Contacts of the helix formed by residues 51 - 61 (chain D) in PDB entry 4PCW
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 ASP 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LYS* 4.0 3.8 + - - -
49D ASP* 3.6 4.5 + - - -
50D PRO* 1.3 71.3 - - - +
52D MET* 1.3 68.5 + - - +
53D VAL* 3.4 27.8 + - - +
54D ASP* 2.8 33.5 + - + +
55D VAL* 3.4 18.9 - - - +
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Residues in contact with MET 52 (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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36D LEU* 4.4 23.8 - - + +
40D PHE* 4.8 12.3 - - + +
42D GLN* 4.4 25.8 - - - +
49D ASP* 5.1 7.7 + - - +
50D PRO 3.2 5.9 + - - +
51D ASP* 1.3 76.2 + - - +
53D VAL* 1.3 65.0 + - + +
55D VAL* 3.7 6.4 + - + +
56D PHE* 3.2 59.6 + - + -
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Residues in contact with VAL 53 (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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29D LYS* 3.6 43.7 - - + +
32D LEU* 4.5 8.9 - - + +
33D LYS* 3.4 37.5 - - + +
36D LEU* 4.8 7.9 - - + -
51D ASP* 3.2 22.8 - - - +
52D MET* 1.3 80.9 - - + +
54D ASP* 1.3 65.1 + - - +
56D PHE* 3.6 3.8 + - - +
57D MET* 3.2 22.5 + - - +
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Residues in contact with ASP 54 (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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29D LYS* 3.3 25.9 + - - +
51D ASP* 2.8 37.4 + - + +
53D VAL* 1.3 75.3 - - - +
55D VAL* 1.3 62.2 + - + +
57D MET* 3.3 2.6 + - - +
58D ASP* 2.8 43.2 + - - +
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Residues in contact with VAL 55 (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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50D PRO* 5.3 8.3 - - + +
51D ASP 3.4 17.3 - - - +
52D MET* 3.7 9.1 + - + +
53D VAL 3.3 0.4 - - - -
54D ASP* 1.3 78.8 - - + +
56D PHE* 1.3 66.0 + - + +
58D ASP* 3.3 6.6 + - - +
59D HIS* 3.1 42.5 + - + +
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Residues in contact with PHE 56 (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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32D LEU* 4.1 14.8 - - + -
36D LEU* 3.4 36.1 - - + -
40D PHE* 5.5 2.7 - + - -
52D MET* 3.2 46.3 + - + +
53D VAL 3.8 7.6 - - - +
54D ASP 3.3 0.2 - - - -
55D VAL* 1.3 82.0 - - + +
57D MET* 1.3 54.9 + - - +
59D HIS* 3.1 1.0 + - - -
60D LEU* 2.7 67.5 + - + +
76D MET* 3.9 28.5 - - + -
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Residues in contact with MET 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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27D LEU 4.2 0.9 - - - +
28D SER 3.9 3.8 - - - -
29D LYS* 3.6 51.8 - - + +
32D LEU* 3.9 11.2 - - + -
53D VAL 3.2 13.0 + - - +
54D ASP* 3.3 9.6 + - - +
56D PHE* 1.3 75.9 - - - +
58D ASP* 1.3 68.8 + - - +
59D HIS 3.3 0.3 + - - -
61D ASP* 3.2 34.7 + - - +
64D HIS* 5.6 1.7 - - - -
66D LYS* 3.8 32.8 - - - +
68D ILE* 3.7 35.7 - - + -
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Residues in contact with ASP 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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52A MET* 3.1 38.5 - - + +
55A VAL* 5.2 1.9 - - - +
54D ASP* 2.8 34.2 + - - +
55D VAL* 3.6 8.5 - - - +
57D MET* 1.3 79.3 - - - +
59D HIS* 1.3 65.0 + - + +
61D ASP 5.0 3.2 - - - +
64D HIS* 5.1 6.4 + - - -
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Residues in contact with HIS 59 (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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52A MET* 5.4 2.2 - - + -
55A VAL* 3.1 39.0 - - + +
59A HIS* 3.1 26.3 + - + -
55D VAL* 3.1 38.3 + - + +
56D PHE* 4.5 0.4 - - - -
57D MET 3.1 0.4 - - - -
58D ASP* 1.3 89.5 - - + +
60D LEU* 1.3 78.9 + - + +
61D ASP 3.5 1.3 - - - -
62D ILE* 3.7 8.7 - - - +
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Residues in contact with LEU 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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59A HIS* 5.0 7.9 - - + -
32D LEU* 5.6 2.7 - - + -
56D PHE* 2.7 55.5 + - + +
59D HIS* 1.3 87.2 - - + +
61D ASP* 1.3 59.3 + - - +
62D ILE* 3.0 14.5 + - - +
68D ILE* 4.2 17.5 - - + -
72D GLU* 3.4 37.7 - - + +
73D PHE* 5.4 0.2 - - - -
75D LEU* 5.3 7.8 - - + +
76D MET* 3.8 35.4 - - + +
79D LYS* 6.1 4.0 - - + -
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Residues in contact with ASP 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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57D MET* 3.2 24.4 + - - +
58D ASP 5.0 2.3 - - - +
59D HIS 4.8 1.3 - - - -
60D LEU* 1.3 74.3 - - - +
62D ILE* 1.3 63.9 + - - +
63D ASP* 2.9 7.1 - - - +
64D HIS* 3.2 27.0 + - + -
65D ASN* 3.0 3.6 + - - +
66D LYS* 2.6 35.0 + - - +
67D LYS 3.5 9.4 - - - -
68D ILE* 3.8 14.3 - - + +
72D GLU* 3.5 2.2 - - - -
102D CA 2.3 32.7 - - - -
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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