Contacts of the helix formed by residues 38 - 48 (chain G) in PDB entry 6WNX
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 38 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G ASP* 4.7 3.8 - - - -
8G THR* 4.6 3.8 - - - -
35G GLU 3.6 6.6 - - - +
36G LEU 3.4 2.8 - - - -
37G VAL* 1.3 83.4 - - - +
39G LYS* 1.3 67.7 + - - +
40G GLU* 3.9 9.9 - - - -
41G TRP* 3.2 40.2 + - - +
42G GLN 3.1 17.0 + - - -
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Residues in contact with LYS 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PRO* 6.0 0.8 - - - +
368A SER* 3.8 28.2 + - - -
38G CYS* 1.3 74.6 - - - +
40G GLU* 1.3 52.6 + - - +
42G GLN* 3.3 21.5 + - - +
43G ARG* 2.7 34.6 + - - +
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Residues in contact with GLU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G ILE 4.5 3.1 - - - +
8G THR* 3.4 39.5 - - + +
11G PRO* 3.7 14.6 - - - +
38G CYS* 3.2 7.3 - - - -
39G LYS* 1.3 76.2 - - - +
41G TRP* 1.3 60.0 + - + +
43G ARG* 2.9 45.7 + - - +
44G VAL* 2.9 33.7 + - + +
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Residues in contact with TRP 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ASP* 2.7 34.3 + - - -
6G PHE 5.4 1.3 - - - -
7G ILE* 3.4 44.8 - - + +
8G THR* 4.0 7.0 - - - -
23G LEU* 4.6 8.0 - - + +
26G LEU* 6.2 0.4 - - + -
34G ALA* 3.4 41.5 - - + +
37G VAL* 3.7 29.7 - - + +
38G CYS* 3.2 26.6 + - - +
40G GLU* 1.3 71.8 - - - +
42G GLN* 1.3 64.9 + - - +
44G VAL* 3.2 2.4 + - - +
45G ILE* 3.0 30.6 + - + +
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Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G GLU* 3.4 40.6 + - + +
38G CYS 3.1 6.1 + - - +
39G LYS* 3.4 24.5 - - - +
41G TRP* 1.3 78.0 - - - +
43G ARG* 1.3 57.8 + - - +
45G ILE* 3.4 4.9 + - - +
46G SER* 2.9 35.5 + - - -
93G ARG* 5.9 4.4 - - - +
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G PRO* 3.9 5.3 - - - +
16G ASP* 3.3 26.0 + - - -
39G LYS 2.7 17.4 + - - +
40G GLU* 2.9 45.3 + - - +
42G GLN* 1.3 73.1 - - - +
44G VAL* 1.3 74.7 + - - +
46G SER* 3.3 4.9 + - - -
47G GLU* 2.8 77.4 + - + +
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Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 3.9 28.5 - - + +
11G PRO* 4.0 7.0 - - + -
16G ASP* 4.9 3.6 - - + +
19G ALA* 4.4 4.0 - - + -
20G GLU* 4.1 26.6 - - + +
23G LEU* 3.7 22.4 - - + -
40G GLU* 2.9 19.0 + - - +
41G TRP 3.2 6.7 + - - +
43G ARG* 1.3 97.1 - - - +
45G ILE* 1.3 58.3 + - - +
47G GLU* 5.0 0.7 - - - -
48G GLY* 2.7 34.3 + - - +
50G LEU* 3.8 1.0 - - - +
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Residues in contact with ILE 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU* 3.8 17.9 - - + -
31G LEU* 3.8 15.5 - - + +
34G ALA* 3.7 18.4 - - + -
35G GLU* 3.5 46.2 - - + +
41G TRP* 3.0 18.9 + - + +
42G GLN* 3.6 6.1 - - - +
44G VAL* 1.3 74.5 - - - +
46G SER* 1.3 64.7 + - - +
49G MET 3.4 2.3 + - - -
50G LEU* 3.2 40.2 + - + +
51G TRP* 3.8 30.1 - - + +
89G ASN* 4.0 2.1 + - - +
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Residues in contact with SER 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G GLN* 2.9 22.4 + - - -
43G ARG* 3.5 7.2 - - - -
45G ILE* 1.3 79.5 - - - +
47G GLU* 1.3 63.1 + - - +
49G MET* 3.3 5.5 + - - +
89G ASN* 3.1 42.6 + - - +
90G SER 5.3 1.2 + - - -
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLU* 4.4 3.6 - - - +
43G ARG* 2.8 64.5 + - + +
44G VAL* 4.5 1.1 - - - +
46G SER* 1.3 70.5 - - - +
48G GLY* 1.3 62.4 + - - +
49G MET* 3.1 16.4 + - - +
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Residues in contact with GLY 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLU* 3.3 30.3 + - - -
44G VAL 2.7 21.7 + - - -
47G GLU* 1.3 69.5 - - - +
49G MET* 1.3 69.4 + - - +
50G LEU* 3.3 9.1 + - - +
53G LYS* 3.1 25.1 + - - +
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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