Contacts of the helix formed by residues 103 - 119 (chain J) 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 ASP 103 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69I GLN* 3.1 18.1 + - - -
68J LEU* 3.9 4.9 - - - +
100J LYS* 3.5 48.0 - - + +
101J ASP 3.3 3.3 - - - +
102J GLY* 1.3 74.3 - - - +
104J TRP* 1.3 60.4 + - - +
105J ASN* 3.1 8.3 + - - +
106J GLU* 2.9 41.4 + - + +
107J PHE* 3.6 18.7 + - - +
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Residues in contact with TRP 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I GLN* 2.6 19.0 + - + +
70I ASN* 4.2 10.1 - - - -
26J HIS 4.1 21.5 - - - -
27J LEU* 4.1 15.0 - - + -
29J GLN* 5.1 4.3 - - + -
30J PRO* 3.9 13.1 - - + +
68J LEU* 3.8 32.1 - - + -
69J GLN 5.9 2.5 - - - -
70J ASN 5.8 2.0 - - - -
71J ALA* 5.8 3.4 - - + -
74J ILE* 4.7 12.3 - - + -
102J GLY 3.3 3.2 + - - +
103J ASP* 1.3 72.3 - - - +
105J ASN* 1.3 64.0 + - - +
106J GLU 3.3 0.2 - - - -
107J PHE* 3.2 22.1 + + - +
108J ARG* 2.8 81.4 + - + +
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Residues in contact with ASN 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I GLN* 3.1 23.1 + - - +
70I ASN* 2.8 30.0 + - - +
32J LEU* 3.3 21.1 - - + +
36J ASP* 5.1 0.7 - - - +
103J ASP* 3.1 6.7 + - - +
104J TRP* 1.3 78.9 - - - +
106J GLU* 1.3 57.5 + - - +
108J ARG* 3.2 30.7 + - - +
109J ARG* 2.9 48.2 + - - +
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Residues in contact with GLU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J HIS* 3.6 2.3 - - - +
99J ILE* 3.2 4.7 - - + -
100J LYS* 2.8 51.0 + - - +
103J ASP* 2.9 24.8 + - + +
105J ASN* 1.3 77.9 - - - +
107J PHE* 1.3 62.9 + - - +
109J ARG* 3.3 16.6 + - - +
110J LYS* 3.0 61.9 + - + +
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Residues in contact with PHE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J LEU* 4.1 9.6 - - + -
61J PHE* 3.6 45.2 - + + -
64J ALA* 4.0 17.0 - - + -
65J VAL* 4.0 17.3 - - + -
68J LEU* 3.7 21.8 - - + -
74J ILE* 4.0 16.8 - - + -
78J LEU* 4.1 2.0 - - + -
99J ILE* 4.0 13.6 - - + +
103J ASP 3.6 16.9 + - - +
104J TRP* 3.2 14.9 + + - +
106J GLU* 1.3 78.9 - - - +
108J ARG* 1.3 66.2 + - - +
110J LYS* 4.1 3.0 - - - +
111J LEU* 2.9 56.8 + - + +
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Residues in contact with ARG 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ASN* 4.0 1.4 - - - +
27J LEU* 3.2 46.9 + - + +
28J LYS* 3.9 3.4 - - - +
29J GLN 3.5 8.3 - - - +
30J PRO* 3.0 48.3 + - - +
31J PRO* 4.1 4.0 - - - +
32J LEU* 4.1 12.9 - - - +
36J ASP* 5.1 6.5 - - - -
104J TRP* 2.8 58.7 + - + +
105J ASN* 3.2 25.9 + - - +
107J PHE* 1.3 73.9 - - - +
109J ARG* 1.3 57.0 + - - +
111J LEU* 4.0 0.5 - - - +
112J THR* 2.5 41.0 + - - +
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Residues in contact with ARG 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F TYR* 4.6 1.8 + - - +
32J LEU* 4.0 16.0 - - - +
36J ASP* 3.0 52.4 + - - +
37J PHE* 4.4 6.5 - - + -
39J ASN* 3.8 19.0 + - - +
40J LEU* 3.7 35.9 - - + +
105J ASN* 2.9 29.2 + - - +
106J GLU* 3.8 20.3 + - - +
108J ARG* 1.3 77.5 - - - +
110J LYS* 1.3 64.6 + - - +
112J THR* 3.3 5.3 + - - -
113J PHE* 3.0 24.1 + - + +
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Residues in contact with LYS 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J LEU* 3.6 20.6 - - + -
44J ASP* 3.6 27.3 + - - -
48J LEU* 3.4 20.8 - - + +
61J PHE* 3.8 15.0 - - + -
97J ILE* 3.8 18.6 - - + +
98J HIS 2.6 27.9 + - - +
99J ILE* 4.3 7.4 - - + -
106J GLU* 3.0 46.6 + - + +
107J PHE* 4.9 0.2 - - - -
109J ARG* 1.3 77.5 - - - +
111J LEU* 1.3 59.4 + - - +
113J PHE 3.3 1.2 + - - -
114J TYR* 2.9 28.4 + - - +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ILE* 4.1 6.1 - - + -
27J LEU* 3.8 20.2 - - + -
61J PHE* 3.5 36.9 - - + -
74J ILE* 4.0 12.1 - - + -
78J LEU* 4.1 17.7 - - + -
107J PHE* 2.9 44.6 + - + +
108J ARG 4.1 1.3 - - - +
110J LYS* 1.3 73.6 - - - +
112J THR* 1.3 67.0 + - - +
114J TYR* 3.3 8.2 + - + -
115J LEU* 2.9 42.9 + - + +
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Residues in contact with THR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F VAL* 3.6 28.3 - - + +
279F TYR* 3.8 19.5 - - + -
24J ILE* 5.5 5.8 - - + -
27J LEU* 4.1 23.2 + - + +
28J LYS* 6.1 2.5 - - + -
108J ARG* 2.5 28.9 + - - +
109J ARG* 3.6 6.5 - - - -
111J LEU* 1.3 77.5 - - - +
113J PHE* 1.3 57.5 + - - +
115J LEU* 3.4 3.8 + - - +
116J LYS* 2.9 27.4 + - - +
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Residues in contact with PHE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F VAL* 4.2 15.9 - - + -
204F GLN* 4.6 14.8 - - + -
279F TYR* 3.2 25.5 + + - +
37J PHE* 4.9 6.7 - + + -
40J LEU* 3.6 32.1 - - + -
45J GLN* 3.6 44.6 - - + -
48J LEU* 4.0 14.1 - - + -
49J MET* 3.6 17.0 - - + -
109J ARG 3.0 10.0 + - - +
110J LYS 3.9 1.8 - - - +
112J THR* 1.3 73.8 - - - +
114J TYR* 1.3 60.8 + - - +
116J LYS* 3.2 4.0 + - + +
117J THR* 2.9 61.0 + - + +
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Residues in contact with TYR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J LEU* 4.0 26.2 - - + +
54J ARG* 3.1 57.1 + - - -
57J ASN* 3.8 20.6 - - + -
58J LEU* 3.9 11.4 - - + +
61J PHE* 4.0 17.0 - + + -
81J LEU* 4.8 6.3 - - + -
85J LEU* 3.4 24.2 - - + +
110J LYS 2.9 16.8 + - - +
111J LEU* 3.5 22.4 - - + +
113J PHE* 1.3 76.6 - - - +
115J LEU* 1.3 69.2 + - + +
117J THR* 2.9 21.3 + - - -
118J LEU* 3.0 24.1 + - + +
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278F VAL* 5.0 2.9 - - + +
20J ILE* 4.4 34.1 - - + +
23J ILE* 3.6 29.6 - - + -
24J ILE* 4.2 9.6 - - + -
27J LEU* 4.0 9.6 - - + -
81J LEU* 4.1 26.7 - - + -
111J LEU* 2.9 42.1 + - + +
112J THR* 3.9 3.6 - - - +
114J TYR* 1.3 81.6 - - + +
116J LYS* 1.3 65.0 + - - +
118J LEU* 3.4 20.7 + - + +
119J GLU* 3.8 9.7 - - - +
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Residues in contact with LYS 116 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203F SER* 3.9 17.8 + - - +
204F GLN* 3.9 11.7 - - - +
232F PHE 4.4 1.2 + - - -
233F ASN* 3.2 29.2 + - - +
234F ARG 4.7 0.4 - - - +
276F GLU* 2.5 39.0 + - - +
278F VAL* 3.9 17.2 - - + +
279F TYR* 3.6 25.6 - - + -
281F PHE* 5.2 0.4 - - - -
112J THR 2.9 18.0 + - - +
113J PHE* 3.6 5.4 - - + +
115J LEU* 1.3 77.7 - - - +
117J THR* 1.3 65.8 + - + +
119J GLU* 3.2 40.4 + - - +
120J ASN 4.6 0.5 + - - -
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Residues in contact with THR 117 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178F GLN* 3.3 24.7 + - + +
201F VAL* 5.3 3.8 - - + -
203F SER* 6.1 1.1 - - - +
48J LEU 4.0 4.5 + - - -
49J MET* 3.6 18.2 - - + -
54J ARG* 2.9 23.6 + - - -
113J PHE* 2.9 48.1 + - + +
114J TYR* 2.9 21.1 + - - -
116J LYS* 1.3 73.7 - - + +
118J LEU* 1.3 64.4 + - - +
119J GLU 3.1 3.3 + - - -
120J ASN* 3.9 6.6 + - - -
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J CYS* 6.1 0.9 - - + -
20J ILE* 4.4 19.7 - - + -
54J ARG* 3.7 21.5 - - - +
81J LEU* 5.6 1.8 - - + -
84J CYS* 3.5 23.8 - - + +
85J LEU* 3.7 31.9 - - + -
86J PRO* 4.9 9.0 - - + -
114J TYR* 3.0 21.7 + - + +
115J LEU* 3.5 19.5 - - + +
116J LYS 3.2 0.8 - - - -
117J THR* 1.3 77.0 + - - +
119J GLU* 1.3 59.4 + - - +
120J ASN* 2.9 18.4 + - - +
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Residues in contact with GLU 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F ARG* 4.0 15.2 + - + +
235F LYS* 3.7 27.1 + - + +
276F GLU* 4.1 1.8 - - - +
277F ARG* 2.9 39.7 + - - +
278F VAL* 3.8 10.2 - - - +
20J ILE* 5.7 2.0 - - + -
115J LEU 3.8 8.7 - - - +
116J LYS* 3.2 44.2 + - - +
117J THR 3.1 1.4 - - - -
118J LEU* 1.3 80.4 - - + +
120J ASN* 1.3 76.6 + - - +
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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