Contacts of the helix formed by residues 55 - 66 (chain A) in PDB entry 5EKD
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 ALA 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A SER* 5.2 0.2 - - - +
51A ASN 3.0 12.0 + - - +
53A LEU 3.4 0.8 - - - -
54A GLY* 1.3 80.2 - - - +
56A ILE* 1.3 66.8 + - + +
57A GLU 3.2 2.9 - - - -
58A SER* 3.0 26.7 + - - -
59A TRP* 3.1 25.1 + - + +
177A PRO* 4.6 9.2 - - - +
178A VAL* 4.8 2.7 - - - -
402A ATP 4.3 27.1 - - - +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 4.1 14.8 - - + -
47A LEU* 3.7 18.8 - - + -
51A ASN 3.1 18.6 + - - +
52A TYR* 3.9 12.6 - - + -
55A ALA* 1.3 74.5 - - + +
57A GLU* 1.3 63.7 + - - +
59A TRP* 2.9 53.1 + - + +
60A VAL* 3.2 15.8 + - + +
99A LEU* 4.0 15.9 - - + -
102A CYS* 4.0 33.2 - - + -
104A ILE* 5.2 1.6 - - + -
402A ATP 6.3 0.4 - - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.0 36.9 + - + +
53A LEU* 3.7 24.0 - - - +
56A ILE* 1.3 75.3 - - - +
58A SER* 1.3 65.3 + - - +
59A TRP 3.2 0.7 + - - -
60A VAL* 3.3 7.0 + - + +
61A ARG* 3.3 18.8 + - - +
281A ALA* 5.0 8.3 - - - +
282A VAL* 6.0 0.2 - - - -
313A LYS* 3.6 31.2 + - - -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 4.6 1.0 + - - -
55A ALA* 3.0 14.1 + - - -
57A GLU* 1.3 76.5 - - - +
59A TRP* 1.3 64.7 + - - +
61A ARG* 3.2 15.9 + - - +
62A LEU* 2.8 42.1 + - - +
177A PRO* 4.2 11.0 - - - +
210A ILE* 4.3 12.4 + - - +
212A THR* 3.4 27.8 - - - +
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Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 3.2 41.8 + - - -
40A GLY* 3.8 15.3 - - - -
41A ILE* 3.7 26.7 - - + -
55A ALA* 3.1 28.9 + - + +
56A ILE* 2.9 33.9 + - + +
58A SER* 1.3 80.6 - - - +
60A VAL* 1.3 63.6 + - - +
62A LEU* 4.4 1.6 - - - -
63A GLN* 3.2 12.1 + - - +
71A TYR* 2.7 67.9 + + + -
72A SER 4.9 1.3 - - - -
99A LEU* 3.9 19.3 - - + -
104A ILE* 4.0 14.5 - - + +
177A PRO* 3.9 14.3 - - + +
402A ATP 6.0 1.1 - - - -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 6.3 0.7 - - + -
56A ILE* 3.2 13.8 + - + +
57A GLU* 3.8 9.2 - - + +
58A SER 3.2 0.2 - - - -
59A TRP* 1.3 74.0 - - - +
61A ARG* 1.3 65.7 + - - +
63A GLN* 3.5 32.2 + - - +
64A ASP* 4.1 7.2 - - - +
102A CYS* 3.5 29.6 - - + +
103A GLY* 4.1 8.3 - - - +
104A ILE* 3.8 20.0 - - + -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU 3.3 8.7 + - - +
58A SER* 3.2 16.7 + - - +
60A VAL* 1.3 79.6 - - - +
62A LEU* 1.3 84.4 + - - +
63A GLN 3.2 0.9 + - - -
64A ASP* 3.2 16.2 + - - +
65A GLU* 2.6 63.5 + - - +
210A ILE* 4.3 18.2 - - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.2 13.9 - - + -
58A SER* 2.8 32.9 + - - +
59A TRP* 4.4 1.8 - - - +
60A VAL 3.3 0.2 - - - -
61A ARG* 1.3 104.2 - - - +
63A GLN* 1.3 62.6 + - - +
64A ASP 3.1 0.2 + - - -
65A GLU* 3.1 3.9 + - - +
66A TYR* 3.0 49.1 + - + +
69A VAL* 3.8 6.5 - - - +
71A TYR* 3.6 11.9 - - - +
177A PRO* 3.5 33.0 - - + -
210A ILE* 4.1 18.4 - - + -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TRP 3.2 11.1 + - - +
60A VAL* 3.6 22.3 + - - +
61A ARG 3.2 1.4 - - - -
62A LEU* 1.3 76.8 - - - +
64A ASP* 1.3 64.2 + - - +
66A TYR 3.5 12.2 - - - +
69A VAL* 4.2 22.2 - - + -
71A TYR* 4.2 0.6 + - + -
103A GLY 2.8 27.5 + - - -
104A ILE* 3.7 5.9 - - - +
105A ASN* 3.0 31.9 + - - +
108A LYS* 4.0 32.9 - - + +
109A SER* 3.2 14.5 + - - +
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.1 8.4 - - - +
61A ARG* 3.2 8.9 + - - +
62A LEU 3.0 0.6 - - - -
63A GLN* 1.3 85.2 + - - +
65A GLU* 1.3 61.4 + - + +
66A TYR 3.7 0.9 - - - -
108A LYS* 2.6 36.8 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 2.6 60.0 + - - +
62A LEU* 3.1 9.8 + - - +
64A ASP* 1.3 83.1 - - + +
66A TYR* 1.3 74.3 + - + +
67A ASP* 5.5 0.7 - - - +
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.5 47.5 - - + +
37A VAL* 3.8 17.5 - - + -
62A LEU* 3.0 31.5 + - + -
63A GLN 3.5 16.6 - - - +
64A ASP 4.8 0.8 - - - -
65A GLU* 1.3 88.1 - - + +
67A ASP* 1.3 65.0 - - - +
68A SER 3.5 6.2 + - - +
69A VAL* 3.8 22.6 - - + +
108A LYS 5.5 1.0 - - - +
175A HIS* 3.6 33.8 + + + -
210A ILE* 5.2 1.9 - - + +
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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