Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 3MPZ
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 CYS 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS 4.4 0.5 - - - +
42A ASN* 4.1 6.1 - - - -
51A GLY 6.0 0.2 - - - -
52A LEU* 1.3 76.5 - - - +
54A ALA* 1.3 66.6 + - - +
55A GLU* 3.6 4.9 - - - +
56A CYS* 3.0 17.4 + - - +
57A ALA* 3.1 12.1 + - - +
88A ARG* 3.5 20.6 - - - +
89A CYS* 3.2 13.9 - - - -
300A ZN 2.3 36.6 - - - -
47B SER* 3.7 15.0 - - - -
49B GLY 5.9 1.1 - - - -
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Residues in contact with ALA 54 (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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26A VAL* 3.8 21.7 - - + +
28A ALA* 3.8 13.7 - - + +
40A GLY* 3.4 19.2 - - - +
41A CYS* 3.6 13.7 - - - +
42A ASN* 3.7 18.5 - - - +
53A CYS* 1.3 72.1 - - - +
55A GLU* 1.3 65.2 + - - +
57A ALA* 3.1 5.2 + - - +
58A VAL* 2.9 29.6 + - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.7 1.7 - - - +
28A ALA* 4.4 10.5 - - + -
53A CYS* 3.6 6.6 - - - +
54A ALA* 1.3 85.0 + - - +
56A CYS* 1.3 63.8 + - - +
58A VAL* 3.3 12.2 + - - +
59A VAL* 3.2 27.5 + - - +
73A LEU* 4.5 11.7 - - + -
75A CYS* 4.0 17.4 - - - -
85A PRO* 3.3 31.3 - - + +
86A CYS 3.9 0.5 + - - -
89A CYS* 3.5 28.0 - - + +
92A VAL* 5.8 0.9 - - - -
93A LEU* 4.3 22.5 - - + +
300A ZN 3.8 2.9 - - - -
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Residues in contact with CYS 56 (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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52A LEU* 4.8 7.6 - - + -
53A CYS 3.0 17.8 + - - +
55A GLU* 1.3 77.4 - - - +
57A ALA* 1.3 62.2 + - - +
59A VAL* 3.2 8.0 + - - +
60A CYS* 3.0 27.7 + - - -
88A ARG* 3.4 46.0 - - - -
89A CYS* 4.1 5.2 - - - -
92A VAL* 4.9 7.9 - - - -
52D LEU* 3.9 30.4 - - + +
60D CYS* 4.9 1.1 - - - -
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Residues in contact with ALA 57 (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 THR 4.2 3.4 - - - +
40A GLY* 3.7 16.6 - - - -
41A CYS 3.8 14.4 - - - +
53A CYS 3.1 6.7 + - - +
54A ALA 3.1 9.4 + - - +
56A CYS* 1.3 76.0 - - - +
58A VAL* 1.3 62.3 + - - +
60A CYS* 3.3 3.8 + - - +
61A ALA* 3.0 23.7 + - - +
60D CYS* 3.5 40.8 - - + +
64D SER* 5.8 0.4 - - - -
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Residues in contact with VAL 58 (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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28A ALA* 3.5 37.0 - - + +
29A ALA 4.4 1.1 - - - +
30A ALA* 3.7 27.1 - - + -
38A VAL* 3.8 11.9 - - + +
39A THR* 3.6 10.5 - - - -
40A GLY 3.5 8.3 - - - +
54A ALA 2.9 16.3 + - - +
55A GLU* 3.4 10.8 - - - +
56A CYS 3.2 0.2 - - - -
57A ALA* 1.3 76.6 - - - +
59A VAL* 1.3 57.5 + - + +
61A ALA* 3.2 4.1 + - - +
62A LEU* 2.8 27.2 + - - +
70A LEU* 4.4 10.3 - - + -
73A LEU* 4.1 10.5 - - + -
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Residues in contact with VAL 59 (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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55A GLU 3.2 13.4 + - - +
56A CYS 3.2 9.0 + - - +
58A VAL* 1.3 72.3 - - - +
60A CYS* 1.3 67.6 + - - +
62A LEU* 3.4 8.9 + - - +
63A HIS* 3.4 21.2 + - + -
70A LEU* 4.2 9.6 - - + -
92A VAL* 3.9 21.5 - - + -
93A LEU* 3.8 22.2 - - + -
96A HIS* 3.4 39.7 - - + +
43D VAL* 3.7 15.7 - - + +
52D LEU* 4.9 2.2 - - + -
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Residues in contact with CYS 60 (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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52A LEU* 6.4 0.2 - - - -
56A CYS* 3.0 20.4 + - - -
57A ALA* 3.3 11.6 + - - +
59A VAL* 1.3 77.2 - - - +
61A ALA* 1.3 56.7 + - - +
63A HIS* 3.3 4.0 + - - +
64A SER* 2.9 30.8 + - - -
41D CYS* 5.0 2.3 - - - +
43D VAL* 4.4 11.9 - - - -
52D LEU* 4.0 29.8 - - - -
56D CYS* 5.0 0.7 - - - -
57D ALA* 3.6 42.4 - - + +
60D CYS* 4.8 6.1 - - + -
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Residues in contact with ALA 61 (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 ARG* 3.5 6.1 + - - -
38A VAL* 4.1 15.3 - - + +
39A THR 4.1 15.3 - - - +
57A ALA 3.0 17.2 + - - +
58A VAL 3.6 4.0 - - - +
60A CYS* 1.3 72.5 - - - +
62A LEU* 1.3 66.7 + - - +
64A SER* 3.5 9.6 + - - +
65A GLY* 2.9 19.9 + - - -
64D SER* 6.1 0.7 - - - +
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Residues in contact with LEU 62 (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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32A VAL* 3.8 28.3 - - + -
36A ARG* 2.9 18.3 + - - +
38A VAL* 4.2 5.5 - - + +
58A VAL 2.8 13.5 + - - +
59A VAL* 3.4 11.0 - - - +
61A ALA* 1.3 75.4 - - - +
63A HIS* 1.3 77.9 + - + +
67A GLY* 2.8 40.2 + - - +
68A GLY 3.7 23.6 - - - +
70A LEU* 3.9 22.2 - - + -
96A HIS* 3.8 22.7 - - + +
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Residues in contact with HIS 63 (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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59A VAL* 3.4 18.8 + - + +
60A CYS 3.3 6.2 + - - +
61A ALA 3.2 0.2 - - - -
62A LEU* 1.3 88.9 - - + +
64A SER* 1.3 64.8 + - - +
65A GLY 3.1 1.8 - - - -
66A GLY 3.0 11.4 + - - -
67A GLY* 3.5 14.4 + - - +
68A GLY 4.6 7.6 - - - -
96A HIS* 3.0 38.2 + + - -
16D HIS* 3.1 36.3 + - - +
18D TYR* 4.0 23.5 - + + +
41D CYS* 4.0 9.4 - - - -
43D VAL* 4.0 14.6 - - + -
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Residues in contact with SER 64 (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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60A CYS 2.9 22.8 + - - -
61A ALA* 3.5 10.7 - - - +
63A HIS* 1.3 73.8 - - - +
65A GLY* 1.3 59.3 + - - +
66A GLY 3.3 1.3 + - - -
13D VAL* 3.8 29.6 - - - +
16D HIS* 4.1 12.6 + - - -
39D THR* 4.4 12.2 + - - -
40D GLY* 4.3 15.7 - - - -
41D CYS* 3.8 5.7 - - - -
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Residues in contact with GLY 65 (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 ARG* 3.5 23.9 + - - -
61A ALA 2.9 17.9 + - - -
63A HIS 3.1 0.2 + - - -
64A SER* 1.3 79.5 + - - +
66A GLY* 1.3 54.4 + - - +
16D HIS* 5.6 0.2 - - - -
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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