Contacts of the helix formed by residues 55 - 64 (chain A) in PDB entry 5EJC
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 TYR 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS* 4.1 6.3 - - + -
28A LEU* 4.2 21.1 - - + -
29A GLU* 3.1 44.2 + - + +
32A LEU* 3.6 22.7 - - + -
51A LEU* 5.3 0.9 - - - -
52A PRO* 3.1 23.0 + - + +
54A MSE 1.3 118.7 - - + +
56A ARG* 1.3 64.8 + - - +
57A ALA 3.4 1.8 - - - -
58A LEU* 3.4 19.1 + - + +
59A VAL* 3.0 27.8 + - + +
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Residues in contact with ARG 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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51A LEU* 3.2 30.2 + - + +
52A PRO 3.1 5.8 + - - +
53A SER* 3.7 31.7 + - - +
54A MSE 3.4 2.0 - - - -
55A TYR* 1.3 78.4 - - - +
57A ALA* 1.3 65.7 + - - +
59A VAL* 3.2 0.5 + - - -
60A TRP* 2.9 62.4 + - + +
144A MSE 5.7 2.9 - - - -
221A GLN* 3.5 48.0 + - - +
222A ARG* 4.1 12.3 - - - +
225A ASP* 3.1 30.1 + - - +
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Residues in contact with ALA 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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53A SER 4.8 1.2 + - - -
54A MSE 4.7 4.8 + - - +
55A TYR 3.4 0.8 - - - -
56A ARG* 1.3 77.9 - - - +
58A LEU* 1.3 63.4 + - - +
60A TRP* 3.8 5.9 - - - +
61A LYS* 3.0 39.2 + - - +
145A VAL* 4.9 19.1 - - + -
150A ASP* 5.0 5.6 - - - +
154A ILE* 4.5 7.1 - - + +
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Residues in contact with LEU 58 (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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32A LEU* 4.2 26.0 - - + -
37A LEU* 5.7 1.3 - - + -
54A MSE 5.1 2.1 + - - +
55A TYR* 3.4 27.7 + - + +
56A ARG 3.2 0.6 - - - -
57A ALA* 1.3 76.7 - - - +
59A VAL* 1.3 64.4 + - - +
61A LYS* 3.2 10.7 + - - +
62A VAL* 3.0 36.8 + - + +
67A LEU* 4.0 21.3 - - + -
74A HIS* 4.2 11.9 - - + +
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Residues in contact with VAL 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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28A LEU* 4.6 6.3 - - + -
32A LEU* 4.5 19.1 - - + -
42A LEU* 4.5 19.7 - - + -
46A SER* 3.9 14.4 - - - +
51A LEU* 4.1 22.4 - - + -
55A TYR* 3.0 27.6 + - + +
56A ARG 3.8 2.5 - - - +
58A LEU* 1.3 75.2 - - + +
60A TRP* 1.3 63.0 + - - +
62A VAL* 3.1 7.7 + - - +
63A LEU* 2.9 46.3 + - + +
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Residues in contact with TRP 60 (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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51A LEU* 3.5 13.5 - - + +
56A ARG* 2.9 43.0 + - + +
57A ALA* 3.8 4.9 - - - +
59A VAL* 1.3 77.3 - - + +
61A LYS* 1.3 58.3 + - - +
63A LEU* 3.4 1.8 + - + +
64A LEU* 2.9 43.8 + - + +
141A MSE 3.8 29.2 - - + -
144A MSE 4.0 17.3 - - + -
145A VAL* 5.2 3.8 - - + -
154A ILE* 3.9 23.8 - - + -
158A PHE* 6.3 1.3 - + - -
221A GLN* 3.6 13.2 - - + -
224A TRP* 3.8 19.1 - + + -
225A ASP* 3.1 42.8 + - - +
228A VAL* 4.2 29.8 - - + +
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Residues in contact with LYS 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 ALA* 3.0 30.6 + - - +
58A LEU* 3.5 8.7 - - - +
60A TRP* 1.3 75.0 - - - +
62A VAL* 1.3 61.2 + - - +
64A LEU 3.6 0.2 + - - -
65A GLY 3.3 2.4 + - - -
66A ILE* 2.9 57.9 + - + -
67A LEU* 3.1 29.5 + - + +
78A MSE 4.3 13.5 - - - +
150A ASP* 3.2 42.0 + - + +
154A ILE* 4.0 18.6 - - + -
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Residues in contact with VAL 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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32A LEU* 6.3 0.9 - - + -
37A LEU* 3.8 28.9 - - + -
39A THR* 4.2 22.3 - - + +
42A LEU* 3.9 24.0 - - + -
58A LEU* 3.0 25.2 + - + +
59A VAL* 3.1 8.9 + - - +
61A LYS* 1.3 75.2 - - - +
63A LEU* 1.3 63.5 + - - +
65A GLY* 3.2 10.7 + - - -
67A LEU* 3.6 20.0 - - + +
68A PRO 4.8 2.9 - - - +
69A PRO* 4.9 1.6 - - + -
74A HIS* 4.1 17.7 - - + +
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Residues in contact with LEU 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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39A THR* 3.8 20.2 - - - +
42A LEU* 3.9 16.4 - - + +
43A CYS* 3.6 26.0 - - - -
46A SER* 4.1 12.3 - - - +
59A VAL* 2.9 37.5 + - + +
60A TRP* 4.0 1.1 - - + +
62A VAL* 1.3 79.2 - - + +
64A LEU* 1.3 62.1 + - - +
65A GLY* 3.1 1.8 + - - -
161A GLN* 5.6 2.6 + - - -
225A ASP 5.4 0.4 - - - +
228A VAL* 3.8 32.0 - - + +
229A SER* 4.2 15.5 - - - -
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Residues in contact with LEU 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 TRP* 2.9 27.2 + - + +
61A LYS 4.3 0.4 - - - +
63A LEU* 1.3 74.5 - - - +
65A GLY* 1.3 57.7 + - - +
66A ILE* 3.4 9.8 + - + -
154A ILE* 3.9 42.6 - - + +
157A ARG* 3.1 53.1 + - + +
158A PHE* 4.3 4.5 - - + +
161A GLN* 3.9 28.7 - - + +
228A VAL* 4.1 22.4 - - + -
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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