Contacts of the helix formed by residues 46 - 55 (chain F) in PDB entry 3MQT
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 PRO 46 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C PHE* 5.3 0.7 - - + -
56C ILE* 3.6 38.1 - - + -
57C GLU 5.8 0.4 - - - +
59C GLU* 4.0 10.5 - - - +
63C LEU* 5.0 2.0 - - + -
92C ILE* 4.1 30.0 - - + -
45F GLY* 1.4 80.5 - - - +
47F PRO* 1.3 66.9 - - + +
48F GLU 3.4 1.6 - - - -
49F CYS* 3.0 11.8 + - + +
50F MET* 2.9 28.7 + - - +
97F LEU* 4.1 16.4 - - + -
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Residues in contact with PRO 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 4.1 2.7 - - - +
14F PRO* 3.6 25.3 - - + +
15F VAL 4.1 3.8 - - - +
16F ASN* 5.1 9.0 - - + +
25F ASN* 3.7 35.9 - - + +
26F THR 3.7 22.7 - - - +
27F VAL* 3.3 16.6 - - + +
45F GLY 3.5 7.9 - - - +
46F PRO* 1.3 84.2 - - + +
48F GLU* 1.3 58.6 + - + +
50F MET 3.4 0.7 + - - -
51F LYS* 3.0 26.3 + - - +
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Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA* 4.7 6.3 - - + +
14F PRO* 3.6 23.0 - - + +
16F ASN* 6.2 2.0 - - + +
46F PRO* 3.4 0.4 - - - +
47F PRO* 1.3 75.0 - - + +
49F CYS* 1.3 62.2 + - - +
51F LYS* 3.4 17.9 + - - +
52F ALA* 2.9 28.4 + - - +
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Residues in contact with CYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C CYS* 4.0 16.3 - - - -
52C ALA* 4.2 10.0 - - - +
53C PHE* 3.8 44.2 - - - +
56C ILE* 4.3 9.8 - - + +
46F PRO* 3.0 25.0 + - + +
48F GLU* 1.3 78.9 - - - +
50F MET* 1.3 56.7 + - - +
52F ALA* 3.1 3.3 + - - +
53F PHE* 2.9 27.7 + - - +
97F LEU* 4.3 14.8 - - - -
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Residues in contact with MET 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.7 15.3 - - + -
27F VAL* 3.7 23.8 - - + -
43F ALA* 4.8 2.2 - - + -
44F ASP 3.5 27.1 - - - +
45F GLY* 3.7 10.8 - - - -
46F PRO* 2.9 22.5 + - - +
48F GLU 3.3 0.2 - - - -
49F CYS* 1.3 75.7 - - - +
51F LYS* 1.3 61.2 + - - +
53F PHE* 3.4 6.8 + - + +
54F SER 3.1 16.8 + - - -
97F LEU* 3.5 57.4 - - + +
100F PHE* 3.8 6.3 - - + -
101F ALA* 3.9 20.4 - - + +
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Residues in contact with LYS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLU* 5.9 0.4 + - - -
12F PHE* 3.8 21.0 + - + +
14F PRO* 3.6 30.0 - - + +
47F PRO 3.0 14.7 + - - +
48F GLU* 3.5 18.8 - - - +
49F CYS 3.2 0.2 - - - -
50F MET* 1.3 74.1 - - - +
52F ALA* 1.3 65.2 + - - +
54F SER* 2.6 25.2 + - - +
55F GLU* 2.7 48.1 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLU* 4.8 3.6 - - + +
49C CYS* 4.1 23.0 - - - +
52C ALA* 4.3 12.3 - - + -
48F GLU 2.9 17.6 + - - +
49F CYS 3.5 4.5 - - - +
51F LYS* 1.3 75.8 - - - +
53F PHE* 1.3 61.2 + - - +
55F GLU* 3.0 19.7 + - - +
56F ILE* 3.3 16.1 + - - +
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Residues in contact with PHE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PRO* 5.4 2.0 - - + -
49C CYS* 3.9 22.8 - - - -
97C LEU* 4.0 14.6 - - + -
49F CYS 2.9 13.6 + - - +
50F MET* 3.4 13.7 - - - +
52F ALA* 1.3 77.2 - - - +
54F SER* 1.3 62.4 + - - +
55F GLU 3.1 0.9 + - - -
56F ILE* 3.4 22.8 - - + +
65F ASN* 5.0 0.2 + - - -
66F ILE* 4.5 18.9 + - + +
89F THR* 5.2 6.7 - - + -
92F ILE* 3.9 35.7 - - + -
93F GLY 5.2 0.4 - - - -
97F LEU* 4.0 15.0 - - + -
98F GLY* 3.6 26.9 - - - -
101F ALA* 3.7 31.9 - - + -
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.5 48.1 - - - +
50F MET 3.1 5.4 + - - -
51F LYS* 2.6 22.2 + - - -
53F PHE* 1.3 77.1 - - - +
55F GLU* 1.3 61.0 + - - +
56F ILE 3.6 0.7 - - - -
65F ASN* 2.7 25.2 + - - +
66F ILE* 4.2 11.7 - - - -
67F LYS* 3.2 21.8 + - - +
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE 4.9 2.6 + - - +
51F LYS* 2.7 58.5 + - - +
52F ALA* 3.0 12.3 + - - +
54F SER* 1.3 86.1 + - - +
56F ILE* 1.3 64.2 + - - +
57F GLU* 3.9 4.5 + - - +
65F ASN* 3.8 2.7 - - - +
67F LYS* 4.3 13.5 + - - +
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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
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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