Contacts of the helix formed by residues 26 - 31 (chain R) in PDB entry 1KD1
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 PRO 26 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3008B G 4.1 7.6 - - - +
20O TYR* 3.6 50.3 - - + +
23O ARG* 4.8 4.0 - - + +
24O LEU* 3.7 38.4 - - + +
27O LEU* 4.8 9.2 - - + -
23R THR* 6.3 0.4 - - + -
24R SER 3.9 5.8 - - - +
25R PRO* 1.3 84.3 - - + +
27R GLN* 1.3 59.0 + - - +
29R ALA* 2.7 30.1 + - + +
30R VAL* 3.2 12.8 + - - +
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Residues in contact with GLN 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3008B G 3.6 43.5 + - - +
3009B C 3.4 21.8 - - - +
23O ARG* 4.8 3.6 + - - +
27O LEU* 5.1 2.2 - - - +
50O LEU* 3.9 27.8 - - - +
51O GLY 2.7 30.7 + - - +
52O PRO* 4.2 8.7 + - - +
54O GLY* 5.0 0.4 - - - -
25R PRO 3.3 1.0 - - - -
26R PRO* 1.3 79.3 - - - +
28R ARG* 1.3 62.1 + - + +
30R VAL* 3.3 12.5 + - - +
31R GLU* 3.4 14.7 + - - +
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Residues in contact with ARG 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3009B C 4.5 9.0 + - - +
3010B C 3.6 23.0 + - - -
24R SER* 3.4 16.1 + - - -
25R PRO* 3.8 27.1 + - - +
27R GLN* 1.3 76.2 - - + +
29R ALA* 1.3 66.3 + - + +
30R VAL 3.2 1.6 - - - -
31R GLU* 3.8 13.2 + - + +
44R ASP* 2.9 29.7 + - - -
88R ALA* 3.4 25.4 - - - +
89R ALA* 4.8 12.3 + - + +
91R LEU 5.1 3.7 - - - +
92R ARG* 3.6 33.1 - - - +
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Residues in contact with ALA 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 4.4 17.9 - - + +
25R PRO 4.7 2.2 - - - +
26R PRO* 2.7 23.1 + - + +
28R ARG* 1.3 77.2 - - + +
30R VAL* 1.3 60.3 + - - +
31R GLU 3.5 0.4 - - - -
47R VAL* 6.1 2.0 - - + -
87R THR* 5.9 0.3 - - - -
88R ALA* 3.5 13.4 + - - +
89R ALA* 3.8 26.6 + - + +
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Residues in contact with VAL 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 3.6 22.2 - - + -
27O LEU* 3.8 35.7 - - + +
28O LYS* 5.7 1.6 - - + -
30O GLY* 6.2 1.3 - - - -
50O LEU* 4.2 23.6 - - + -
26R PRO 3.2 17.4 + - - +
27R GLN* 3.3 4.7 + - - +
28R ARG 3.2 0.4 - - - -
29R ALA* 1.3 83.7 - - - +
31R GLU* 1.3 66.8 - - - +
32R GLU* 3.4 19.1 + - + +
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Residues in contact with GLU 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R GLN* 3.4 13.7 + - - +
28R ARG* 3.8 18.2 - - + +
29R ALA 3.5 1.0 - - - -
30R VAL* 1.3 80.8 - - - +
32R GLU* 1.3 66.1 + - - +
33R PHE* 3.8 24.1 - - + -
71R TYR* 3.4 8.8 + - - -
88R ALA* 3.4 15.6 - - - +
93R ARG* 3.0 37.3 + - - +
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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