Contacts of the helix formed by residues 41 - 50 (chain I) in PDB entry 6NMY
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 ASN 41 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39I ASN 3.3 6.9 + - - +
40I LEU* 1.3 77.5 - - - +
42I GLY* 1.3 71.3 + - - +
43I GLU* 3.5 22.6 + - - +
44I ASP* 3.0 26.9 + - - +
45I GLN* 3.1 9.7 + - - +
54M LYS* 4.7 9.6 + - - +
57M ASP* 5.4 6.7 - - - +
58M TYR* 3.2 38.6 - - + +
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Residues in contact with GLY 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LEU 3.5 2.2 + - - -
41I ASN* 1.3 78.7 + - - +
43I GLU* 1.3 56.3 + - - +
45I GLN* 3.2 17.7 + - - +
46I ASP* 2.9 29.1 + - - +
72M ALA* 3.9 18.0 - - - +
199M PHE* 5.8 6.5 - - - -
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Residues in contact with GLU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASN* 3.1 12.2 + - - +
42I GLY* 1.3 73.9 - - - +
44I ASP* 1.3 65.5 + - - +
46I ASP* 3.2 3.1 + - - -
47I ILE* 2.9 33.7 + - + +
54M LYS* 2.7 35.6 + - - +
58M TYR* 3.5 32.1 - - + +
60M MET* 5.5 0.2 - - - +
70M PHE* 3.5 24.5 - - + +
71M GLY* 2.8 24.4 + - - -
72M ALA* 3.1 23.7 + - - +
73M ILE* 3.8 0.7 - - - +
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Residues in contact with ASP 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I LEU* 3.9 19.3 - - + +
41I ASN* 3.0 17.8 + - - +
43I GLU* 1.3 76.0 - - - +
45I GLN* 1.3 57.3 + - - +
47I ILE* 3.7 2.0 - - - +
48I LEU* 2.9 38.9 + - + +
97I ILE* 3.3 29.2 - - + +
110I LYS* 3.7 18.1 + - - -
58M TYR* 2.9 35.5 + - - -
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Residues in contact with GLN 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I PHE* 3.7 19.2 + - - +
40I LEU* 3.0 35.5 + - + +
41I ASN 3.1 11.1 + - - +
42I GLY* 3.3 15.6 - - - +
43I GLU 3.2 0.2 - - - -
44I ASP* 1.3 77.6 - - - +
46I ASP* 1.3 57.1 + - - +
48I LEU 3.3 0.9 + - - -
49I MET* 2.9 41.6 + - + +
113I PHE* 3.7 26.6 - - + -
201M VAL* 3.5 25.6 - - - +
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Residues in contact with ASP 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLY 2.9 16.0 + - - +
43I GLU 3.7 4.3 - - - +
45I GLN* 1.3 75.8 - - - +
47I ILE* 1.3 63.1 + - - +
49I MET* 3.9 11.1 - - - +
50I GLU* 3.1 22.3 + - - +
94I ARG* 2.7 37.5 + - - +
71M GLY* 3.5 32.1 - - - +
72M ALA* 5.0 0.4 - - + -
179M SER* 5.6 1.9 + - - -
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Residues in contact with ILE 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLU* 2.9 37.6 + - + +
44I ASP* 3.7 4.9 - - - +
46I ASP* 1.3 79.4 - - - +
48I LEU* 1.3 61.2 + - - +
50I GLU* 3.5 15.1 + - - +
53I LEU* 4.0 8.6 - - + +
57I ASN* 3.1 15.6 + - - +
94I ARG* 3.3 43.5 - - - +
95I HIS 4.2 9.4 - - - +
96I PRO 4.2 2.0 - - - +
97I ILE* 3.8 44.6 - - + +
58M TYR* 4.7 7.2 - - - +
60M MET* 4.5 10.3 - - + -
69M GLN 5.1 0.2 - - - +
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Residues in contact with LEU 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I LEU* 4.2 3.6 - - + -
44I ASP* 2.9 24.6 + - + +
45I GLN 3.9 2.7 - - - +
47I ILE* 1.3 79.2 - - + +
49I MET* 1.3 61.2 + - - +
50I GLU 3.5 1.6 + - - +
54I ARG* 3.6 21.8 + - - -
57I ASN* 3.7 10.4 + - - +
61I PHE* 4.1 20.9 - - + -
97I ILE* 4.1 27.6 - - + -
110I LYS* 3.5 38.1 - - + +
113I PHE* 4.0 22.7 - - + -
114I TYR* 4.1 21.9 - - + -
117I THR* 4.2 1.9 + - - -
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Residues in contact with MET 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I GLN* 2.9 42.3 + - + +
46I ASP* 4.0 11.0 - - - +
47I ILE 3.3 0.2 - - - -
48I LEU* 1.3 75.8 - - - +
50I GLU* 1.3 66.0 + - - +
51I ASN* 3.1 5.0 + - - +
54I ARG* 3.8 14.5 + - - +
113I PHE* 3.7 18.6 - - + -
117I THR* 3.7 23.3 - - + -
178M GLN* 3.9 30.7 + - - +
179M SER* 4.0 26.2 - - - +
201M VAL* 3.9 18.4 - - + -
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ASP 3.1 17.0 + - - +
47I ILE 3.7 8.9 - - - +
48I LEU 3.3 4.1 - - - +
49I MET* 1.3 75.4 - - - +
51I ASN* 1.3 68.4 + - - +
52I ASN* 3.8 15.0 + - - +
53I LEU* 3.3 43.5 + - + +
54I ARG* 3.7 10.6 + - - +
93I THR* 5.4 8.0 + - - -
94I ARG* 3.7 23.0 + - - +
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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