Contacts of the helix formed by residues 28 - 33 (chain D) in PDB entry 4K9P
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 GLU 28 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D PRO* 5.1 1.6 - - + -
25D GLY* 2.9 26.1 + - - +
27D ASN* 1.3 78.8 - - - +
29D LEU* 1.3 65.5 + - - +
30D PRO* 3.3 3.1 - - - -
31D PHE* 3.1 10.8 + - + +
32D LEU* 3.0 29.5 + - + +
68D ASN* 3.3 26.0 - - - +
69D LEU 3.2 21.3 - - - +
70D HIS* 2.6 40.6 + - - +
71D SER 3.4 1.0 + - - -
97D GLY* 2.9 33.0 + - - +
163D TRP* 5.8 0.2 - - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B LEU* 3.8 12.1 - - + +
464B PHE* 3.6 34.5 - - + +
465B ALA* 3.6 21.3 - - + +
468B LEU* 4.6 11.0 - - + -
473B VAL* 3.9 28.6 - - + +
476B LEU* 4.6 12.6 - - + -
24D PRO* 5.4 1.1 - - + -
25D GLY 3.3 15.8 + - - +
26D SER* 3.6 11.7 - - - +
28D GLU* 1.3 77.4 - - - +
30D PRO* 1.3 65.8 - - + +
32D LEU* 3.0 8.0 + - + +
33D LYS* 2.8 33.1 + - - +
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Residues in contact with PRO 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B LEU* 4.5 20.4 - - + -
5D HIS* 3.6 14.6 - - - -
26D SER 3.5 9.4 - - - +
27D ASN 3.8 5.4 - - - +
28D GLU 3.4 4.3 - - - -
29D LEU* 1.3 97.6 - - + +
31D PHE* 1.3 57.3 + - - +
33D LYS* 3.7 22.2 - - + +
160D TYR* 3.4 45.8 - - + +
163D TRP* 3.9 13.4 - - + +
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Residues in contact with PHE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D HIS* 3.1 16.7 + + - -
8D THR* 4.4 10.3 - - + -
9D TYR* 2.8 56.4 + + - -
12D LEU* 4.8 3.1 - - + -
20D VAL* 5.1 5.4 - - + -
28D GLU* 3.1 10.2 + - - +
29D LEU 3.1 0.6 - - - -
30D PRO* 1.3 81.5 - - - +
32D LEU* 1.3 71.3 + - + +
33D LYS 3.3 0.4 - - - -
66D PHE* 4.0 27.8 - + - -
68D ASN* 3.8 33.9 - - + +
95D THR* 5.1 0.2 - - - -
163D TRP* 3.4 58.2 - + + +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ASN 3.6 5.2 - - - +
473B VAL* 4.1 17.0 - - + -
474B PRO* 3.7 13.7 - - + +
9D TYR* 4.2 2.0 - - - -
20D VAL* 4.9 1.1 - - + -
24D PRO* 3.9 28.7 - - + -
28D GLU* 3.0 21.1 + - + +
29D LEU* 3.0 5.9 + - + +
31D PHE* 1.3 94.3 - - + +
33D LYS* 1.3 67.4 + - - +
34D ASP 3.6 0.2 + - - -
35D PHE* 3.2 33.3 + - + +
41D TYR* 3.8 35.0 - - + +
68D ASN* 4.1 11.4 - - - +
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B LEU* 4.0 20.8 + - + +
469B GLU* 3.9 11.9 + - - +
470B ALA* 3.6 36.1 - - + +
471B GLU* 4.2 3.7 + - - +
473B VAL* 3.6 11.2 - - - +
5D HIS* 2.9 30.1 + - + +
29D LEU 2.8 14.4 + - - +
30D PRO* 3.7 21.5 - - + +
31D PHE 3.3 0.8 - - - -
32D LEU* 1.3 77.7 - - - +
34D ASP* 1.3 79.8 + - + +
35D PHE 3.3 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