Contacts of the helix formed by residues 46 - 55 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 5.5 0.7 - - + -
56E ILE* 3.5 39.5 - - + -
57E GLU 5.8 0.7 - - - +
59E GLU* 4.2 10.7 - - - +
63E LEU* 4.8 2.9 - - + -
92E ILE* 4.0 30.5 - - + -
45H GLY* 1.3 81.2 - - - +
47H PRO* 1.3 67.5 - - + +
48H GLU 3.4 1.8 - - - -
49H CYS* 3.1 9.7 + - + +
50H MET* 2.9 35.8 + - - +
97H LEU* 4.3 8.1 - - + -
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Residues in contact with PRO 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLU* 4.5 0.7 - - - +
14H PRO* 3.7 27.0 - - + +
15H VAL 4.6 0.9 - - - +
16H ASN* 3.9 12.8 - - - +
25H ASN* 3.7 40.2 - - + +
26H THR 3.7 21.5 - - - +
27H VAL* 3.5 13.8 - - + +
45H GLY 3.2 7.4 - - - +
46H PRO* 1.3 85.3 - - + +
48H GLU* 1.3 59.3 + - + +
50H MET* 3.3 2.6 + - - +
51H LYS* 3.0 26.9 + - - +
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA* 4.7 5.1 - - + +
14H PRO* 3.8 26.4 - - + +
16H ASN* 5.6 8.5 - - + +
46H PRO* 3.4 0.6 - - - +
47H PRO* 1.3 80.6 - - + +
49H CYS* 1.3 64.3 + - - +
51H LYS* 3.3 18.6 + - - +
52H ALA* 3.1 21.3 + - - +
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Residues in contact with CYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E CYS* 4.0 14.7 - - - -
52E ALA* 4.0 14.0 - - + +
53E PHE* 3.9 39.9 - - - -
56E ILE* 4.2 12.2 - - + +
97E LEU* 5.4 0.4 - - - -
46H PRO* 3.1 23.3 + - + +
48H GLU* 1.3 79.6 - - - +
50H MET* 1.3 57.9 + - - +
52H ALA* 3.3 3.1 + - - +
53H PHE* 3.0 26.2 + - - +
97H LEU* 4.2 15.3 - - - -
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Residues in contact with MET 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PHE* 3.6 20.4 - - + -
27H VAL* 3.8 19.5 - - + -
43H ALA* 4.7 2.9 - - + -
44H ASP 3.5 26.5 - - - +
45H GLY* 3.8 11.9 - - - +
46H PRO* 2.9 19.9 + - - +
47H PRO 3.3 0.2 + - - -
49H CYS* 1.3 75.2 - - - +
51H LYS* 1.3 61.7 + - - +
53H PHE* 3.5 5.5 + - + +
54H SER 3.1 16.8 + - - -
97H LEU* 3.5 57.2 - - + +
100H PHE* 3.7 8.1 - - + -
101H ALA* 3.9 21.1 - - + +
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Residues in contact with LYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PHE* 3.7 19.5 + - + +
14H PRO* 3.5 30.3 - - + -
27H VAL* 5.3 0.6 - - + +
47H PRO 3.0 13.2 + - - +
48H GLU* 3.5 18.6 - - - +
49H CYS 3.2 0.2 - - - -
50H MET* 1.3 78.3 - - - +
52H ALA* 1.3 61.8 - - - +
54H SER* 2.7 24.2 + - - +
55H GLU* 2.8 46.8 + - - +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E GLU* 4.6 4.7 - - + +
49E CYS* 4.0 23.6 - - - +
52E ALA* 4.3 11.0 - - + -
48H GLU 3.1 13.7 + - - +
49H CYS 3.3 6.9 + - - +
51H LYS* 1.3 74.6 - - - +
53H PHE* 1.3 64.1 + - - +
55H GLU* 2.9 19.6 + - - +
56H ILE* 3.2 17.3 + - - +
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Residues in contact with PHE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PRO* 5.3 1.6 - - + -
49E CYS* 3.8 20.7 - - - -
97E LEU* 3.9 15.5 - - + -
49H CYS 3.0 14.4 + - - +
50H MET* 3.5 13.9 - - + +
52H ALA* 1.3 74.9 - - - +
54H SER* 1.3 65.1 + - - +
55H GLU 3.3 0.9 + - - -
56H ILE* 3.4 22.4 - - + +
66H ILE* 4.6 20.1 + - + +
89H THR* 5.3 6.1 - - + -
92H ILE* 3.9 37.0 - - + -
93H GLY* 5.1 0.9 - - - -
97H LEU* 3.8 18.8 - - + -
98H GLY* 3.6 26.7 - - - -
101H ALA* 3.8 30.1 - - + -
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Residues in contact with SER 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PHE* 3.5 49.1 + - - +
50H MET 3.1 5.8 + - - -
51H LYS* 2.7 20.9 + - - -
53H PHE* 1.3 77.3 - - - +
55H GLU* 1.3 64.0 + - - +
56H ILE 3.5 0.7 - - - -
65H ASN* 2.8 19.2 + - - +
66H ILE* 4.2 11.4 - - - -
67H LYS* 3.4 22.9 + - - +
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Residues in contact with GLU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLU* 6.1 1.6 - - - +
12H PHE* 4.9 2.8 + - - +
51H LYS* 2.8 58.3 + - - +
52H ALA* 2.9 10.1 + - - +
54H SER* 1.3 84.1 + - - +
56H ILE* 1.3 64.4 + - - +
57H GLU* 4.5 5.2 - - - +
65H ASN* 3.7 3.6 - - - +
67H LYS* 4.3 13.3 + - - +
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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