Contacts of the helix formed by residues 38 - 51 (chain G) in PDB entry 4UIS
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 SER 38 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34G THR* 3.9 1.7 - - - +
36G SER* 3.2 14.0 - - - +
37G PRO* 1.3 81.6 - - - +
39G LEU* 1.3 61.6 - - - +
40G ASN* 3.4 24.3 + - - +
41G ALA* 3.4 24.3 + - - +
42G ALA 3.9 2.1 + - - -
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Residues in contact with LEU 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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17G ILE* 3.5 31.2 - - + -
25G TYR* 3.5 37.5 - - + +
37G PRO 3.2 5.6 + - - -
38G SER* 1.3 70.5 - - - +
40G ASN* 1.3 61.8 + - - +
42G ALA* 2.8 26.0 + - + +
43G LYS* 2.9 36.1 + - - +
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Residues in contact with ASN 40 (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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38G SER* 3.2 11.2 + - - +
39G LEU* 1.3 80.6 - - - +
41G ALA* 1.3 57.0 + - - +
43G LYS* 3.4 27.0 + - - +
44G SER* 2.9 30.3 + - - -
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Residues in contact with ALA 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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34G THR* 3.8 18.4 - - + +
36G SER* 4.4 9.0 - - - -
38G SER* 3.4 20.6 + - - +
39G LEU 3.1 0.6 - - - -
40G ASN* 1.3 77.2 - - - +
42G ALA* 1.3 58.2 + - - +
44G SER* 3.8 5.5 - - - -
45G GLU* 2.9 38.1 + - + +
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Residues in contact with ALA 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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17G ILE* 4.5 0.7 - - + -
25G TYR* 4.1 9.4 - - + -
33G LEU* 3.2 41.7 - - + +
34G THR* 3.6 14.6 - - + +
39G LEU* 2.8 29.3 + - + +
41G ALA* 1.3 79.2 - - - +
43G LYS* 1.3 56.2 + - - +
46G LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 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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17G ILE* 3.6 20.6 - - + -
39G LEU* 2.9 33.5 + - + +
40G ASN* 3.7 26.4 + - - +
42G ALA* 1.3 76.3 - - - +
44G SER* 1.3 58.1 + - - +
46G LEU* 3.4 9.7 - - + +
47G ASP* 2.8 36.3 + - - +
55G ASN* 3.3 40.9 + - - +
56G GLY* 4.5 6.3 - - - +
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Residues in contact with SER 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ASN 2.9 18.0 + - - -
41G ALA* 3.8 7.0 - - - -
43G LYS* 1.3 74.1 - - - +
45G GLU* 1.3 62.8 + - - +
46G LEU 3.1 1.1 - - - -
47G ASP* 2.8 29.6 + - - +
48G LYS* 2.9 27.0 + - - +
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Residues in contact with GLU 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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33G LEU* 3.9 29.2 - - + +
34G THR* 5.1 3.4 - - - -
41G ALA* 2.9 23.1 + - + +
42G ALA 4.1 2.5 - - - +
44G SER* 1.3 76.6 + - - +
46G LEU* 1.3 57.6 + - - +
48G LYS* 2.8 35.9 + - - +
49G ALA* 2.9 29.2 + - - +
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Residues in contact with LEU 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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17G ILE* 3.7 19.3 - - + -
27G ILE* 3.6 44.4 - - + -
33G LEU* 4.0 8.9 - - + +
42G ALA 2.9 19.7 + - - +
43G LYS* 3.4 7.4 - - - +
45G GLU* 1.3 78.2 - - - +
47G ASP* 1.3 56.7 + - - +
49G ALA* 4.2 2.5 - - + -
50G ILE* 2.9 60.1 + - + +
52G ARG 4.3 0.2 - - - +
54G CYS* 3.6 29.4 - - + -
55G ASN 5.1 0.2 - - - +
56G GLY 4.4 4.7 - - - +
58G ILE* 4.8 2.7 - - + -
66G LEU* 4.3 7.9 - - + -
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Residues in contact with ASP 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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43G LYS* 2.8 26.5 + - - +
44G SER* 2.8 20.8 + - - +
46G LEU* 1.3 76.5 - - - +
48G LYS* 1.3 58.5 + - + +
51G GLY* 2.9 26.7 + - - -
52G ARG* 3.0 20.3 + - - +
53G ASN* 3.3 33.6 + - - +
54G CYS* 3.3 7.4 + - - +
55G ASN 4.6 2.1 + - - -
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Residues in contact with LYS 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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44G SER* 2.9 30.2 + - - +
45G GLU* 2.8 47.3 + - - +
46G LEU 3.2 0.2 - - - -
47G ASP* 1.3 78.6 - - + +
49G ALA* 1.3 63.4 + - - +
50G ILE 3.2 0.8 + - - -
51G GLY* 3.5 9.3 + - - -
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Residues in contact with ALA 49 (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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31G HIS* 4.7 9.2 - - + +
45G GLU 2.9 17.4 + - - +
46G LEU* 3.4 7.6 + - - +
48G LYS* 1.3 78.9 - - - +
50G ILE* 1.3 63.5 + - + +
66G LEU* 4.0 23.3 - - + -
69G GLN* 3.7 21.9 + - - +
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Residues in contact with ILE 50 (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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46G LEU* 2.9 34.9 + - + +
49G ALA* 1.3 84.3 - - - +
51G GLY* 1.3 60.7 + - - +
52G ARG* 3.7 8.4 - - + +
54G CYS* 3.5 19.3 - - - -
58G ILE* 4.6 3.8 - - + -
62G GLU* 3.3 49.8 - - + +
66G LEU* 4.1 32.3 - - + -
69G GLN* 5.4 0.4 - - - +
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Residues in contact with GLY 51 (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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47G ASP 2.9 15.6 + - - -
48G LYS* 3.5 8.7 + - - -
50G ILE* 1.3 78.1 - - - +
52G ARG* 1.3 61.0 + - - +
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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