Contacts of the helix formed by residues 74 - 84 (chain C) in PDB entry 2Q2U
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 THR 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLY 5.3 1.1 - - - +
73C ALA* 1.3 80.3 - - - +
75C PHE* 1.3 64.5 + - - +
76C GLN* 3.3 20.4 - - + +
77C ASP* 3.0 34.3 + - - +
78C THR* 3.1 21.9 + - - -
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Residues in contact with PHE 75 (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 ASP* 3.1 50.7 - - - +
30C GLY* 3.7 16.6 - - - -
31C ILE* 4.7 2.9 - - + -
74C THR* 1.3 71.3 - - - +
76C GLN* 1.3 75.1 + - - +
78C THR* 2.9 9.3 + - - -
79C THR* 2.7 47.7 + - - -
279C GLY* 4.8 8.0 - - - -
285C ARG* 3.7 20.6 - - - -
13I G 5.1 7.0 - - - -
14I G 6.5 0.9 - - - -
30J OMC 3.4 16.6 - - - -
31J C 3.3 32.3 - - - -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.3 17.4 + - + +
75C PHE* 1.3 97.7 - - - +
77C ASP* 1.3 62.4 + - - +
79C THR* 3.5 10.4 + - - -
80C SER* 3.3 19.4 + - - -
279C GLY* 3.5 22.6 + - - +
281C LYS* 3.2 51.7 - - + +
14I G 3.9 16.3 - - - +
15I T 3.8 23.4 - - - +
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Residues in contact with ASP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.9 1.1 - - + -
73C ALA* 3.8 16.9 - - + +
74C THR* 3.0 40.8 + - - +
75C PHE 3.0 0.6 - - - -
76C GLN* 1.3 76.1 - - - +
78C THR* 1.3 67.3 + - - +
80C SER* 3.0 16.2 + - - -
81C ALA* 3.0 13.5 + - - +
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP 5.5 1.1 + - - -
30C GLY* 4.9 5.6 - - - -
31C ILE* 4.6 6.1 - - + -
68C ILE 3.8 9.9 - - - +
69C SER* 3.7 15.1 + - - +
70C ILE* 3.3 52.5 + - + +
73C ALA 4.7 0.3 + - - -
74C THR 3.1 11.2 + - - -
75C PHE* 2.9 13.7 + - + -
77C ASP* 1.3 76.9 - - - +
79C THR* 1.3 64.3 + - - +
81C ALA* 3.1 10.3 + - - -
82C VAL* 3.3 21.0 + - + +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 3.9 10.1 - - - +
75C PHE* 2.7 49.1 + - + -
76C GLN* 3.5 12.5 - - - -
78C THR* 1.3 74.1 - - - +
80C SER* 1.3 57.6 + - - +
82C VAL* 3.8 0.7 - - - +
83C MET* 2.9 50.4 + - + +
14I G 5.2 5.4 - - - +
15I T 3.9 22.9 - - - +
30J OMC 3.9 17.7 - - - +
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Residues in contact with SER 80 (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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76C GLN 3.3 7.0 + - - -
77C ASP* 3.0 10.3 + - - -
79C THR* 1.3 76.3 - - - +
81C ALA* 1.3 58.1 + - - +
82C VAL 2.9 11.3 + - - -
84C THR* 2.8 30.8 + - - -
86C HIS* 4.4 5.5 - - - -
15I T 3.4 11.0 + - - -
16I C 2.4 31.8 + - - -
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Residues in contact with ALA 81 (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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49C ASN* 3.1 25.2 + - - +
52C MET* 3.2 11.5 - - + +
70C ILE* 3.9 17.5 - - + -
77C ASP 3.0 12.9 + - - +
78C THR 3.1 7.6 + - - +
80C SER* 1.3 76.0 + - - +
82C VAL* 1.3 57.6 + - - +
84C THR 5.4 0.2 - - - -
86C HIS* 5.2 2.9 - - - -
89C TYR* 3.2 35.7 - - + +
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Residues in contact with VAL 82 (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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31C ILE* 3.8 27.8 - - + -
47C ILE* 3.7 27.8 - - + -
48C ARG* 3.7 6.2 + - - +
49C ASN* 3.3 26.1 + - - -
52C MET* 3.6 15.9 - - + -
68C ILE* 3.7 27.8 - - + -
78C THR* 3.3 22.1 + - + +
80C SER 2.9 0.4 - - - -
81C ALA* 1.3 83.9 - - - +
83C MET* 1.3 64.0 + - - +
84C THR 3.2 4.3 - - - -
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Residues in contact with MET 83 (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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31C ILE* 4.7 5.4 - - + -
48C ARG* 2.7 55.5 + - + +
79C THR* 2.9 36.1 + - + +
82C VAL* 1.3 87.6 - - - +
84C THR* 1.3 57.1 + - - +
14I G 6.1 0.9 - - - +
15I T 5.5 5.4 - - - +
16I C 3.3 23.4 - - - +
28J A 6.0 1.6 - - + -
29J C 3.7 28.7 - - - +
30J OMC 3.3 40.6 - - - +
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Residues in contact with THR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ARG* 4.1 2.5 - - - -
49C ASN* 3.2 21.3 - - - +
80C SER* 2.8 23.7 + - - -
82C VAL 3.2 0.8 - - - -
83C MET* 1.3 78.7 - - - +
85C GLY* 1.3 55.8 - - - +
86C HIS* 2.7 42.4 + - + +
16I C 2.9 28.7 + - - +
17I G 3.2 24.5 - - - +
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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
------------------------------------------------------------
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