Contacts of the helix formed by residues 45 - 59 (chain B) in PDB entry 3ECS
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 LEU 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 GLN* 3.1 35.5 + - + +
44B GLY* 1.3 94.4 - - - +
46B ARG* 1.3 55.6 + - - +
47B ALA* 3.1 7.0 - - - +
48B ASN* 2.8 46.9 - - - +
49B LEU* 4.1 2.4 + - - +
90B LYS* 5.3 1.1 - - - +
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Residues in contact with ARG 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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33B PHE* 4.8 0.2 - - - -
34B LEU* 5.3 6.5 - - + +
37B ASP* 3.0 37.5 + - - +
38B LYS 2.7 30.3 + - - -
43B GLN* 4.1 24.4 + - - +
44B GLY 3.8 1.6 + - - -
45B LEU* 1.3 74.9 - - - +
47B ALA* 1.3 56.3 + - - +
48B ASN 2.8 6.5 + - - -
49B LEU* 2.9 33.3 + - - +
50B THR* 2.9 27.8 + - - -
88B LYS* 4.0 20.6 - - + +
91B LYS* 6.1 0.9 - - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 6.1 0.9 - - - -
44B GLY 5.8 1.3 - - - +
45B LEU* 4.9 1.8 - - - -
46B ARG* 1.3 77.6 - - - +
48B ASN* 1.3 65.9 + - - +
50B THR* 3.1 28.9 - - + +
51B SER* 3.3 8.5 + - - -
73B LEU* 5.1 6.8 - - + +
93B MSE 6.2 4.3 - - - -
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Residues in contact with ASN 48 (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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43B GLN* 5.0 0.9 + - - -
45B LEU* 2.8 57.7 + - - +
47B ALA* 1.3 87.1 - - - +
49B LEU* 1.3 68.3 + - + +
51B SER* 2.9 24.1 + - - -
52B ALA* 3.5 4.2 + - - +
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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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33B PHE* 4.1 16.2 - - + -
37B ASP* 3.7 8.5 - - - +
43B GLN* 5.1 2.5 - - - +
45B LEU 4.7 2.7 - - - +
46B ARG* 2.9 52.8 + - - +
48B ASN* 1.3 77.1 - - + +
50B THR* 1.3 62.9 + - - +
51B SER 2.9 6.4 + - - -
52B ALA* 3.0 20.2 + - + +
53B ILE* 3.1 21.5 + - + +
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.9 7.6 + - - +
33B PHE* 3.7 17.5 - - - -
34B LEU* 3.8 21.4 - - - +
46B ARG 2.9 13.2 + - - -
47B ALA* 3.1 25.8 - - - +
48B ASN 3.2 0.4 - - - -
49B LEU* 1.3 77.4 - - - +
51B SER* 1.3 62.2 + - - +
53B ILE* 3.8 3.3 - - - +
54B GLU* 3.0 33.3 + - - +
72B PHE* 5.5 6.6 - - - -
73B LEU* 3.8 27.2 - - + +
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Residues in contact with SER 51 (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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47B ALA 3.3 15.1 + - - -
48B ASN* 2.9 10.3 + - - -
49B LEU 2.9 0.6 - - - -
50B THR* 1.3 78.4 - - - +
52B ALA* 1.3 54.4 + - - +
53B ILE 2.7 14.8 + - - -
54B GLU* 3.0 16.9 + - - +
55B THR* 3.2 16.6 + - - -
73B LEU* 5.5 5.5 - - - +
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Residues in contact with ALA 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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3B ASP* 5.0 0.2 - - - +
48B ASN 3.5 5.1 + - - +
49B LEU* 3.0 15.9 + - + +
51B SER* 1.3 77.5 - - - +
53B ILE* 1.3 68.5 + - + +
55B THR* 4.3 8.0 - - - -
56B LEU* 3.4 19.2 + - - +
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Residues in contact with ILE 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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2B ASP 6.1 0.4 - - - -
3B ASP* 4.0 10.8 - - - +
6B LEU* 3.4 33.9 - - + +
30B LEU* 3.8 21.5 - - + -
33B PHE* 3.3 37.0 - - + -
49B LEU* 3.1 20.3 + - + +
50B THR 3.8 3.4 - - - +
51B SER 2.8 0.2 - - - -
52B ALA* 1.3 92.4 - - + +
54B GLU* 1.3 59.7 + - - +
55B THR 2.8 9.4 + - - -
56B LEU* 3.0 24.4 + - + +
57B CYS* 3.4 10.2 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.2 26.4 - - + +
50B THR* 3.0 22.2 + - - +
51B SER* 3.0 7.4 + - - +
53B ILE* 1.3 77.7 - - - +
55B THR* 1.3 57.8 + - - +
57B CYS* 4.4 4.0 - - - +
58B GLY* 3.2 20.5 + - - -
65B VAL* 5.6 1.1 - - - +
69B GLY* 3.1 36.1 - - - +
70B GLU* 3.4 8.3 + - - -
72B PHE* 4.8 0.9 - - - -
73B LEU* 3.2 30.5 - - - +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER 3.2 13.8 + - - -
52B ALA* 4.6 8.0 - - - -
53B ILE 2.8 0.4 - - - -
54B GLU* 1.3 77.9 - - - +
56B LEU* 1.3 69.1 + - + +
57B CYS 3.2 1.3 - - - -
58B GLY* 3.4 2.3 - - - +
59B VAL* 3.1 22.7 + - + +
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Residues in contact with LEU 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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3B ASP* 3.0 48.2 - - + +
6B LEU* 3.8 24.5 - - + -
7B ILE* 4.8 21.3 - - + +
52B ALA 3.4 22.4 - - - +
53B ILE* 3.0 7.6 + - + +
55B THR* 1.3 80.3 - - + +
57B CYS* 1.3 56.0 + - - +
59B VAL* 2.7 32.2 - - + +
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Residues in contact with CYS 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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6B LEU* 4.4 19.1 - - - -
7B ILE* 5.9 2.7 - - - -
10B PHE* 4.2 30.7 - - + -
26B ALA* 4.9 6.3 - - + -
29B THR* 4.1 19.7 - - - -
30B LEU* 5.2 7.0 - - + -
53B ILE 3.4 10.5 + - - +
54B GLU* 4.4 4.5 - - - +
55B THR 3.2 0.2 - - - -
56B LEU* 1.3 73.9 - - - +
58B GLY* 1.3 59.9 + - - +
59B VAL 2.6 18.1 + - - -
60B ASP* 3.1 21.8 + - - +
65B VAL* 4.1 14.6 - - + -
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Residues in contact with GLY 58 (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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54B GLU 3.2 14.6 + - - -
55B THR* 3.1 9.8 + - - -
57B CYS* 1.3 77.7 - - - +
59B VAL* 1.3 50.9 + - - +
60B ASP* 2.6 21.2 + - - +
62B SER 5.5 0.3 - - - +
65B VAL* 4.0 15.7 - - - +
66B SER* 5.5 7.4 - - - -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 3.1 9.3 + - + +
56B LEU* 2.7 32.3 - - + +
57B CYS 2.6 7.6 + - - +
58B GLY* 1.3 67.9 - - - +
60B ASP* 1.3 57.5 + - - +
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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