Contacts of the strand formed by residues 14 - 20 (chain C) in PDB entry 2I3T
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 ILE 14 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C PRO* 4.6 9.0 - - + -
12C ASP 3.7 12.1 - - - +
13C TYR* 1.3 90.9 - - - +
15C SER* 1.3 62.2 + - - +
16C ASP 4.0 15.9 - - - +
17C ILE* 4.5 3.8 - - + -
28C ILE* 4.1 10.3 - - + -
29C THR 3.7 12.3 - - - +
30C SER* 4.8 3.6 - - - +
298C VAL* 3.6 13.0 - - + +
299C LYS* 5.0 3.0 - - + +
310C ALA* 3.7 25.1 - - + -
312C SER* 3.0 11.0 + - - +
331C SER* 3.8 18.6 - - - +
332C SER 4.2 0.2 - - - +
333C ILE* 3.4 39.3 - - + -
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Residues in contact with SER 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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13C TYR* 4.0 3.6 + - - -
14C ILE* 1.3 73.9 - - - +
16C ASP* 1.3 64.6 + - - +
29C THR* 2.9 23.5 + - - -
30C SER* 4.1 0.3 + - - -
31C TRP* 4.0 16.8 - - - +
59C LEU 2.6 27.6 + - - -
60C LEU* 3.3 24.4 - - - +
106C ARG* 5.7 1.7 + - - -
298C VAL* 5.7 0.4 - - - -
299C LYS* 4.0 16.6 + - - +
382D GLU* 5.9 3.6 - - - -
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Residues in contact with ASP 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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14C ILE* 3.8 2.5 - - - +
15C SER* 1.3 81.5 - - - +
17C ILE* 1.3 85.7 + - - +
18C LYS* 2.9 30.8 + - - -
27C LEU 4.4 0.7 - - - -
28C ILE* 3.5 6.4 - - - +
29C THR* 3.1 39.3 + - - +
61C CYS* 3.4 16.9 - - - +
62C CYS* 3.0 27.6 + - - +
106C ARG* 5.5 5.8 - - - +
107C ILE 5.4 0.7 + - - +
299C LYS* 3.4 18.6 - - - +
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Residues in contact with ILE 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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14C ILE* 4.5 4.5 - - + -
16C ASP* 1.3 92.6 + - - +
18C LYS* 1.3 71.0 + - - +
26C LEU* 4.4 7.6 - - + -
27C LEU 3.4 7.0 - - - +
28C ILE* 4.3 11.7 - - + -
299C LYS* 3.7 27.2 - - + +
300C ILE 5.1 0.3 - - - +
301C ALA* 3.6 30.8 - - + +
308C CYS* 3.7 31.2 - - + +
309C LEU 3.8 6.5 - - - -
310C ALA* 3.6 37.9 - - + +
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Residues in contact with LYS 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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16C ASP* 2.9 36.3 + - - +
17C ILE* 1.3 78.3 + - - +
19C ILE* 1.3 64.4 + - - +
20C ILE 4.1 0.3 + - - -
26C LEU* 3.6 3.5 - - - +
27C LEU* 2.8 48.5 + - + +
62C CYS* 3.3 24.3 + - - +
63C ASN* 3.3 33.4 - - - +
64C PHE* 4.4 15.5 - - + -
106C ARG* 6.2 2.8 - - - +
107C ILE 4.4 4.3 + - - -
109C LYS* 5.7 1.1 - - - +
299C LYS* 5.5 1.0 - - - +
301C ALA* 4.8 0.9 - - - -
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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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18C LYS* 1.3 76.2 - - - +
20C ILE* 1.3 64.2 + - - +
21C PRO* 3.1 22.4 - - + +
25C LEU 3.7 9.9 - - - +
26C LEU* 3.8 14.4 - - + -
40C PHE* 4.1 16.4 - - + -
64C PHE* 3.5 13.5 - - - -
301C ALA* 3.8 36.2 - - + +
302C CYS 4.1 2.5 - - - +
303C SER* 3.6 38.8 - - - +
306C ILE* 3.7 17.0 - - + -
308C CYS* 4.3 4.3 - - + -
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Residues in contact with ILE 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 ILE* 1.3 72.8 - - - +
21C PRO* 1.3 66.4 - - + +
22C SER* 3.7 17.7 - - - +
23C LYS* 3.1 12.7 + - + +
24C SER 3.0 17.7 + - - -
25C LEU* 2.9 37.6 + - + +
27C LEU* 3.8 35.9 - - + -
64C PHE* 3.5 38.4 - - + -
66C ASP* 4.4 1.3 - - - +
70C LEU* 4.0 26.5 - - + -
72C ILE* 5.0 0.2 - - + -
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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