Contacts of the helix formed by residues 56 - 65 (chain D) in PDB entry 3KHU
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 GLY 56 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLU 3.3 0.8 + - - -
55D PRO* 1.3 70.1 - - - +
57D LEU* 1.3 61.8 + - - +
58D LYS 3.4 2.5 - - - -
59D GLU* 3.4 28.3 + - - +
60D VAL* 3.2 28.1 + - - +
169D ILE* 3.9 11.0 - - - -
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Residues in contact with LEU 57 (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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18D PRO* 4.0 34.5 - - + -
21D SER* 4.4 4.5 - - - -
45D TRP* 4.0 24.5 - - + -
50D LEU* 3.8 8.7 - - + -
52D ILE* 3.7 26.5 - - + +
54D GLU* 3.2 27.0 + - + +
55D PRO 3.2 3.2 + - - -
56D GLY* 1.3 75.4 - - - +
58D LYS* 1.3 68.5 + - - +
60D VAL* 3.2 2.8 + - + +
61D VAL* 3.0 38.1 + - + +
169D ILE* 3.9 17.5 - - + -
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Residues in contact with LYS 58 (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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48D PRO* 3.4 29.3 + - - +
50D LEU* 3.8 20.5 - - + +
54D GLU 4.5 2.2 + - - -
56D GLY 3.4 0.2 - - - -
57D LEU* 1.3 79.1 - - - +
59D GLU* 1.3 71.6 + - - +
61D VAL* 3.8 1.0 - - - +
62D GLU* 2.9 64.5 + - + +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLY* 3.4 35.5 + - - +
58D LYS* 1.3 90.6 - - - +
60D VAL* 1.3 64.7 + - + +
62D GLU* 4.1 9.0 - - - +
63D SER* 3.2 24.3 + - - -
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Residues in contact with VAL 60 (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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21D SER* 3.7 34.8 - - - +
22D VAL* 4.1 8.1 - - + +
25D HIS* 3.9 18.4 - - + +
56D GLY 3.2 18.4 + - - +
57D LEU* 3.2 9.2 + - + +
59D GLU* 1.3 75.0 - - + +
61D VAL* 1.3 63.5 + - - +
63D SER* 2.7 22.9 + - - -
64D CYS* 3.5 8.0 - - - -
169D ILE* 4.3 13.2 - - + -
173D LYS* 4.2 28.3 - - - +
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Residues in contact with VAL 61 (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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21D SER* 3.7 22.0 - - - +
45D TRP* 4.3 9.2 - - + +
50D LEU* 3.9 16.8 - - + -
57D LEU* 3.0 33.8 + - + +
58D LYS 3.8 3.1 - - - +
60D VAL* 1.3 75.6 - - - +
62D GLU* 1.3 60.5 + - + +
64D CYS* 3.2 1.7 + - - -
65D ARG* 2.8 69.3 + - + +
69D LEU* 4.2 7.0 - - + -
71D PHE* 4.1 13.0 - - + -
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Residues in contact with GLU 62 (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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48D PRO* 4.9 8.1 - - - +
58D LYS* 2.9 59.5 + - + +
59D GLU* 4.2 7.1 - - - +
61D VAL* 1.3 76.3 - - + +
63D SER* 1.3 61.9 + - - +
64D CYS 3.3 0.3 + - - -
65D ARG* 4.1 31.8 + - - +
67D LYS* 5.2 4.2 + - - -
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Residues in contact with SER 63 (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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25D HIS* 2.9 31.9 + - - -
59D GLU 3.2 13.4 + - - -
60D VAL 2.7 20.1 + - - -
62D GLU* 1.3 77.9 - - - +
64D CYS* 1.3 59.1 + - - +
67D LYS* 4.0 21.3 + - - +
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Residues in contact with CYS 64 (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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21D SER 4.1 2.5 - - - -
24D ALA* 3.9 1.8 - - - +
25D HIS* 3.7 32.1 - - - +
60D VAL 3.5 16.6 - - - -
61D VAL 3.2 2.0 + - - -
62D GLU 3.2 0.4 - - - -
63D SER* 1.3 81.5 - - - +
65D ARG* 1.3 67.7 + - - +
67D LYS* 3.0 23.6 + - + -
68D ASN* 3.2 17.5 + - - +
69D LEU* 3.2 36.7 + - - -
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Residues in contact with ARG 65 (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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45D TRP 2.8 36.4 + - - -
46D ASN* 3.6 26.0 + - - +
47D SER 3.0 26.0 + - - -
48D PRO* 5.4 1.0 - - - +
50D LEU* 4.3 2.8 - - - +
61D VAL* 2.8 41.9 + - + +
62D GLU* 4.1 30.6 + - - +
64D CYS* 1.3 73.6 + - - +
66D GLY* 1.3 63.1 + - - +
67D LYS* 3.4 8.8 + - - +
69D LEU* 3.4 15.9 - - + +
70D PHE* 5.5 0.4 - - - -
71D PHE* 4.3 11.4 - - + -
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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