Contacts of the helix formed by residues 48 - 58 (chain C) in PDB entry 3P05
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 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C PRO* 4.6 0.9 - - + -
2C ILE* 4.1 13.0 - - + -
12C HIS* 4.0 24.7 - - + +
47C ALA* 1.3 76.2 - - - +
49C PRO* 1.3 76.5 - - - +
50C GLN* 3.5 5.0 + - - +
51C ASP* 2.9 42.9 + - - +
52C LEU* 3.0 13.5 + - - +
111C LEU* 4.2 10.1 - - + +
114C GLN* 3.7 10.3 - - + +
115C ILE* 4.7 3.4 - - + -
118C MET* 4.0 16.4 - - + -
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Residues in contact with PRO 49 (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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48C THR* 1.3 83.1 - - - +
50C GLN* 1.3 55.3 + - - +
52C LEU* 3.2 4.4 + - + +
53C ASN* 2.9 35.3 + - - -
103C ASP 4.6 0.9 - - - +
104C ILE 3.4 27.4 - - - +
106C GLY* 3.9 15.0 - - - -
114C GLN* 3.4 22.7 - - + +
118C MET* 4.2 0.7 - - - -
126C VAL* 3.8 37.5 - - + +
127C GLY* 4.0 6.3 - - - +
130C TYR* 3.8 14.1 - - + -
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Residues in contact with GLN 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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12C HIS* 4.9 2.3 + - - -
48C THR* 3.1 3.9 - - - +
49C PRO* 1.3 77.9 - - - +
51C ASP* 1.3 69.8 + - - +
53C ASN* 3.3 9.2 + - + +
54C THR* 3.1 26.5 + - - +
106C GLY* 5.7 0.7 - - - -
111C LEU* 3.8 39.6 - - + +
114C GLN* 3.2 23.4 + - - +
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Residues in contact with ASP 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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1C PRO* 2.5 39.7 - - + +
12C HIS* 4.6 4.3 + - - -
14C ALA* 4.8 0.9 - - - -
15C ILE* 3.9 30.6 + - + +
47C ALA* 3.6 11.0 - - + -
48C THR* 2.9 31.8 + - - +
50C GLN* 1.3 82.9 - - - +
52C LEU* 1.3 62.9 + - - +
54C THR* 3.2 9.5 + - - -
55C MET* 3.1 26.3 + - - +
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Residues in contact with LEU 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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40C PHE* 3.8 30.9 - - + -
44C SER* 3.9 12.1 - - - +
47C ALA* 3.8 20.6 - - + -
48C THR 3.0 18.5 + - - +
49C PRO* 3.6 7.6 - - + +
50C GLN 3.2 0.2 - - - -
51C ASP* 1.3 76.8 - - - +
53C ASN* 1.3 62.5 + - - +
55C MET* 3.2 9.1 + - - +
56C LEU* 3.1 27.0 + - - +
127C GLY* 3.6 24.9 - - - +
130C TYR* 3.7 29.4 - - + -
131C LYS* 4.1 11.0 - - + +
134C ILE* 4.0 8.1 - - + -
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Residues in contact with ASN 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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49C PRO 2.9 20.4 + - - +
50C GLN* 3.8 6.9 - - - +
52C LEU* 1.3 73.2 - - - +
54C THR* 1.3 58.5 + - - +
56C LEU* 3.1 8.4 + - - +
57C ASN* 2.8 46.6 + - - +
105C ALA 3.0 21.4 + - - +
106C GLY* 4.0 14.3 + - - -
107C THR* 5.1 3.6 - - - +
130C TYR* 2.8 25.7 + - - -
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Residues in contact with THR 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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38B PRO* 5.0 4.5 - - + +
42B ALA* 3.9 28.1 - - + +
15C ILE* 4.3 11.7 - - + +
20C LEU* 4.0 17.0 - - + -
50C GLN* 3.1 18.6 + - - +
51C ASP* 3.2 11.8 + - - -
53C ASN* 1.3 75.5 - - - +
55C MET* 1.3 60.1 + - - +
57C ASN* 3.5 5.5 + - - +
58C THR* 2.9 38.4 + - + +
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Residues in contact with MET 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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15C ILE* 3.7 20.2 - - + -
19C THR* 5.3 2.5 - - + -
20C LEU* 4.6 2.7 - - + -
23C TRP* 2.8 59.5 + - + +
40C PHE* 3.9 22.7 - - + -
43C LEU* 4.1 26.2 - - + +
44C SER* 4.0 20.9 - - - -
47C ALA* 5.4 2.5 - - - -
51C ASP 3.1 16.3 + - - +
52C LEU* 3.2 16.6 + - - +
54C THR* 1.3 76.3 - - - +
56C LEU* 1.3 65.5 + - + +
58C THR* 3.2 12.0 + - - -
59C VAL* 3.6 4.0 - - - +
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Residues in contact with LEU 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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23C TRP* 5.0 8.5 - - + -
40C PHE* 4.8 10.3 - - + -
52C LEU 3.1 13.6 + - - +
53C ASN* 3.1 9.8 + - - +
55C MET* 1.3 79.8 - - - +
57C ASN* 1.3 64.5 + - - +
58C THR 3.3 0.7 + - - -
59C VAL* 3.5 10.4 + - - +
66C MET* 3.5 28.2 - - + +
69C LEU* 3.9 25.6 - - + -
73C ILE* 4.2 16.2 - - + -
130C TYR* 4.2 8.3 - - - +
134C ILE* 4.0 39.7 - - + -
138C LEU* 6.0 1.8 - - + -
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Residues in contact with ASN 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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35B GLU* 3.8 0.9 - - - +
38B PRO* 3.3 23.7 - - + +
173B ARG* 2.7 33.4 + - - +
53C ASN* 2.8 31.2 + - - +
54C THR* 4.1 4.6 - - - +
56C LEU* 1.3 78.4 - - - +
58C THR* 1.3 59.0 + - - +
59C VAL 3.3 0.8 + - - -
70C LYS* 5.5 5.2 + - - -
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Residues in contact with THR 58 (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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30B LYS* 3.3 21.8 + - - -
35B GLU* 3.5 7.6 - - - +
38B PRO* 4.1 6.5 - - + -
39B MET* 3.7 51.8 - - + +
20C LEU* 3.7 14.5 - - + +
23C TRP* 4.1 1.0 - - - -
24C VAL* 3.6 11.9 - - - +
54C THR* 2.9 30.6 + - + +
55C MET* 3.2 8.1 + - - -
56C LEU 3.2 0.6 - - - -
57C ASN* 1.3 77.6 - - - +
59C VAL* 1.3 64.4 + - - +
60C GLY 3.5 0.2 + - - -
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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