Contacts of the helix formed by residues 38 - 51 (chain C) in PDB entry 1EZF
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 ASN 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C SER* 1.3 63.8 + - - +
40C LEU* 3.3 5.9 - - - +
41C LYS* 3.4 27.0 + - - +
42C THR* 2.8 33.7 + - - +
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 1.3 76.1 + - - +
40C LEU* 1.3 60.7 + - - +
42C THR* 3.3 2.9 + - - -
43C CYS* 2.9 32.1 + - - -
127C THR* 3.7 21.2 - - - +
130C LEU* 3.6 24.7 - - - +
131C GLU* 2.9 25.7 + - - -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 4.2 16.2 - - + +
38C ASN 3.3 3.2 - - - +
39C SER* 1.3 80.2 + - - +
41C LYS* 1.3 64.7 + - + +
43C CYS* 3.1 10.1 + - + +
44C TYR* 3.0 47.1 + - + -
67C ASN* 3.5 35.4 - - + +
70C CYS* 5.8 0.2 - - - -
71C ILE* 4.9 6.3 - - + -
131C GLU* 3.4 34.6 - - + +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLN* 2.8 34.1 + - - +
364A SER* 4.0 24.3 + - - +
365A THR* 3.8 16.2 + - - +
367A ARG* 5.0 2.3 + - - -
368A THR* 3.5 33.3 - - + +
38C ASN* 3.4 27.6 + - - +
39C SER 3.2 0.2 - - - -
40C LEU* 1.3 78.4 - - + +
42C THR* 1.3 63.8 + - - +
44C TYR* 3.0 4.5 + - - +
45C LYS* 2.9 21.4 + - - +
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Residues in contact with THR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 2.8 23.3 + - - +
39C SER* 3.6 5.9 - - - -
41C LYS* 1.3 75.3 - - - +
43C CYS* 1.3 63.1 + - - +
45C LYS* 3.1 20.0 + - - +
46C TYR* 3.0 58.0 + - + +
124C ASP* 4.0 1.8 - - - +
127C THR* 3.8 16.2 - - + +
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Residues in contact with CYS 43 (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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39C SER 2.9 20.5 + - - -
40C LEU* 3.1 13.2 + - + +
42C THR* 1.3 77.6 - - - +
44C TYR* 1.3 57.8 + - - +
46C TYR* 3.3 4.8 + - - +
47C LEU* 2.9 24.4 + - - +
70C CYS* 4.3 4.9 - - - -
71C ILE* 3.7 20.9 - - + -
74C LEU* 3.3 24.6 - - + +
127C THR* 3.8 13.5 - - - -
128C ILE* 4.0 13.5 - - - -
131C GLU* 3.5 22.2 - - - -
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Residues in contact with TYR 44 (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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367A ARG* 3.5 25.8 - - - -
368A THR* 3.3 31.6 - - + -
40C LEU* 3.0 42.2 + - + -
41C LYS 3.0 1.5 + - - +
43C CYS* 1.3 72.7 - - - +
45C LYS* 1.3 62.6 + - - +
47C LEU* 3.3 12.9 + - + +
48C ASN* 2.7 34.9 + - - -
58C ILE* 5.4 0.4 - - + -
59C GLN* 3.7 32.1 - - + -
66C ARG* 3.3 26.7 - - + +
67C ASN* 2.8 33.4 + - - -
70C CYS* 4.0 20.6 - - + -
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Residues in contact with LYS 45 (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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346A TYR* 3.8 26.2 - - + +
364A SER* 5.9 0.2 - - - +
367A ARG* 3.5 22.3 - - - +
41C LYS 2.9 11.5 + - - +
42C THR* 3.4 19.9 - - - +
44C TYR* 1.3 75.1 - - - +
46C TYR* 1.3 76.7 + - + +
48C ASN* 3.0 6.2 + - - +
49C GLN* 2.9 50.6 + - + +
120C GLN* 5.1 2.2 + - - -
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Residues in contact with TYR 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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42C THR* 3.0 35.6 + - + +
43C CYS* 3.5 8.5 - - - +
45C LYS* 1.3 88.5 + - + +
47C LEU* 1.3 51.8 + - - +
49C GLN* 3.1 24.6 + - + +
50C THR* 2.7 45.7 + - + +
74C LEU* 4.0 11.2 - - + -
120C GLN* 2.8 42.7 + - + -
121C VAL* 5.0 5.4 - - + -
124C ASP* 2.6 45.4 + - + +
127C THR* 4.8 0.9 - - - -
128C ILE* 4.2 22.9 - - + -
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Residues in contact with LEU 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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43C CYS 2.9 14.2 + - - +
44C TYR* 3.5 24.9 - - + +
45C LYS 3.2 0.2 - - - -
46C TYR* 1.3 74.7 - - - +
48C ASN* 1.3 58.4 + - - +
50C THR* 3.2 5.8 + - - -
51C SER* 2.9 35.7 + - - -
55C ALA* 3.8 24.7 - - + +
58C ILE* 3.8 33.0 - - + -
59C GLN* 4.5 2.2 - - - +
70C CYS* 3.8 26.9 - - - +
73C TYR* 3.6 35.4 - - + -
74C LEU* 3.7 4.7 - - + +
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Residues in contact with ASN 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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343A GLU* 3.4 39.9 - - + +
347A HIS* 5.2 9.4 + - + +
367A ARG* 3.2 19.9 - - - +
44C TYR 2.7 23.2 + - - +
45C LYS 3.0 7.0 + - - +
47C LEU* 1.3 78.8 - - - +
49C GLN* 1.3 58.9 + - - +
51C SER 3.2 18.7 - - - +
55C ALA* 3.3 20.0 - - - +
56C ALA 4.9 0.7 + - - -
59C GLN* 2.9 26.9 + - - +
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Residues in contact with GLN 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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347A HIS* 5.7 5.2 - - - +
45C LYS* 2.9 35.4 + - + +
46C TYR* 3.3 38.8 - - - +
48C ASN* 1.3 75.9 - - - +
50C THR* 1.3 63.9 + - + +
51C SER 3.5 0.4 - - - -
117C LYS* 4.9 10.4 + - - -
118C ASP* 4.5 4.2 - - - +
120C GLN* 3.6 22.8 + - - +
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Residues in contact with THR 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 TYR* 2.7 30.0 + - + +
47C LEU* 3.2 12.3 + - - -
49C GLN* 1.3 85.7 - - + +
51C SER* 1.3 58.5 + - - +
52C ARG* 4.1 1.9 + - - +
73C TYR* 4.0 7.2 - - - -
74C LEU* 3.8 10.0 - - + +
77C ARG* 2.8 48.1 + - + -
118C ASP* 3.5 31.4 - - + +
120C GLN* 6.5 0.9 - - + -
121C VAL* 5.0 8.7 - - + +
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 2.9 17.7 + - - -
48C ASN* 3.2 15.7 - - - +
49C GLN 3.5 0.6 - - - -
50C THR* 1.3 77.0 - - - +
52C ARG* 1.3 65.4 + - - +
53C SER* 3.2 1.7 + - - -
54C PHE* 3.1 18.7 + - - +
55C ALA* 3.1 32.5 + - - +
73C TYR* 3.6 22.9 + - - -
995C IN0 3.8 2.5 + - - -
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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