Contacts of the strand formed by residues 12 - 16 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG 3.8 0.4 - - - -
11E THR* 1.3 78.6 + - - +
13E ILE* 1.3 69.1 + - - +
14E VAL* 6.0 0.2 - - - -
36E GLY 5.5 0.2 + - - -
37E PHE* 5.3 5.6 - - - -
38E GLY* 2.8 34.0 + - - +
39E GLY 3.3 0.5 + - - -
329E LEU* 3.9 9.1 - - - +
335E PHE* 4.2 0.6 - - - -
336E THR* 2.4 37.7 + - - -
338E VAL* 5.3 3.1 - - - +
395E VAL* 4.5 23.0 - - - +
398E ARG* 3.8 6.2 - - - +
399E ASN* 4.5 1.2 - - - +
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Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 4.7 1.1 - - + -
12E SER* 1.3 82.8 - - - +
14E VAL* 1.3 58.0 + - - +
37E PHE* 5.7 0.7 - - - -
39E GLY 3.1 15.3 - - - +
40E VAL 4.7 0.7 - - - +
41E GLN* 4.4 10.5 - - + +
94E TYR* 4.0 27.8 - - + -
229E PHE* 5.5 0.7 - - + -
231E PHE* 4.1 25.1 - - + -
293E LEU* 4.6 8.1 - - + -
335E PHE* 3.4 25.4 - - + -
336E THR 3.2 3.5 + - - +
337E ARG* 3.6 35.0 - - + -
338E VAL* 2.7 32.1 + - - +
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Residues in contact with VAL 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E SER* 6.0 0.4 - - - -
13E ILE* 1.3 79.7 - - - +
15E HIS* 1.3 56.6 + - - +
16E LEU* 3.4 25.8 + - + -
32E LEU* 4.1 19.5 - - + -
37E PHE* 3.3 33.7 - - + -
39E GLY 3.0 11.5 + - - +
40E VAL* 3.3 5.4 - - + -
41E GLN* 2.7 32.5 + - - -
337E ARG* 4.9 0.2 - - - -
338E VAL* 3.1 25.8 - - + +
340E SER* 5.1 0.9 - - - -
386E HIS* 3.9 9.4 - - + -
395E VAL* 5.8 0.2 - - + -
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 1.3 71.2 - - - +
16E LEU* 1.3 57.7 + - - +
17E PHE* 3.0 35.8 + + + -
41E GLN* 3.1 51.7 + - + -
42E VAL 4.8 0.7 - - - -
43E SER* 4.3 13.0 - - - -
62E TYR* 5.1 4.8 + - - -
96E ASP* 5.5 0.7 - - - -
298E ASN* 5.8 0.2 - - - -
299E HIS* 3.8 22.6 - + + +
337E ARG* 4.5 15.8 - - - +
338E VAL 2.8 15.0 + - - +
339E MET* 3.8 28.9 - - + -
340E SER* 2.9 29.5 + - - +
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 3.4 14.5 + - + -
15E HIS* 1.3 70.1 - - - +
17E PHE* 1.3 63.9 + - - +
18E GLU 3.2 0.5 + - - -
19E TRP* 3.0 57.8 + - + +
24E ILE* 4.0 16.6 - - + +
27E GLU* 4.6 3.8 - - + -
32E LEU* 4.2 12.6 - - + -
40E VAL* 3.6 36.3 - - + -
41E GLN 3.3 10.9 + - - +
43E SER* 4.7 4.3 + - - -
340E SER* 3.7 26.2 - - - +
386E HIS* 3.9 16.6 - - + +
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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