Contacts of the helix formed by residues 103 - 122 (chain I) in PDB entry 5UWC
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68I LEU* 4.2 2.3 - - - +
99I ILE* 4.7 0.3 - - - +
100I LYS* 3.3 33.6 + - + +
101I ASP 3.2 3.9 + - - +
102I GLY* 1.3 73.6 - - - +
104I TRP* 1.3 62.2 + - - +
105I ASN* 3.5 10.6 + - - +
106I GLU* 3.2 35.9 + - + +
107I PHE* 3.2 22.7 + - - +
109I ARG* 5.7 0.2 + - - -
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Residues in contact with TRP 104 (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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26I HIS 3.8 25.1 - - - -
27I LEU* 4.2 23.6 - - + -
29I GLN* 5.1 2.2 - - + -
30I PRO* 3.4 25.7 - - + +
68I LEU* 3.7 28.5 - - + -
69I GLN 5.7 3.6 - - - -
70I ASN 6.0 1.8 - - - -
71I ALA* 4.9 15.3 - - + -
74I ILE* 5.0 6.5 - - + -
102I GLY 3.1 8.2 + - - +
103I ASP* 1.3 69.8 + - - +
105I ASN* 1.3 68.8 + - - +
107I PHE* 3.4 15.8 + + - +
108I ARG* 3.0 61.1 + - - +
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Residues in contact with ASN 105 (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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30I PRO* 5.5 1.9 - - - +
33I PRO* 5.8 4.5 - - - +
103I ASP* 3.4 8.6 + - - +
104I TRP* 1.3 91.9 - - - +
106I GLU* 1.3 57.5 + - - +
108I ARG* 3.4 20.0 + - - +
109I ARG* 3.1 41.5 + - - +
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Residues in contact with GLU 106 (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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98I HIS 4.5 0.8 - - - +
99I ILE* 3.7 2.7 - - + -
100I LYS* 2.9 40.7 + - - +
103I ASP* 3.2 25.7 + - - +
104I TRP 3.3 0.2 - - - -
105I ASN* 1.3 74.7 - - - +
107I PHE* 1.3 60.6 + - - +
109I ARG* 3.3 29.1 + - - +
110I LYS* 2.9 68.1 + - + +
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Residues in contact with PHE 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 4.0 15.5 - - + -
61I PHE* 3.5 43.0 - + - -
64I ALA* 3.9 17.0 - - + -
65I VAL* 3.8 27.1 - - + -
68I LEU* 3.8 20.9 - - + -
71I ALA* 6.0 0.4 - - + -
74I ILE* 4.1 8.7 - - + -
78I LEU* 4.1 5.8 - - + -
99I ILE* 4.1 13.1 - - + +
103I ASP 3.2 15.4 + - - +
104I TRP* 3.6 15.0 - + - +
106I GLU* 1.3 79.0 - - - +
108I ARG* 1.3 53.0 - - - +
110I LYS* 3.8 1.5 - - - -
111I LEU* 2.7 65.1 + - + +
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Residues in contact with ARG 108 (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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27I LEU* 2.7 57.0 + - + +
28I LYS* 3.7 2.2 - - - +
30I PRO* 3.6 13.7 - - - +
31I PRO* 3.3 33.7 - - - +
33I PRO* 4.0 18.8 + - - +
35I LEU* 3.7 23.2 - - + +
104I TRP* 3.0 50.9 + - + +
105I ASN* 3.4 21.2 + - - +
107I PHE* 1.3 72.7 - - + +
109I ARG* 1.3 63.6 + - - +
111I LEU 4.5 0.4 - - - +
112I THR* 2.7 37.5 + - - +
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Residues in contact with ARG 109 (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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279G TYR* 4.5 2.3 + - - -
35I LEU* 3.9 17.7 - - + -
36I ASP 4.9 3.4 - - - +
39I ASN* 3.2 43.2 + - - +
40I LEU* 3.6 28.3 - - + +
105I ASN* 3.1 47.9 + - - +
106I GLU* 3.3 32.7 + - - +
108I ARG* 1.3 78.1 - - - +
110I LYS* 1.3 65.3 + - + +
112I THR* 4.2 1.7 - - - -
113I PHE* 3.6 13.2 + - - +
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Residues in contact with LYS 110 (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* 4.0 18.2 - - + -
44I ASP* 3.8 23.9 + - - -
48I LEU* 3.4 20.9 - - + +
61I PHE* 3.6 15.0 - - + -
97I ILE* 3.9 21.4 - - + +
98I HIS 2.7 27.4 + - - +
99I ILE* 4.3 6.3 - - + -
106I GLU* 2.9 49.7 + - + +
107I PHE 4.0 1.6 - - - +
109I ARG* 1.3 80.5 - - + +
111I LEU* 1.3 59.6 + - - +
113I PHE 3.5 1.2 + - - -
114I TYR* 3.1 24.6 + - - +
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Residues in contact with LEU 111 (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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23I ILE* 3.9 15.5 - - + -
27I LEU* 3.8 22.9 - - + -
61I PHE* 3.5 35.3 - - + -
74I ILE* 4.3 0.4 - - + -
78I LEU* 4.1 23.1 - - + -
107I PHE* 2.7 50.9 + - + +
110I LYS* 1.3 70.9 - - - +
112I THR* 1.3 65.0 + - - +
114I TYR* 3.4 7.8 + - + -
115I LEU* 3.0 38.2 + - + +
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Residues in contact with THR 112 (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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278G VAL* 3.4 28.9 - - + -
279G TYR* 3.5 16.8 - - + +
24I ILE* 4.0 15.6 - - + +
27I LEU* 3.5 15.3 - - - +
28I LYS* 5.3 0.6 - - + +
35I LEU* 3.4 28.2 - - + +
108I ARG 2.7 25.3 + - - -
109I ARG 4.2 1.6 - - - -
111I LEU* 1.3 76.5 - - - +
113I PHE* 1.3 56.2 + - - +
115I LEU* 3.4 1.7 + - - +
116I TRP* 2.8 31.5 + - - +
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Residues in contact with PHE 113 (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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201G VAL* 4.6 4.0 - - + -
204G GLN* 3.4 25.6 - - - -
279G TYR* 3.3 13.1 + - - +
37I PHE* 4.2 8.3 - - + -
40I LEU* 3.6 24.7 - - + -
45I GLN* 3.6 46.9 - - + -
48I LEU* 3.9 18.6 - - + -
49I MET* 3.8 13.2 - - + -
109I ARG 3.6 3.9 + - - +
110I LYS 3.5 4.4 + - - +
111I LEU 3.3 0.2 - - - -
112I THR* 1.3 75.9 - - - +
114I TYR* 1.3 65.0 + - - +
116I TRP* 3.8 24.6 - + - +
117I THR* 2.9 46.4 + - + +
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Residues in contact with TYR 114 (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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48I LEU* 3.7 22.4 - - + -
54I ARG* 2.6 75.9 + - - -
57I ASN* 3.6 23.6 - - + -
58I LEU* 3.7 14.7 - - + +
61I PHE* 3.9 18.2 - + + -
81I LEU* 4.7 8.3 - - + -
85I LEU* 3.6 17.3 - - + +
110I LYS 3.1 17.1 + - - +
111I LEU* 3.5 15.0 - - + +
112I THR 3.3 0.2 - - - -
113I PHE* 1.3 77.2 - - - +
115I LEU* 1.3 79.6 + - + +
117I THR* 2.9 12.6 + - - -
118I LEU* 3.0 13.1 + - + +
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Residues in contact with LEU 115 (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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20I ILE* 3.9 25.8 - - + +
23I ILE* 3.6 37.7 - - + -
24I ILE* 3.8 24.2 - - + -
81I LEU* 3.8 26.5 - - + -
111I LEU* 3.0 29.4 + - + +
114I TYR* 1.3 89.7 - - + +
116I TRP* 1.3 67.2 + - - +
118I LEU* 3.4 12.0 - - + +
119I GLU* 3.0 26.3 + - - +
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Residues in contact with TRP 116 (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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201G VAL* 4.9 0.7 - - + -
203G SER* 3.1 40.4 - - - -
204G GLN* 3.8 12.1 - - - -
233G ASN* 3.4 14.3 + - - -
276G GLU* 3.1 29.9 + - - -
278G VAL* 3.7 22.2 - - + -
279G TYR* 3.4 24.9 - + + -
281G PHE* 4.2 10.8 - + - -
24I ILE* 4.9 0.8 - - - +
37I PHE* 3.8 17.0 - + - -
112I THR 2.8 19.5 + - - +
113I PHE* 3.8 32.5 - + - +
115I LEU* 1.3 77.4 - - - +
117I THR* 1.3 64.6 + - + +
119I GLU* 3.4 4.0 + - + +
120I ASN* 3.0 53.7 + - - +
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Residues in contact with THR 117 (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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178G GLN* 3.0 37.2 + - - +
201G VAL* 5.2 3.1 - - + -
203G SER* 5.2 2.7 - - - +
48I LEU 4.1 3.5 + - - -
49I MET* 3.8 13.6 - - + +
54I ARG* 2.9 25.4 + - - -
113I PHE* 2.9 49.6 + - + +
114I TYR* 2.9 12.3 + - - -
116I TRP* 1.3 81.1 - - + +
118I LEU* 1.3 62.5 + - - +
120I ASN* 4.4 3.4 - - - +
121I ALA* 3.1 9.0 + - - +
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Residues in contact with LEU 118 (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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20I ILE* 3.8 24.5 - - + -
54I ARG* 3.4 19.5 - - - +
81I LEU* 4.8 1.6 - - + -
84I CYS* 3.6 26.0 - - + +
85I LEU* 4.2 17.5 - - + -
86I PRO* 3.9 22.2 - - + -
114I TYR* 3.0 24.2 + - + +
115I LEU* 3.4 21.1 - - + +
117I THR* 1.3 78.1 + - - +
119I GLU* 1.3 61.7 - - - +
121I ALA* 3.4 4.9 + - + +
122I GLN* 3.2 25.1 + - + +
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Residues in contact with GLU 119 (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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234G ARG* 3.5 7.0 - - + +
235G LYS* 3.1 51.3 + - + -
16I CYS* 4.7 3.1 - - - +
17I SER* 3.7 17.2 + - - -
20I ILE* 3.6 29.2 - - + +
21I ASP* 5.9 1.1 - - - +
115I LEU 3.0 16.5 + - - +
116I TRP* 4.1 3.8 - - + +
118I LEU* 1.3 76.7 - - - +
120I ASN* 1.3 63.6 + - - +
122I GLN* 3.4 32.7 - - - +
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Residues in contact with ASN 120 (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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178G GLN* 3.7 14.9 + - - +
203G SER* 3.8 6.0 + - - -
231G HIS 5.1 0.5 - - - +
232G PHE* 3.3 22.7 + - - +
233G ASN* 3.5 8.4 + - - +
234G ARG* 3.1 53.0 + - - +
235G LYS* 4.5 3.1 + - - +
276G GLU* 5.0 1.0 - - - +
116I TRP* 3.0 58.3 + - - +
117I THR* 3.9 1.2 - - - +
118I LEU 3.3 0.2 - - - -
119I GLU* 1.3 78.8 - - - +
121I ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 121 (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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176G GLY 5.7 2.9 - - - +
178G GLN* 3.2 25.9 - - + +
54I ARG* 5.6 2.0 - - - +
117I THR 3.1 12.9 + - - +
118I LEU* 3.8 6.3 - - + +
120I ASN* 1.3 75.5 - - - +
122I GLN* 1.3 60.3 + - - +
123I ALA* 3.0 11.2 + - - +
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Residues in contact with GLN 122 (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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234G ARG* 4.3 5.4 - - - +
16I CYS* 6.3 2.7 - - + -
84I CYS 4.0 17.4 - - - +
85I LEU 5.1 0.9 - - - -
86I PRO* 4.9 13.0 - - - +
118I LEU* 3.2 19.0 + - + +
119I GLU* 3.4 32.1 + - - +
120I ASN 3.3 1.7 - - - -
121I ALA* 1.3 74.5 + - - +
123I ALA* 1.3 63.6 + - - +
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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