Contacts of the helix formed by residues 51 - 63 (chain D) in PDB entry 4HSZ
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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35D LYS* 4.0 0.7 - - - -
49D ARG* 2.6 56.1 + - - +
50D THR* 1.3 84.5 + - - +
52D GLU* 1.3 63.3 + - + +
53D ALA* 3.3 9.8 - - - +
54D ALA* 3.2 14.2 + - - +
55D PHE* 3.4 15.8 + - - +
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Residues in contact with GLU 52 (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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35D LYS* 3.9 18.9 - - - +
51D ASP* 1.3 72.7 - - - +
53D ALA* 1.3 70.9 + - + +
55D PHE* 3.3 4.7 + - + +
56D GLN* 2.8 45.7 + - - +
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Residues in contact with ALA 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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49D ARG* 3.9 8.3 - - - +
51D ASP* 3.3 12.2 + - - +
52D GLU* 1.3 91.3 - - + +
54D ALA* 1.3 61.7 + - - +
56D GLN* 3.3 15.7 + - - +
57D LYS* 3.4 13.2 + - - +
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Residues in contact with ALA 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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49D ARG* 3.8 33.4 - - + +
51D ASP* 3.2 25.7 + - - +
52D GLU 3.3 0.4 - - - -
53D ALA* 1.3 79.9 - - - +
55D PHE* 1.3 61.6 + - - +
57D LYS* 3.7 6.7 + - - +
58D LEU* 3.6 15.9 + - - +
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Residues in contact with PHE 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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31D LYS* 3.2 39.9 - - + -
34D LEU* 3.5 32.3 - - + -
35D LYS* 3.6 49.6 - - + +
38D LEU* 3.9 13.0 - - + -
50D THR 5.2 0.7 - - - +
51D ASP 3.4 6.7 + - - +
52D GLU* 3.3 8.8 + - + +
54D ALA* 1.3 77.3 - - - +
56D GLN* 1.3 65.2 + - + +
58D LEU* 3.1 16.3 + - + +
59D MET* 2.8 39.1 + - + -
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Residues in contact with GLN 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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31D LYS* 2.7 46.3 - - + +
52D GLU* 2.8 33.0 + - - +
53D ALA* 3.3 9.6 + - - +
55D PHE* 1.3 80.2 - - + +
57D LYS* 1.3 56.6 + - - +
59D MET* 3.3 6.0 + - - +
60D SER* 2.9 33.8 + - - -
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Residues in contact with LYS 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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53D ALA 3.4 9.9 + - - +
54D ALA* 4.0 8.7 - - - +
55D PHE 3.2 0.4 - - - -
56D GLN* 1.3 76.0 - - - +
58D LEU* 1.3 65.0 + - - +
60D SER* 3.5 18.1 + - - +
61D ASN* 3.6 12.3 + - - +
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Residues in contact with LEU 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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34D LEU* 4.8 0.4 - - + -
38D LEU* 3.2 36.1 - - + -
54D ALA 3.6 7.3 + - - +
55D PHE* 3.1 23.6 + - + +
57D LYS* 1.3 77.4 - - - +
59D MET* 1.3 65.8 + - - +
61D ASN* 3.1 20.7 + - + +
62D LEU* 3.5 32.8 + - + +
78D PHE* 4.6 13.5 - - + -
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Residues in contact with MET 59 (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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29D LEU 4.7 0.4 - - - +
30D ASN 3.9 3.8 - - - +
31D LYS* 3.3 59.9 - - + +
34D LEU* 3.2 38.8 - - + -
55D PHE* 2.8 20.6 + - + +
56D GLN* 3.4 13.7 - - - +
58D LEU* 1.3 78.2 - - - +
60D SER* 1.3 63.5 + - - +
61D ASN 3.0 1.6 + - - -
62D LEU* 3.2 11.7 + - - +
63D ASP* 3.2 19.1 + - + +
68D ASN* 5.0 2.7 - - - -
69D GLU* 5.0 7.6 - - - -
70D VAL* 4.0 17.3 - - + -
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Residues in contact with SER 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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56D GLN* 2.9 20.5 + - - -
57D LYS* 3.5 14.6 + - - +
58D LEU 3.3 0.2 - - - -
59D MET* 1.3 76.7 - - - +
61D ASN* 1.3 59.8 + - - +
63D ASP* 4.2 16.7 - - - +
64D SER* 5.6 0.3 - - - -
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Residues in contact with ASN 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 LYS 3.6 11.0 + - - +
58D LEU* 3.1 16.0 + - + +
59D MET 3.0 1.0 - - - -
60D SER* 1.3 80.3 + - - +
62D LEU* 1.3 65.0 + - + +
63D ASP 5.0 0.7 - - - -
64D SER* 5.0 6.3 - - - -
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Residues in contact with LEU 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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34D LEU* 4.0 30.1 - - + -
58D LEU* 3.5 29.8 - - + +
59D MET* 3.2 4.2 + - - +
61D ASN* 1.3 83.3 - - + +
63D ASP* 1.3 52.0 + - - +
64D SER* 2.6 27.6 + - - -
70D VAL* 4.1 17.5 - - + -
74D GLU* 3.7 19.1 - - - +
77D VAL* 6.1 3.4 - - + -
78D PHE* 3.5 53.6 - - + -
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Residues in contact with ASP 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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59D MET* 3.2 18.8 + - + +
60D SER* 4.2 13.6 + - - +
61D ASN 3.7 0.2 - - - -
62D LEU* 1.3 73.3 - - - +
64D SER* 1.3 56.4 + - - +
65D ASN* 2.6 29.6 - - - +
66D ARG* 3.1 19.3 + - - +
67D ASP* 2.7 13.1 + - - +
68D ASN* 2.7 27.7 + - - -
69D GLU 3.5 14.8 - - - +
70D VAL* 4.2 5.2 - - + +
74D GLU* 3.8 7.0 - - - -
102D CA 2.7 7.8 - - - -
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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