Contacts of the helix formed by residues 30 - 42 (chain w) in PDB entry 5Z58
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 LYS 30 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26w MET* 3.3 17.2 + - - +
27w LEU 4.2 3.4 + - - +
28w THR 4.1 0.8 - - - -
29w LYS* 1.3 67.9 - - - +
31w SER* 1.3 66.6 + - - +
33w LEU* 2.9 17.7 + - - +
34w ARG* 2.9 14.8 + - + +
58w ARG* 4.5 25.5 - - + +
59w ASP 4.6 13.2 - - - +
60w LEU* 4.8 8.7 - - + +
65w ASP* 5.2 3.2 - - + +
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Residues in contact with SER 31 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29w LYS* 2.9 7.8 + - - -
30w LYS* 1.3 76.4 - - - +
32w THR* 1.3 60.5 + - - +
34w ARG* 3.0 10.3 + - - -
35w ASP* 2.7 38.3 + - - +
58w ARG* 5.6 9.3 - - - +
68w ARG* 6.1 5.8 - - - -
84w PHE* 5.7 8.1 - - - -
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Residues in contact with THR 32 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25w GLU* 5.1 4.5 - - - -
26w MET* 4.7 13.5 - - - -
29w LYS* 2.9 17.0 + - - +
31w SER* 1.3 78.7 - - - +
33w LEU* 1.3 59.8 + - - +
35w ASP* 4.3 2.9 - - - +
36w GLN* 3.6 17.0 + - - +
84w PHE* 5.5 15.1 - - - +
87w ARG* 5.7 8.1 - - - -
88w LEU* 5.7 9.4 - - - +
254w GLU* 5.4 1.9 - - - +
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Residues in contact with LEU 33 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244u CYS* 5.0 14.4 - - + -
26w MET* 4.7 17.2 - - + +
30w LYS* 2.9 8.7 + - - +
32w THR* 1.3 76.0 - - - +
34w ARG* 1.3 57.7 + - - +
36w GLN* 3.0 8.2 + - - +
37w ILE* 2.6 38.2 + - + +
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Residues in contact with ARG 34 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30w LYS* 2.9 17.2 + - + +
31w SER* 3.6 8.7 - - - +
33w LEU* 1.3 77.2 - - - +
35w ASP* 1.3 67.7 + - - +
37w ILE* 2.9 6.1 + - - +
38w ASN* 2.8 23.0 + - - +
55w GLY* 5.0 16.8 - - - +
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Residues in contact with ASP 35 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31w SER* 2.7 23.9 + - - +
32w THR* 4.3 3.1 - - - +
34w ARG* 1.3 73.1 - - - +
36w GLN* 1.3 69.1 + - - +
38w ASN* 3.0 13.0 + - - +
39w SER* 3.3 10.1 + - - -
84w PHE* 6.3 2.9 - - + -
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Residues in contact with GLN 36 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32w THR 3.6 13.5 + - - +
33w LEU* 3.0 10.4 + - - +
35w ASP* 1.3 81.7 - - - +
37w ILE* 1.3 66.2 + - - +
39w SER* 3.0 15.6 + - - -
40w ASP* 3.0 12.5 + - - +
252w TRP* 6.3 3.1 - - - -
254w GLU* 3.8 28.0 - - + -
255w LEU* 5.6 4.4 - - + +
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Residues in contact with ILE 37 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33w LEU* 2.6 21.6 + - + +
34w ARG* 3.6 6.7 - - - +
36w GLN* 1.3 71.5 - - - +
38w ASN* 1.3 64.8 + - - +
40w ASP* 2.9 11.9 + - - +
41w HIS* 2.8 21.9 + - - +
47w GLN* 5.6 1.2 - - - +
48w ASP 5.7 2.5 - - - +
49w ARG* 5.3 11.9 - - + -
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Residues in contact with ASN 38 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34w ARG 2.8 12.0 + - - +
35w ASP* 3.4 11.4 - - - +
37w ILE* 1.3 74.8 - - - +
39w SER* 1.3 63.8 + - - +
41w HIS* 2.9 24.2 - - - +
42w ARG* 3.6 4.0 + - - +
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Residues in contact with SER 39 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35w ASP 3.3 6.0 + - - -
36w GLN* 3.0 11.2 + - - -
38w ASN* 1.3 77.5 - - - +
40w ASP* 1.3 65.2 + - - +
42w ARG* 2.9 20.0 + - - +
43w THR* 3.5 8.4 + - - -
252w TRP* 5.2 14.8 - - - -
255w LEU* 6.3 2.0 - - - -
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Residues in contact with ASP 40 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36w GLN 3.0 11.1 + - - +
37w ILE* 2.9 15.0 + - - +
39w SER* 1.3 76.0 - - - +
41w HIS* 1.3 63.4 + - - +
43w THR* 2.9 8.1 + - - +
44w ARG* 2.9 29.5 + - + +
47w GLN* 4.8 9.6 - - + -
255w LEU* 5.3 12.9 - - + +
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Residues in contact with HIS 41 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37w ILE 2.8 10.8 + - - +
38w ASN* 2.9 19.3 + - - +
40w ASP* 1.3 78.8 - - - +
42w ARG* 1.3 57.5 + - + +
43w THR 3.5 0.5 + - - -
44w ARG 3.5 15.1 - - - +
45w ALA* 3.6 14.2 - - - +
47w GLN* 4.5 15.4 - - + +
49w ARG* 5.2 11.2 - - + -
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Residues in contact with ARG 42 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38w ASN 3.6 3.6 + - - +
39w SER* 2.9 11.7 + - - +
41w HIS* 1.3 77.9 - - + +
43w THR* 1.3 59.1 + - - +
45w ALA 5.2 0.7 - - - -
333w ILE* 5.9 9.3 - - + +
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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