Contacts of the helix formed by residues 38 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A SER* 1.3 62.5 + - - +
40A LEU* 3.4 3.3 - - - +
41A LYS* 3.4 29.2 + - - +
42A THR* 2.7 39.6 + - - -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 1.3 78.0 + - - +
40A LEU* 1.3 56.9 + - - +
42A THR* 2.9 11.6 + - - -
43A CYS* 2.8 30.0 + - - -
127A THR* 3.8 19.2 - - - +
130A LEU* 4.3 21.0 - - - +
131A GLU* 2.7 30.5 + - - -
134A ASN* 5.4 0.2 + - - -
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Residues in contact with LEU 40 (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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38A ASN 3.4 1.9 - - - +
39A SER* 1.3 80.5 + - - +
41A LYS* 1.3 59.5 + - + +
43A CYS* 3.1 8.1 + - + +
44A TYR* 2.9 49.9 + - + -
67A ASN* 3.7 40.4 - - + +
71A ILE* 5.0 6.3 - - + -
131A GLU* 3.3 34.9 + - + +
368B THR* 4.3 13.7 - - - +
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Residues in contact with LYS 41 (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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38A ASN* 3.4 32.2 + - - +
39A SER 3.1 0.4 - - - -
40A LEU* 1.3 79.5 - - + +
42A THR* 1.3 63.0 + - - +
44A TYR* 3.1 4.2 + - - +
45A LYS* 2.9 21.8 + - - +
361B GLN* 5.5 6.9 - - - +
364B SER* 5.2 15.7 - - - +
365B THR* 4.3 17.5 + - - +
367B ARG* 6.0 0.3 - - - -
368B THR* 3.2 34.7 - - + +
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Residues in contact with THR 42 (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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38A ASN* 2.7 33.5 + - - -
39A SER* 2.9 9.3 + - - -
41A LYS* 1.3 74.7 - - - +
43A CYS* 1.3 64.0 + - - +
45A LYS* 3.0 18.2 + - - +
46A TYR* 2.9 63.1 + - + +
124A ASP* 4.0 6.7 - - - +
127A THR* 3.9 9.8 - - + +
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Residues in contact with CYS 43 (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 SER 2.8 16.5 + - - -
40A LEU* 3.3 11.2 - - + +
42A THR* 1.3 76.5 - - - +
44A TYR* 1.3 56.9 + - - +
46A TYR* 3.3 5.1 + - - -
47A LEU* 2.9 24.4 + - - +
70A CYS* 4.4 5.4 - - - -
71A ILE* 3.9 19.3 - - + -
74A LEU* 3.1 24.0 - - + +
127A THR* 3.9 15.7 - - - -
128A ILE* 4.0 15.5 - - - -
131A GLU* 3.7 23.6 - - - -
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Residues in contact with TYR 44 (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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40A LEU* 2.9 39.3 + - + -
41A LYS 3.1 0.2 + - - -
43A CYS* 1.3 74.9 - - - +
45A LYS* 1.3 60.5 + - - +
46A TYR 3.3 0.2 - - - -
47A LEU* 3.5 7.5 + - + +
48A ASN* 2.7 35.0 + - - -
58A ILE* 5.4 0.2 - - + -
59A GLN* 3.7 36.6 - - + -
66A ARG* 3.3 37.5 + - + +
67A ASN* 2.7 36.4 + - - -
70A CYS* 3.7 25.3 - - + +
367B ARG* 4.0 11.2 - - + -
368B THR* 3.4 34.3 - - + -
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Residues in contact with LYS 45 (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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41A LYS 2.9 12.4 + - - +
42A THR* 3.0 18.9 + - - +
44A TYR* 1.3 75.6 - - - +
46A TYR* 1.3 86.7 + - - +
48A ASN* 3.4 7.6 + - - +
49A GLN* 3.0 55.7 + - + +
346B TYR* 4.7 17.0 - - + +
364B SER* 5.9 0.9 - - - +
367B ARG* 4.7 16.7 - - - +
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Residues in contact with TYR 46 (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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42A THR* 2.9 32.3 + - + +
43A CYS* 3.6 7.0 - - - +
45A LYS* 1.3 99.7 + - - +
47A LEU* 1.3 56.1 + - - +
49A GLN* 2.8 23.4 + - - +
50A THR* 2.7 41.1 + - + +
74A LEU* 3.9 14.1 - - + -
120A GLN* 4.4 19.1 + - + +
121A VAL* 4.9 8.1 - - + -
124A ASP* 2.5 44.1 + - + +
127A THR* 5.0 2.2 - - - -
128A ILE* 4.1 27.6 - - + -
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Residues in contact with LEU 47 (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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43A CYS 2.9 16.5 + - - +
44A TYR* 3.6 19.1 - - + +
45A LYS 3.3 0.2 - - - -
46A TYR* 1.3 76.6 - - - +
48A ASN* 1.3 57.9 + - - +
50A THR* 3.2 6.3 + - - -
51A SER* 2.8 34.0 + - - -
55A ALA* 4.1 23.8 - - + +
58A ILE* 4.0 29.6 - - + -
59A GLN* 4.4 1.3 - - - +
70A CYS* 3.9 27.8 - - - +
73A TYR* 3.4 42.2 - - + -
74A LEU* 3.7 5.5 - - + +
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Residues in contact with ASN 48 (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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44A TYR 2.7 25.0 + - - +
45A LYS 3.8 4.0 - - - +
46A TYR 3.2 0.2 - - - -
47A LEU* 1.3 79.5 - - - +
49A GLN* 1.3 59.8 + - + +
51A SER 2.5 24.7 - - - +
55A ALA* 3.2 20.3 - - - +
56A ALA 4.8 1.0 + - - -
59A GLN* 2.9 25.8 + - - +
343B GLU* 3.2 36.9 - - + +
347B HIS* 5.7 2.8 + - - -
367B ARG* 3.3 21.1 - - - +
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Residues in contact with GLN 49 (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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45A LYS* 3.0 48.3 + - + +
46A TYR* 2.8 27.3 + - - +
48A ASN* 1.3 79.9 - - + +
50A THR* 1.3 61.7 + - + +
51A SER 4.9 0.9 - - - +
117A LYS* 5.8 4.2 - - - -
118A ASP* 4.7 4.3 - - - +
120A GLN* 4.9 10.4 - - - +
346B TYR* 5.9 0.6 + - + -
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Residues in contact with THR 50 (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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46A TYR* 2.7 24.0 + - + +
47A LEU* 3.2 9.4 + - - -
49A GLN* 1.3 77.2 - - + +
51A SER* 1.3 57.2 + - - +
52A ARG 4.3 0.4 - - - -
73A TYR* 3.2 21.5 + - - -
74A LEU* 4.0 9.0 - - + +
77A ARG* 3.0 52.3 + - + +
118A ASP* 4.1 24.9 - - + +
121A VAL* 4.9 7.6 - - + -
991A IN0 4.7 4.7 - - - +
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Residues in contact with SER 51 (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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47A LEU* 2.8 16.9 + - - -
48A ASN* 2.5 26.2 - - - +
49A GLN 3.3 1.3 - - - -
50A THR* 1.3 80.8 - - - +
52A ARG* 1.3 62.4 + - - +
53A SER 3.5 0.2 - - - -
54A PHE* 3.3 30.3 + - - +
55A ALA* 3.4 17.9 + - - +
58A ILE* 5.9 0.2 - - - -
73A TYR* 3.2 22.2 + - - -
991A IN0 4.2 5.2 + - - -
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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