.7 - + - -
113C ILE* 3.7 29.4 - - + -
114C SER 4.1 1.3 - - - -
115C GLY 2.7 44.1 + - - +
117C HIS* 4.1 13.5 - - + +
76D VAL* 3.5 16.3 - - - +
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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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19C TRP* 1.3 92.3 + - - +
21C CYS* 1.3 62.1 + - - +
30C PHE* 5.1 2.8 - - - -
113C ILE 3.0 14.1 - - - -
76D VAL* 4.1 17.2 - - - +
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Residues in contact with CYS 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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19C TRP* 3.9 18.8 - - + -
20C GLY* 1.3 75.0 - - - +
22C GLU* 1.3 60.7 + - - +
23C LEU* 4.6 6.3 - - - -
30C PHE* 3.7 50.3 - - + -
102C PHE* 4.7 2.2 - - - -
111C LEU 3.7 0.7 - - - +
112C TYR* 3.3 7.2 - - - +
113C ILE* 2.9 53.7 + - - -
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Residues in contact with GLU 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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21C CYS* 1.3 77.6 - - - +
23C LEU* 1.3 79.1 + - - +
24C ASN* 2.9 27.1 + - - +
27C ASN* 4.3 7.8 - - - +
30C PHE* 5.1 5.3 - - - +
110C PRO* 3.0 28.3 - - + +
111C LEU 3.3 5.2 - - - +
112C TYR* 3.4 24.3 + - + -
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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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21C CYS* 4.6 7.2 - - - -
22C GLU* 1.3 79.7 - - - +
24C ASN* 1.3 63.8 + - - +
27C ASN 3.6 3.8 - - - +
28C LYS 3.7 14.1 - - - +
29C THR 3.8 3.4 - - - -
30C PHE* 3.7 35.2 - - + +
63C VAL* 4.1 23.3 - - + -
102C PHE* 3.8 9.4 - - + +
104C LEU* 3.8 36.1 - - + +
109C GLY* 4.0 0.7 - - - -
110C PRO* 3.3 1.6 - - - +
111C LEU* 2.8 44.6 + - + +
113C ILE* 4.1 11.9 - - + -
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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