Contacts of the helix formed by residues 26 - 36 (chain C) in PDB entry 5GQQ
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 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLY* 5.2 0.2 - - - -
23C SER* 3.2 18.3 + - - -
24C ASP 3.2 0.6 - - - -
25C GLN* 1.3 82.6 + - - +
27C PHE* 1.3 64.1 + - - +
28C LEU 3.5 2.0 - - - -
29C TRP* 3.3 17.7 + - - +
30C ASN* 2.9 40.5 + - - -
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Residues in contact with PHE 27 (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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23C SER 3.1 11.2 + - - +
24C ASP* 3.4 21.3 + - - +
25C GLN 3.4 0.6 - - - -
26C SER* 1.3 75.3 - - - +
28C LEU* 1.3 71.4 + - + +
30C ASN* 3.0 9.8 + - + +
31C VAL* 2.8 48.8 + - + +
34C ARG* 5.8 4.0 - - - -
89C TRP* 3.5 36.3 - + - -
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Residues in contact with LEU 28 (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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25C GLN 5.1 1.2 + - - -
26C SER 3.5 0.2 - - - -
27C PHE* 1.3 90.4 - - + +
29C TRP* 1.3 58.1 + - - +
31C VAL* 3.3 4.3 + - + +
32C PHE* 2.8 30.1 + - - +
82C PHE* 3.7 16.0 - - + -
85C PHE* 4.3 9.2 - - + -
86C THR* 4.2 26.5 - - + +
89C TRP* 3.6 53.4 - - + +
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Residues in contact with TRP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN 5.7 0.4 + - - +
26C SER* 3.3 21.4 + - - +
28C LEU* 1.3 77.4 - - - +
30C ASN* 1.3 65.5 + - - +
32C PHE* 3.2 24.1 + + - +
33C GLN* 2.8 68.6 + - + +
82C PHE* 3.4 46.5 - + + -
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Residues in contact with ASN 30 (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 GLY* 3.5 30.5 - - - -
26C SER* 2.9 30.4 + - - -
27C PHE* 3.5 9.9 - - + +
29C TRP* 1.3 79.4 - - - +
31C VAL* 1.3 65.9 + - + +
33C GLN* 3.3 21.6 + - - +
34C ARG* 3.2 21.7 + - - +
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Residues in contact with VAL 31 (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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100A PHE* 4.6 5.2 - - + -
27C PHE* 2.8 49.9 + - + +
28C LEU* 3.6 9.2 - - - +
30C ASN* 1.3 73.5 - - - +
32C PHE* 1.3 67.8 + - - +
34C ARG* 3.2 27.9 + - - +
35C VAL* 3.0 30.8 + - + +
85C PHE* 3.9 23.1 - - + -
89C TRP* 4.2 16.8 - - + -
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Residues in contact with PHE 32 (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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28C LEU 2.8 18.3 + - - +
29C TRP* 3.4 33.4 - + - +
31C VAL* 1.3 72.5 - - - +
33C GLN* 1.3 62.9 + - + +
35C VAL* 3.3 2.0 + - - +
36C ASP* 2.8 50.6 + - + +
41C GLY* 3.4 32.1 - - - -
42C VAL 4.3 0.2 - - - -
43C ILE* 3.4 35.6 - - + +
80C VAL 3.9 2.5 - - - -
81C ASN 3.6 6.7 - - - -
82C PHE* 3.4 37.5 - + + -
85C PHE* 3.6 24.2 - - + -
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Residues in contact with GLN 33 (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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29C TRP* 2.8 68.6 + - + +
30C ASN* 3.3 18.5 - - - +
31C VAL 3.2 0.4 - - - -
32C PHE* 1.3 81.0 - - + +
34C ARG* 1.3 60.6 + - - +
36C ASP* 3.3 22.1 - - - +
37C LYS* 4.9 0.5 - - - -
39C ARG* 5.7 1.7 - - - +
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Residues in contact with ARG 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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56A MET* 3.2 34.6 - - - +
100A PHE* 3.2 24.0 + - - +
102A GLU* 3.9 33.4 + - - +
27C PHE* 5.8 3.8 - - - -
30C ASN 3.2 9.5 + - - +
31C VAL* 3.2 39.1 + - - +
33C GLN* 1.3 76.4 - - - +
35C VAL* 1.3 74.6 + - + +
37C LYS* 3.9 18.2 + - - +
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Residues in contact with VAL 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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56A MET* 5.2 1.1 - - + -
100A PHE* 4.8 4.5 - - + -
31C VAL* 3.0 30.3 + - + +
32C PHE 3.7 2.7 - - - +
34C ARG* 1.3 84.9 - - + +
36C ASP* 1.3 57.5 + - - +
37C LYS* 2.8 15.0 + - - +
43C ILE* 3.6 31.6 - - + -
47C GLU* 3.4 35.8 - - - +
48C LEU* 4.3 5.4 - - + -
51C ALA* 3.6 25.6 - - + -
85C PHE* 4.7 7.4 - - + -
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Residues in contact with ASP 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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32C PHE* 2.8 32.2 + - + +
33C GLN* 3.3 15.8 - - - +
34C ARG 3.3 0.6 - - - -
35C VAL* 1.3 72.3 - - - +
37C LYS* 1.3 57.5 + - - +
38C ASP* 3.1 6.2 - - - +
39C ARG* 3.0 21.0 + - - +
40C SER 3.2 6.1 + - - -
41C GLY* 2.8 30.7 + - - -
42C VAL 3.3 6.2 - - - +
43C ILE* 4.2 6.5 - - + +
47C GLU* 4.0 5.6 - - - -
201C CA 2.3 31.6 - - - -
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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