Contacts of the helix formed by residues 33 - 45 (chain C) in PDB entry 4GGF
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 ASN 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.7 36.5 + - - +
27C GLY* 5.1 1.8 - - - +
31C THR 3.8 1.0 + - - -
32C LEU* 1.3 76.0 - - - +
34C GLN* 1.3 66.2 + - - +
35C GLY* 3.2 5.5 + - - -
36C GLU* 2.8 39.7 + - - +
37C PHE* 3.0 20.1 + - - +
63C MET* 3.9 2.5 - - - -
72C LYS 4.2 8.1 - - - +
73C GLN* 4.4 17.4 - - + +
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASN* 1.3 77.8 - - - +
35C GLY* 1.3 58.5 + - - +
37C PHE* 3.4 1.4 + - + +
38C LYS* 2.9 56.3 + - + +
60C GLU* 3.4 35.4 + - + +
63C MET* 3.7 28.6 - - + +
72C LYS 4.4 2.2 + - - +
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 6.3 2.5 - - - -
33C ASN* 3.2 6.6 + - - -
34C GLN* 1.3 78.8 - - - +
36C GLU* 1.3 56.0 + - - +
38C LYS* 3.5 8.6 + - - +
39C GLU* 3.0 28.4 + - - +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.0 33.0 - - + +
23C SER* 3.1 0.7 - - - +
25C LYS* 4.4 9.6 - - + -
26C LEU* 2.7 31.1 + - + +
31C THR 3.0 5.2 - - - +
32C LEU* 3.1 11.6 - - + -
33C ASN* 2.8 43.8 + - - +
35C GLY* 1.3 74.1 - - - +
37C PHE* 1.3 63.9 + - - +
39C GLU* 3.3 8.5 + - - +
40C LEU* 3.0 22.7 + - - +
204C CA 2.4 31.2 - - - -
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.2 19.4 - - + +
33C ASN 3.0 16.6 + - - +
34C GLN* 3.7 4.7 - - + +
36C GLU* 1.3 77.6 - - - +
38C LYS* 1.3 58.4 + - + +
40C LEU* 3.2 7.4 + - + +
41C VAL* 2.9 56.6 + - + +
59C ILE* 3.8 24.0 - - + -
62C ILE* 4.0 21.3 - - + -
63C MET* 3.7 38.4 - - + -
66C LEU* 4.1 4.9 - - + -
74C LEU* 3.6 21.3 - - + -
79C PHE* 4.4 8.1 - + - -
82C LEU* 3.9 18.2 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 2.9 41.1 + - + +
35C GLY* 3.8 7.2 - - - +
37C PHE* 1.3 75.7 - - + +
39C GLU* 1.3 58.8 + - - +
41C VAL* 3.4 1.6 + - - +
42C ARG* 2.9 32.1 + - - +
53C ASN* 4.9 0.7 - - - +
56C GLU* 2.7 38.9 + - + +
59C ILE* 3.8 24.9 - - + +
60C GLU* 2.8 41.3 + - - +
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.3 18.6 - - + -
25C LYS* 2.8 37.5 + - - +
35C GLY 3.0 17.3 + - - +
36C GLU* 3.6 6.9 - - - +
37C PHE 3.2 0.4 - - - -
38C LYS* 1.3 72.9 - - - +
40C LEU* 1.3 66.7 + - - +
42C ARG* 3.3 26.3 + - - +
43C LYS* 2.7 54.0 + - + +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.2 11.9 - - + -
18C THR* 4.0 16.8 - - + +
19C PHE* 4.2 4.7 - - - -
22C TYR* 3.6 39.4 - - + -
32C LEU* 4.2 15.5 - - + -
36C GLU 3.0 10.7 + - - +
37C PHE* 3.5 9.0 - - + +
39C GLU* 1.3 76.2 - - - +
41C VAL* 1.3 64.1 + - + +
44C ASP* 2.7 29.0 + - + -
45C LEU* 3.5 22.8 + - + -
79C PHE* 3.8 35.2 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 2.9 53.7 + - + +
38C LYS* 3.9 6.1 - - - +
40C LEU* 1.3 77.2 - - + +
42C ARG* 1.3 62.9 + - - +
45C LEU* 3.1 36.6 + - + -
49C LEU* 3.7 23.3 - - + -
53C ASN* 3.1 35.4 + - - +
59C ILE* 3.9 16.6 - - + -
82C LEU* 4.8 0.2 - - + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS 2.9 17.0 + - - +
39C GLU* 3.7 28.8 + - - +
41C VAL* 1.3 78.5 - - - +
43C LYS* 1.3 80.5 + - + +
46C GLN* 3.3 23.2 + - - +
53C ASN* 3.4 16.6 + - - +
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A THR* 3.6 2.9 - - - +
22C TYR* 3.7 22.4 - - + +
25C LYS* 5.2 0.4 - - - +
39C GLU* 2.7 44.8 + - + +
42C ARG* 1.3 109.6 - - - +
44C ASP* 1.3 66.9 + - - +
45C LEU 3.4 0.2 - - - -
46C GLN* 2.9 32.5 + - - +
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 2.6 34.2 + - - +
5A LEU* 3.9 25.4 + - + +
6A GLU* 3.5 1.7 - - - +
18C THR* 3.9 13.5 - - + -
21C GLN* 4.2 6.0 + - - -
22C TYR* 2.5 43.1 + - - -
40C LEU* 2.7 16.0 + - + +
43C LYS* 1.3 76.4 - - - +
45C LEU* 1.3 66.2 + - - +
46C GLN 3.5 0.4 - - - -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.7 19.5 - - + -
6A GLU* 3.3 18.4 - - + -
9A LEU* 4.6 4.3 - - + -
40C LEU* 3.5 17.4 + - + -
41C VAL* 3.1 20.2 + - + +
44C ASP* 1.3 85.0 - - - +
46C GLN* 1.3 64.7 + - - +
47C ASN 3.2 2.7 - - - -
48C PHE* 4.3 7.0 - - + -
49C LEU* 2.9 40.7 + - + +
53C ASN* 3.4 7.4 + - - -
82C LEU* 4.2 7.2 - - + -
83C MET* 4.0 15.9 - - + -
86C LEU* 3.8 31.4 - - + -
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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