Contacts of the helix formed by residues 45 - 58 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PRO 5.0 2.9 - - - +
44B LYS* 1.3 77.2 - - - +
46B ASP* 1.3 68.9 + - - +
47B LYS* 3.9 4.8 + - - +
48B GLU* 2.7 58.8 + - - +
49B LEU* 2.8 11.7 + - - -
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LYS 4.2 0.2 + - - -
45B THR* 1.3 72.0 - - - +
47B LYS* 1.3 58.5 + - - +
49B LEU* 3.5 9.3 - - - +
50B ALA* 3.0 27.0 + - - +
89B LEU* 4.4 9.6 - - + +
94B ILE* 3.1 43.9 - - + +
97B MET* 4.6 1.7 - - - +
98B ARG* 2.9 25.8 + - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 2.8 5.7 + - - +
46B ASP* 1.3 75.0 - - - +
48B GLU* 1.3 62.9 - - + +
50B ALA* 3.0 2.6 + - + +
51B VAL* 2.8 52.1 + - + +
65B CYS 5.6 2.7 - - - -
66B ASN* 5.8 6.4 - - - +
70B LEU* 4.6 19.0 - - + +
89B LEU* 4.0 22.4 - - + +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO 4.1 3.1 - - - +
44B LYS* 3.4 27.7 - - + +
45B THR* 2.7 56.6 + - - +
47B LYS* 1.3 74.2 - - + +
49B LEU* 1.3 63.5 + - - +
51B VAL* 3.8 5.9 - - - +
52B GLN* 2.9 25.8 + - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LYS* 4.4 12.1 - - + +
45B THR 2.8 11.4 + - - +
46B ASP* 3.5 10.5 - - - +
48B GLU* 1.3 77.2 - - - +
50B ALA* 1.3 52.3 + - - +
52B GLN* 3.1 12.0 + - + +
53B TYR* 2.7 46.0 + - + +
94B ILE* 4.7 4.7 - - + +
97B MET* 4.1 26.0 - - + +
98B ARG* 3.4 43.3 - - + +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP 3.0 16.7 + - - +
47B LYS* 3.0 5.8 + - + +
49B LEU* 1.3 75.7 - - - +
51B VAL* 1.3 56.4 + - + +
53B TYR* 3.1 0.7 + - - +
54B LEU* 2.7 49.1 + - + +
70B LEU* 5.2 3.4 - - + -
74B LEU* 5.0 1.8 - - + -
89B LEU* 3.8 18.4 - - + -
97B MET* 3.3 31.0 - - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 2.8 46.7 + - + +
48B GLU* 3.9 5.2 - - - +
50B ALA* 1.3 72.4 - - + +
52B GLN* 1.3 57.7 + - - +
54B LEU* 4.3 7.1 - - - +
55B ASN* 2.9 32.3 + - + +
60B CYS* 4.7 0.7 - - - -
62B LYS* 4.5 12.6 - - - +
65B CYS* 3.9 35.9 - - + +
70B LEU* 4.8 9.4 - - + -
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LYS* 4.0 24.1 + - - +
48B GLU 2.9 13.5 + - - +
49B LEU* 3.4 13.7 - - + +
51B VAL* 1.3 74.8 - - - +
53B TYR* 1.3 64.9 + - - +
55B ASN* 2.9 10.5 + - + +
56B THR* 2.8 36.6 + - - +
185B ASP* 5.3 13.7 + - - +
190B LEU* 6.0 3.6 - - - +
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Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 2.7 28.0 + - + +
50B ALA 3.5 3.8 - - - +
52B GLN* 1.3 72.5 - - - +
54B LEU* 1.3 59.7 + - + +
56B THR* 4.4 0.7 - - - -
57B PHE* 2.9 74.6 + + + +
58B TYR* 4.1 20.0 - + - -
77B MET* 4.7 2.9 - - - -
81B PHE* 3.6 18.0 - + - -
96B THR* 4.7 1.3 + - + +
97B MET* 3.2 63.0 - - + -
101B ARG* 2.9 35.1 + - + -
424B ILE* 4.2 9.7 - - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 2.7 23.2 + - + +
51B VAL 4.3 0.9 - - - +
53B TYR* 1.3 77.3 - - + +
55B ASN* 1.3 58.0 + - - +
58B TYR* 2.9 33.0 + - + +
59B GLY 2.9 9.0 + - - -
60B CYS* 3.5 18.1 + - - -
65B CYS* 4.6 2.2 - - - -
70B LEU* 3.4 28.5 - - + +
73B THR* 3.6 32.3 - - + +
74B LEU* 3.3 27.1 - - + -
77B MET* 4.0 26.0 - - + -
97B MET* 5.0 3.8 - - - -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 2.9 21.4 + - + +
52B GLN* 2.9 11.9 + - - +
54B LEU* 1.3 79.2 - - - +
56B THR* 1.3 63.7 + - - +
59B GLY* 3.9 11.3 + - - -
60B CYS* 3.0 24.5 - - - +
61B PRO 5.3 0.2 - - - -
62B LYS* 3.3 47.3 + - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLN* 2.8 26.0 + - - +
53B TYR* 4.1 2.1 - - - -
55B ASN* 1.3 82.0 + - - +
57B PHE* 1.3 87.7 + - + +
58B TYR 3.6 0.4 + - - -
59B GLY* 4.7 1.6 + - - -
103B GLY 4.8 7.6 - - - +
105B PRO* 4.2 15.2 - - - +
182B TYR* 6.2 4.0 - - + -
190B LEU* 5.0 11.6 - - + +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 2.9 56.6 + + - +
56B THR* 1.3 93.6 - - + +
58B TYR* 1.3 77.1 + - + +
59B GLY 3.8 0.2 - - - -
101B ARG* 3.2 39.9 - - - -
102B CYS 3.6 6.1 - - - -
103B GLY* 3.8 11.4 - - - -
104B ASN 3.5 10.3 - - - -
105B PRO* 4.0 4.0 - - - -
106B ASP* 3.0 28.3 + - - +
107B VAL* 3.5 8.5 + - - +
190B LEU* 3.1 33.7 - - + -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 4.1 11.9 - + - -
54B LEU* 2.9 24.7 + - + +
57B PHE* 1.3 85.4 - - + +
59B GLY* 1.3 63.1 + - - +
60B CYS 3.4 1.7 + - - -
73B THR* 4.0 21.3 - - + +
76B LYS* 3.9 20.0 + - + +
77B MET* 3.2 41.9 - - + -
80B PHE* 3.3 14.6 - + + +
81B PHE* 3.2 16.1 - - - -
106B ASP* 2.6 42.5 + - + +
107B VAL* 3.4 37.1 - - + +
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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