Contacts of the helix formed by residues 49 - 57 (chain C) in PDB entry 2V5Q
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 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.7 3.1 - - - -
40C VAL 4.9 3.1 - - - -
41C ASN* 4.3 14.4 - - + +
42C ALA 3.3 12.6 - - - +
43C VAL* 4.8 4.5 - - + -
47C GLY 4.1 6.7 - - - +
48C LEU* 1.3 77.0 - - - +
50C PRO* 1.4 75.4 - - - +
51C LEU* 3.4 10.5 + - - +
52C HIS* 2.8 36.6 + - - +
53C LEU* 3.0 21.8 + - - +
72C ASP 5.2 1.0 + - - -
75C ALA* 3.9 22.8 - - + +
83C PRO* 4.7 0.3 - - - +
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Residues in contact with PRO 50 (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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18C LEU* 3.8 25.1 - - + -
19C LEU* 3.5 18.1 - - + +
22C ALA* 3.5 19.7 - - + +
39C ASP 4.6 1.8 - - - +
40C VAL 3.4 20.0 - - - +
42C ALA* 3.2 16.6 - - + +
49C THR* 1.4 86.2 - - - +
51C LEU* 1.3 54.9 + - - +
53C LEU* 3.3 1.7 + - + -
54C ALA* 2.9 31.9 + - - +
66C LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 51 (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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40C VAL 5.1 0.6 + - - -
49C THR* 3.1 10.1 + - - +
50C PRO* 1.3 77.3 - - - +
52C HIS* 1.3 64.7 + - - +
54C ALA* 3.4 0.6 + - - -
55C ALA* 2.9 26.6 + - + +
63C VAL* 3.7 45.8 - - + +
66C LEU* 3.8 10.7 - - + +
67C LEU* 3.7 27.1 - - + -
71C ALA* 4.2 14.8 - - + -
72C ASP 3.8 22.7 - - - +
73C VAL* 3.9 8.5 - - - -
83C PRO* 3.8 17.3 - - + -
99C LEU* 4.1 6.1 - - + -
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Residues in contact with HIS 52 (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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47C GLY 3.9 14.6 - - - -
48C LEU* 3.6 24.0 - - + -
49C THR* 2.8 37.1 + - + +
51C LEU* 1.3 77.0 - - - +
53C LEU* 1.3 58.8 + - - +
55C ALA* 3.3 1.0 + - - +
56C VAL* 2.9 33.8 + - - +
75C ALA* 3.0 33.3 + - + -
77C ASP* 3.8 4.5 + - + -
81C PHE 2.7 29.4 + - - -
82C THR 3.7 2.5 - - - -
83C PRO* 3.6 23.3 - - + +
86C LEU* 3.7 18.6 - - + +
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Residues in contact with LEU 53 (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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19C LEU* 3.4 50.5 - - + +
22C ALA 4.4 2.0 - - - -
23C ARG* 3.5 58.1 - - + +
44C ASP* 4.9 3.8 - - + +
48C LEU* 3.9 26.9 - - + -
49C THR 3.0 13.5 + - - +
50C PRO* 3.8 4.3 - - + +
51C LEU 3.2 0.2 - - - -
52C HIS* 1.3 78.6 - - - +
54C ALA* 1.3 60.1 + - - +
56C VAL* 3.6 8.3 - - + +
57C SER* 2.7 32.4 + - - -
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Residues in contact with ALA 54 (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 ALA 3.9 12.5 + - - +
50C PRO 2.9 16.8 + - - +
51C LEU 4.1 0.7 - - - +
53C LEU* 1.3 76.0 - - - +
55C ALA* 1.3 63.7 - - - +
57C SER 3.3 0.9 + - - -
58C GLY 3.1 4.0 + - - -
59C HIS* 2.9 34.1 + - + +
62C ILE* 3.5 30.7 - - + -
63C VAL* 3.7 17.7 - - + +
66C LEU* 4.4 1.6 - - + -
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Residues in contact with ALA 55 (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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51C LEU* 2.9 19.3 + - + +
52C HIS 3.6 4.5 - - - +
54C ALA* 1.3 77.3 - - - +
56C VAL* 1.3 62.6 + - - +
58C GLY 3.2 10.2 + - - -
63C VAL* 3.6 11.3 - - + +
83C PRO* 3.6 30.7 - - + +
86C LEU* 5.0 0.2 - - + -
87C ALA* 4.3 5.1 - - + -
90C THR* 4.2 0.9 + - - -
92C HIS* 3.4 14.4 - - - -
95C ILE* 3.6 21.5 - - + +
99C LEU* 4.7 0.7 - - + -
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Residues in contact with VAL 56 (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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320B THR* 4.1 16.2 - - + -
321B ILE* 4.1 29.8 - - + +
23C ARG* 5.9 2.7 - - - +
48C LEU* 6.3 0.2 - - + -
52C HIS 2.9 17.0 + - - +
53C LEU* 3.6 20.4 - - + +
55C ALA* 1.3 76.5 - - - +
57C SER* 1.3 67.6 + - - +
58C GLY 3.4 0.6 + - - -
86C LEU* 3.9 24.0 - - + -
89C MET* 4.0 11.7 - - + -
90C THR* 3.7 35.0 - - + +
92C HIS* 3.8 4.9 + - - -
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Residues in contact with SER 57 (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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321B ILE* 5.7 2.5 - - - +
23C ARG* 3.7 18.2 + - - +
53C LEU 2.7 22.8 + - - -
54C ALA 4.1 0.2 - - - -
55C ALA 3.2 0.8 - - - -
56C VAL* 1.3 84.6 - - - +
58C GLY* 1.3 61.4 + - - +
59C HIS* 3.4 34.3 + - - -
92C HIS* 4.0 3.8 - - - -
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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