Contacts of the strand formed by residues 12 - 16 (chain C) in PDB entry 1KXT
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG 3.7 0.8 - - - -
11C THR* 1.3 79.7 + - - +
13C ILE* 1.3 66.3 + - - +
36C GLY 5.5 0.2 + - - -
37C PHE* 5.2 7.0 - - - -
38C GLY* 2.7 37.9 + - - +
39C GLY 3.1 0.7 + - - -
329C LEU* 3.7 9.1 - - - +
335C PHE* 4.0 3.3 - - - -
336C THR* 2.7 29.3 + - - -
338C VAL* 4.9 3.8 - - - -
395C VAL* 4.4 22.5 - - - +
398C ARG* 3.7 9.5 - - - +
399C ASN* 4.7 0.8 - - - +
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Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C THR* 4.6 0.2 - - + -
12C SER* 1.3 75.3 - - - +
14C VAL* 1.3 59.3 + - - +
37C PHE* 5.6 0.7 - - - -
38C GLY 4.2 1.1 - - - -
39C GLY* 3.1 34.5 - - - +
40C VAL* 4.4 1.1 - - - +
41C GLN* 5.0 5.2 - - + +
94C TYR* 3.5 24.0 - - + +
229C PHE* 4.9 2.5 - - + -
231C PHE* 4.4 25.1 - - + -
293C LEU* 4.5 6.5 - - + -
335C PHE* 3.7 30.7 - - + -
336C THR 3.4 6.8 + - - +
337C ARG* 3.3 18.5 - - + -
338C VAL* 2.8 31.7 + - - +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 6.2 0.2 - - - -
13C ILE* 1.3 76.1 - - - +
15C HIS* 1.3 54.7 + - - +
16C LEU* 3.5 22.9 + - + -
32C LEU* 4.3 7.6 - - + -
37C PHE* 3.1 41.5 - - + -
39C GLY 2.9 12.1 + - - +
40C VAL* 3.3 17.0 - - + -
41C GLN* 2.7 32.8 + - - -
337C ARG* 5.1 0.9 - - - -
338C VAL* 3.2 21.1 - - + +
340C SER* 5.2 1.6 - - - -
386C HIS* 3.9 11.0 - - + -
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 1.3 71.5 - - - +
16C LEU* 1.3 61.3 + - - +
17C PHE* 2.9 38.4 + + + -
41C GLN* 3.2 51.0 + - + -
42C VAL 4.8 0.2 - - - -
43C SER* 4.2 13.9 - - - -
62C TYR* 5.2 3.1 + - - -
298C ASN* 5.6 0.9 - - + -
299C HIS* 3.9 21.9 - + + +
337C ARG* 4.5 13.6 - - - +
338C VAL 2.8 14.4 + - - +
339C MET* 3.8 27.4 - - - -
340C SER 2.9 28.8 + - - +
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Residues in contact with LEU 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 VAL* 3.5 17.2 + - + -
15C HIS* 1.3 70.0 - - - +
17C PHE* 1.3 64.7 + - - +
18C GLU 3.2 1.2 + - - -
19C TRP* 3.1 47.1 + - + +
24C ILE* 3.7 28.8 - - + +
27C GLU* 4.8 1.1 - - + -
32C LEU* 4.2 10.8 - - + -
40C VAL* 3.7 32.3 - - + -
41C GLN 3.4 10.0 + - - +
43C SER* 4.4 5.4 + - - -
340C SER* 3.8 23.6 - - - +
386C HIS* 4.1 17.7 - - + +
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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