Contacts of the helix formed by residues 36 - 49 (chain A) in PDB entry 1MZW
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 VAL 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.0 14.5 + - + +
35A VAL* 1.3 88.8 - - + +
37A PRO* 1.3 61.9 - - - +
39A THR* 4.1 4.0 - - - -
40A ALA* 2.9 25.0 + - - +
98A GLU* 3.1 21.1 - - + +
99A ASN* 3.4 27.6 - - - +
139A VAL* 3.9 18.4 - - + -
140A VAL 3.9 5.4 - - - +
141A PHE* 3.7 35.7 - - + +
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Residues in contact with PRO 37 (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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33A ALA* 3.2 30.1 - - + +
34A ASP 4.9 0.7 - - - -
35A VAL 3.5 7.4 - - - +
36A VAL* 1.3 88.6 - - - +
38A LYS* 1.3 58.7 + - + +
40A ALA* 3.9 0.5 - - - +
41A GLU* 2.9 33.0 + - - +
98A GLU* 3.2 15.9 - - - +
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Residues in contact with LYS 38 (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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37A PRO* 1.3 76.2 - - + +
39A THR* 1.3 63.5 + - - +
41A GLU* 4.7 0.2 - - - -
42A ASN* 3.1 14.4 + - - +
91A TYR* 2.6 43.3 + - + +
95A PHE* 4.8 6.3 - - + -
96A ALA* 5.6 9.0 + - - +
98A GLU* 2.9 44.4 + - + +
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Residues in contact with THR 39 (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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36A VAL* 3.7 11.0 - - - +
38A LYS* 1.3 72.9 - - - +
40A ALA* 1.3 61.8 + - - +
42A ASN* 3.4 4.3 + - - +
43A PHE* 3.2 21.1 + - - +
95A PHE* 3.9 22.3 - - + -
98A GLU* 2.8 32.3 + - - +
112A MET* 3.5 36.2 - - + +
120A ASN* 5.9 0.7 + - - -
139A VAL* 4.2 8.9 - - + +
141A PHE* 3.8 18.8 - - + -
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Residues in contact with ALA 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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11A PRO* 5.8 1.3 - - + -
31A LEU* 3.4 32.5 - - + +
32A PHE 4.2 3.1 - - - +
33A ALA* 3.8 29.4 - - + +
36A VAL* 2.9 16.8 + - + +
37A PRO 3.9 1.6 - - - +
39A THR* 1.3 78.0 - - - +
41A GLU* 1.3 56.8 + - - +
43A PHE* 3.3 1.0 + - - +
44A ARG* 2.9 25.5 + - - +
141A PHE* 4.6 10.5 - - - +
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Residues in contact with GLU 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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37A PRO 2.9 19.5 + - - +
38A LYS* 3.8 3.6 - - - +
40A ALA* 1.3 74.5 - - - +
42A ASN* 1.3 64.6 + - - +
44A ARG* 2.8 44.2 + - - -
45A GLN* 2.9 48.2 + - - +
90A ILE* 4.1 7.0 - - + -
91A TYR* 4.1 4.5 - - - +
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Residues in contact with ASN 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 LYS 3.1 14.0 + - - +
39A THR 3.6 8.6 + - - +
41A GLU* 1.3 77.0 - - - +
43A PHE* 1.3 65.2 + - - +
45A GLN* 3.6 2.9 + - - +
46A PHE* 3.3 35.0 + - - -
60A TYR* 4.9 1.4 + - - -
89A SER* 3.3 6.6 - - - -
90A ILE* 2.9 42.3 + - - +
91A TYR* 4.0 10.3 - - + -
95A PHE* 3.8 17.2 - - + -
112A MET* 4.4 7.1 - - - +
121A GLY 3.0 25.2 + - - -
122A CYS* 4.7 1.0 - - - +
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Residues in contact with PHE 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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13A VAL* 4.1 10.1 - - + -
15A PHE* 3.4 28.7 - + - -
29A ILE* 4.7 4.3 - - + -
31A LEU* 3.7 21.3 - - + -
39A THR 3.2 10.9 + - - +
40A ALA 3.6 7.0 - - - +
41A GLU 3.2 0.4 - - - -
42A ASN* 1.3 79.6 - - - +
44A ARG* 1.3 64.6 + - - +
46A PHE* 3.0 12.5 + - - +
47A CYS* 3.1 31.2 + - - -
60A TYR* 3.3 24.4 - + - -
110A LEU* 4.4 8.7 - - + -
112A MET* 5.1 4.9 - - - -
124A PHE* 3.5 29.2 - + + -
141A PHE* 3.3 33.7 - + + -
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Residues in contact with ARG 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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11A PRO* 4.0 19.5 - - + +
13A VAL* 4.0 19.1 - - + -
31A LEU* 3.6 12.9 - - + +
40A ALA 2.9 21.1 + - - +
41A GLU* 2.8 44.1 + - - +
43A PHE* 1.3 71.5 - - - +
45A GLN* 1.3 63.6 + - - +
47A CYS* 2.9 6.4 + - - +
48A THR* 2.9 36.8 + - + +
50A GLU* 2.9 30.6 + - - -
176A GLU* 3.0 37.0 + - - +
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Residues in contact with GLN 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 GLU* 2.9 51.9 + - - +
42A ASN 3.9 4.3 - - - +
44A ARG* 1.3 83.9 - - - +
46A PHE* 1.3 59.2 + - - +
47A CYS 3.0 0.2 - - - -
48A THR* 3.3 8.8 + - - +
49A GLY* 2.8 28.1 + - - -
50A GLU* 3.4 14.5 + - + +
51A PHE* 3.4 33.1 + - + +
58A ILE 4.3 0.7 - - - +
90A ILE* 3.7 23.9 - - + +
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Residues in contact with PHE 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 ASN* 3.3 34.6 + - - -
43A PHE 3.0 3.6 + - - +
45A GLN* 1.3 79.2 - - - +
47A CYS* 1.3 58.5 + - - +
49A GLY 4.2 0.9 - - - -
51A PHE* 4.3 3.6 - + + -
58A ILE* 3.6 33.7 - - + -
59A GLY* 3.3 10.7 - - - -
60A TYR* 2.9 63.9 + - + +
79A PHE* 3.7 26.5 - + - -
88A ALA 3.7 13.9 - - - -
89A SER* 3.6 27.1 - - - -
90A ILE* 3.9 10.8 - - + -
122A CYS* 3.8 6.7 - - + -
121B PHE* 3.7 4.9 - - - -
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Residues in contact with CYS 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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13A VAL* 3.8 19.3 - - + -
15A PHE* 3.7 21.3 - - - -
43A PHE* 3.1 42.3 + - - -
44A ARG 2.9 10.4 + - - +
46A PHE* 1.3 79.8 - - - +
48A THR* 1.3 60.2 + - - +
49A GLY 3.5 0.2 - - - -
60A TYR* 3.9 2.5 - - - -
174A CYS* 3.4 16.9 - - - +
175A GLY* 3.3 36.4 + - - +
121B PHE* 3.6 3.3 - - - -
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Residues in contact with THR 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 ARG* 2.9 35.9 + - + +
45A GLN* 3.3 6.4 + - - -
47A CYS* 1.3 79.1 - - + +
49A GLY* 1.3 56.1 + - - +
50A GLU* 3.0 35.1 + - - +
175A GLY* 4.6 1.3 - - - -
176A GLU* 3.8 28.7 - - + +
119B THR* 4.2 19.2 - - + +
120B LEU 3.7 3.5 - - - +
121B PHE* 3.6 3.3 - - - +
122B GLY* 2.7 27.4 + - - -
123B GLU 4.4 0.5 + - - +
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Residues in contact with GLY 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 GLN 2.8 12.9 + - - -
47A CYS 3.5 2.6 - - - -
48A THR* 1.3 75.1 - - - +
50A GLU* 1.3 62.7 + - - +
51A PHE 3.2 5.6 + - - +
52A ARG* 4.5 4.9 + - - -
57A PRO* 3.4 22.1 - - - +
58A ILE 4.0 4.9 - - - -
121B PHE* 3.4 29.7 - - - -
122B GLY* 3.8 8.3 - - - -
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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