Contacts of the helix formed by residues 45 - 57 (chain C) in PDB entry 1EAK
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 THR 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LYS* 1.3 77.3 - - - +
46C ASP* 1.3 69.4 - - - +
47C LYS* 4.1 5.3 - - - +
48C GLU* 3.0 47.1 + - - +
49C LEU* 2.8 22.8 + - - +
98C ARG* 5.4 2.0 - - - -
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 1.3 73.8 - - - +
47C LYS* 1.3 56.9 + - - +
49C LEU* 3.4 7.3 - - - +
50C ALA* 3.1 25.5 + - - +
89C LEU* 4.2 7.0 - - + +
91C GLN* 4.9 4.7 - - - +
94C ILE* 3.3 33.1 - - + +
98C ARG* 2.9 32.7 + - - +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 3.1 5.1 - - - +
46C ASP* 1.3 75.6 - - - +
48C GLU* 1.3 68.9 + - - +
49C LEU 3.0 1.5 + - - -
50C ALA* 3.1 1.7 + - - +
51C VAL* 3.0 44.4 + - + +
66C ASN* 3.1 35.3 + - - +
70C LEU* 4.5 10.3 - - + +
89C LEU* 4.3 18.8 - - + -
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO 4.1 2.1 - - - +
44C LYS* 3.4 33.0 + - + +
45C THR* 3.0 47.2 + - - +
47C LYS* 1.3 79.3 - - - +
49C LEU* 1.3 66.7 + - - +
51C VAL* 3.5 6.6 + - - +
52C GLN* 3.1 18.9 + - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS* 4.4 14.5 - - + +
45C THR 2.8 17.1 + - - +
46C ASP* 3.4 5.8 - - - +
48C GLU* 1.3 76.4 - - - +
50C ALA* 1.3 67.5 + - - +
52C GLN* 2.8 24.4 + - + +
53C TYR* 2.8 20.6 + - + +
94C ILE* 4.6 7.4 - - + -
97C MET* 4.1 29.6 - - + +
98C ARG* 4.0 43.7 - - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASP 3.1 3.6 + - - +
47C LYS 3.1 5.3 + - - +
49C LEU* 1.3 78.8 - - - +
51C VAL* 1.3 53.6 + - + +
53C TYR* 3.1 0.9 + - - +
54C LEU* 2.8 42.2 + - + +
70C LEU* 5.3 0.4 - - + -
74C LEU* 4.8 4.7 - - + -
89C LEU* 3.0 49.8 - - + -
97C MET* 3.4 19.7 - - + -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LYS* 3.0 43.4 + - + +
48C GLU* 3.8 4.9 - - - +
50C ALA* 1.3 75.9 - - + +
52C GLN* 1.3 61.8 + - - +
54C LEU* 3.7 3.9 + - - +
55C ASN* 3.1 23.4 + - - +
62C LYS* 4.3 12.6 - - - +
65C CYS* 3.9 40.0 - - + +
66C ASN* 5.9 0.2 - - - +
70C LEU* 5.0 7.9 - - + -
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Residues in contact with GLN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS* 4.6 18.0 - - - +
48C GLU 3.1 12.5 + - - +
49C LEU* 2.8 21.0 + - + +
51C VAL* 1.3 70.0 - - - +
53C TYR* 1.3 59.0 + - - +
55C ASN* 2.8 9.2 + - + +
56C THR* 2.8 43.6 + - - +
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Residues in contact with TYR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 2.8 19.7 + - + +
50C ALA 3.4 7.4 - - - +
52C GLN* 1.3 77.7 - - - +
54C LEU* 1.3 57.3 + - - +
57C PHE* 3.0 62.4 + + - +
58C TYR* 3.7 23.3 - + - -
77C MET* 4.2 6.7 - - + -
81C PHE* 3.8 11.3 - + - -
96C THR* 4.0 10.1 + - - -
97C MET* 3.1 60.6 - - + -
101C ARG* 3.1 38.7 + - + -
190C LEU* 6.2 0.2 - - + -
424C ILE* 4.0 5.7 - - - +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA* 2.8 24.4 + - - +
51C VAL 4.2 2.5 - - - +
53C TYR* 1.3 75.9 - - + +
55C ASN* 1.3 57.9 + - - +
58C TYR* 2.8 65.2 + - + +
60C CYS* 2.9 19.9 + - + -
65C CYS* 4.4 3.6 - - - -
70C LEU* 3.3 34.3 - - + -
73C THR* 3.8 21.1 - - + -
74C LEU* 3.6 23.6 - - + +
77C MET* 3.8 15.5 - - + -
97C MET* 4.8 4.0 - - - -
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL 3.1 18.6 + - - +
52C GLN* 2.8 10.8 + - + +
54C LEU* 1.3 79.0 - - - +
56C THR* 1.3 65.2 + - - +
59C GLY* 3.5 14.8 + - - -
60C CYS 2.8 27.0 + - - +
62C LYS* 3.1 43.9 - - - +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLN* 2.8 32.4 + - - +
55C ASN* 1.3 76.6 - - - +
57C PHE* 1.3 89.4 - - + +
59C GLY 4.6 1.2 + - - -
103C GLY 4.6 8.7 - - - +
105C PRO* 4.3 15.8 - - - +
182C TYR* 6.5 1.1 - - + -
190C LEU* 4.9 12.7 - - + +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 3.0 53.8 + + - +
56C THR* 1.3 93.9 - - + +
58C TYR* 1.3 68.4 + - + +
59C GLY 3.7 0.4 - - - -
101C ARG* 2.9 44.2 - - - +
102C CYS 3.4 8.7 - - - -
103C GLY* 3.8 13.2 - - - -
104C ASN 3.2 13.9 - - - -
105C PRO* 3.9 4.7 - - - +
106C ASP* 3.1 30.2 + - - +
107C VAL* 3.5 11.0 + - - +
190C LEU* 3.1 33.7 - - + -
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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