Contacts of the helix formed by residues 39 - 46 (chain D) in PDB entry 4YC6
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU 4.0 1.2 + - - -
38D MET* 1.3 73.5 - - - +
40D GLU* 1.3 67.6 + - - +
41D SER* 3.3 16.1 + - - -
42D GLU* 2.9 32.9 + - - +
43D TRP* 2.9 26.1 + - - -
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Residues in contact with GLU 40 (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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39D SER* 1.3 74.0 - - - +
41D SER* 1.3 65.6 + - - +
43D TRP* 3.4 32.7 + - + +
44D ARG* 3.0 58.3 + - - +
52D GLN* 3.2 38.6 + - - +
53D GLY* 3.4 13.9 + - - -
54D TRP 4.2 2.9 - - - +
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Residues in contact with SER 41 (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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39D SER* 3.3 17.3 + - - -
40D GLU* 1.3 76.6 - - - +
42D GLU* 1.3 61.1 - - - +
44D ARG* 3.3 6.9 + - - +
45D ASN* 3.0 34.2 + - - +
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Residues in contact with GLU 42 (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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33D PRO* 4.4 3.1 - - - +
36D HIS* 3.3 27.9 + - - -
37D LEU 5.0 0.2 - - - +
38D MET* 3.6 31.5 - - + +
39D SER* 2.9 36.9 + - - +
41D SER* 1.3 81.0 + - - +
43D TRP* 1.3 61.5 + - - +
45D ASN* 3.4 17.5 - - - +
46D LEU* 3.7 4.5 + - - +
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Residues in contact with TRP 43 (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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38D MET* 3.8 32.4 + - + +
39D SER 2.9 25.7 + - - -
40D GLU* 3.4 38.5 - - + +
42D GLU* 1.3 72.1 - - - +
44D ARG* 1.3 112.1 + - + +
45D ASN 3.1 1.6 - - - -
46D LEU* 3.0 17.0 + - - +
48D VAL* 3.4 38.0 + - + +
50D GLN* 3.5 28.7 - - + -
51D SER 4.2 5.6 - - - -
54D TRP* 3.5 25.1 + - + -
55D VAL* 5.2 0.2 - - - +
56D HIS* 4.4 4.8 - - + +
67D LEU* 4.6 7.2 - - + -
69D PHE* 3.6 32.1 - + + -
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Residues in contact with ARG 44 (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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89A LYS* 4.5 18.6 - - - +
40D GLU* 3.0 49.9 + - - +
41D SER* 3.7 6.7 - - - +
43D TRP* 1.3 90.0 - - + +
45D ASN* 1.3 56.8 + - - +
47D GLY* 2.7 28.1 + - - -
48D VAL 3.5 20.3 + - - +
49D GLN* 4.6 1.8 - - - +
50D GLN 3.0 31.1 + - - +
51D SER 3.8 13.1 + - - -
52D GLN* 4.1 2.6 - - - +
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Residues in contact with ASN 45 (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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9A LYS* 5.5 5.5 + - - +
41D SER* 3.0 19.7 + - - +
42D GLU* 3.4 13.0 - - - +
43D TRP 3.1 0.2 - - - -
44D ARG* 1.3 75.4 - - - +
46D LEU* 1.3 62.4 + - + +
47D GLY* 3.1 1.7 + - - -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.1 10.0 - - - +
24D LEU* 3.9 27.0 - - + +
28D ILE* 4.0 33.7 - - + +
31D LEU* 4.7 17.7 - - + +
32D VAL* 4.1 7.9 - - + -
38D MET* 3.5 32.3 - - + -
42D GLU 4.0 8.3 - - - +
43D TRP* 3.0 10.0 + - - +
45D ASN* 1.3 79.3 - - + +
47D GLY* 1.3 58.1 + - - +
48D VAL* 4.7 6.5 - - + -
67D LEU* 4.4 6.1 - - + -
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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