Contacts of the strand formed by residues 109 - 129 (chain B) in PDB entry 3UAJ
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 GLY 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLN* 3.9 25.0 + - - +
75B PRO* 3.4 14.0 - - - +
98B ASP* 4.9 0.2 - - - -
99B ARG 2.9 29.7 + - - +
108B PHE* 1.3 76.5 - - - +
110B LYS* 1.3 64.0 + - - -
111B GLY 3.4 0.2 + - - -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 5.5 2.5 - - - -
316A GLN* 3.7 20.6 - - - +
75B PRO* 4.3 10.4 - - - +
96B VAL* 4.0 42.8 + - + +
97B VAL 3.4 6.3 - - - +
98B ASP* 3.6 22.5 + - - +
109B GLY* 1.3 69.1 - - - -
111B GLY* 1.3 60.9 + - - +
112B GLY 4.2 0.5 + - - -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG 3.4 16.4 - - - -
74B CYS 4.6 0.9 - - - -
75B PRO* 4.5 7.6 - - - -
96B VAL* 3.4 3.2 - - - -
97B VAL* 2.8 43.2 + - - +
99B ARG* 3.8 9.4 - - - +
109B GLY 3.4 3.0 + - - -
110B LYS* 1.3 72.9 - - - +
112B GLY* 1.3 64.6 + - - -
113B VAL* 3.7 0.6 + - - -
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.2 30.7 + - - +
74B CYS 5.3 0.6 + - - -
79B GLU* 5.2 9.2 - - - -
80B PRO* 3.4 22.8 - - - +
95B ASP 3.6 7.0 - - - -
96B VAL* 3.8 10.7 - - - +
110B LYS 4.2 0.6 + - - -
111B GLY* 1.3 70.7 - - - -
113B VAL* 1.3 59.1 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 5.6 5.4 - - + -
71B ALA 3.5 4.5 - - - +
72B THR* 3.8 30.3 - - + -
80B PRO* 3.9 2.4 - - - +
93B ARG 4.1 0.5 - - - +
94B ARG* 3.7 3.2 + - - +
95B ASP* 2.9 55.1 + - + +
97B VAL* 3.8 39.9 - - + -
99B ARG* 4.4 3.6 - - - +
111B GLY 4.3 0.9 - - - +
112B GLY* 1.3 77.9 - - - +
114B VAL* 1.3 62.1 + - - +
115B THR* 5.4 2.5 - - - +
242B VAL* 5.8 0.9 - - + -
243B PRO* 6.3 1.8 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR 3.8 1.7 - - - +
70B THR* 3.6 3.2 - - - +
71B ALA* 3.0 43.6 + - + -
80B PRO* 3.6 33.4 - - + +
82B LEU* 3.8 10.9 - - + +
85B GLU* 3.7 26.0 - - - +
92B CYS* 4.5 3.6 - - + -
93B ARG 3.5 16.2 - - - +
94B ARG* 3.9 14.8 - - + -
113B VAL* 1.3 74.7 - - - +
115B THR* 1.3 63.2 + - - +
116B CYS* 4.4 11.4 - - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.9 24.7 - - + -
69B THR 3.6 5.8 - - - +
70B THR* 3.7 19.7 - - + +
92B CYS* 3.4 4.5 - - - -
93B ARG 3.3 28.4 + - - -
113B VAL* 5.4 2.6 - - - +
114B VAL* 1.3 75.1 + - - +
116B CYS* 1.3 64.1 + - - +
240B PHE* 3.4 29.7 - - + -
249B ASP* 5.4 8.7 + - - +
250B VAL* 4.7 5.4 - - + -
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Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN 3.5 2.1 - - - +
68B ILE* 3.5 4.4 - - - -
69B THR* 2.9 46.5 + - - +
82B LEU* 3.8 18.8 - - + -
84B GLU* 3.9 18.2 - - + -
85B GLU* 4.0 9.6 - - - -
90B TYR* 4.1 2.5 - - + -
91B ILE 3.4 3.6 - - - -
92B CYS* 2.0 47.6 - - - -
114B VAL* 4.4 2.0 - - - -
115B THR* 1.3 74.1 - - - +
117B ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.6 12.3 - - + -
66B SER 3.8 8.7 - - - +
67B ASN 4.0 0.9 - - - -
68B ILE* 4.3 15.7 - - + -
90B TYR* 3.4 6.2 - - - -
91B ILE* 2.9 44.3 + - + +
116B CYS* 1.3 73.9 - - - +
118B LYS* 1.3 62.1 + - - +
238B VAL* 5.6 0.2 - - + -
240B PHE* 5.2 0.9 - - + -
250B VAL* 4.4 22.2 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 3.7 5.7 - - - +
65B ILE* 3.7 4.3 - - - +
66B SER* 2.8 48.4 + - - +
67B ASN* 3.8 15.5 + - - +
89B GLN* 3.5 41.1 + - - +
90B TYR* 3.4 37.8 - - + +
91B ILE* 5.4 0.2 - - - -
117B ALA* 1.3 69.1 - - - +
119B PHE* 1.3 63.9 + - - +
120B SER* 3.9 4.2 + - - -
1001B NAG 4.4 17.7 + - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 4.1 13.9 - - - -
63B ALA* 3.8 29.4 - - + -
64B SER 4.4 2.7 - - - -
65B ILE* 6.1 1.3 - - + -
89B GLN* 3.1 38.2 + - - +
91B ILE* 4.8 6.7 - - + -
117B ALA 3.6 1.0 + - - -
118B LYS* 1.3 71.2 - - - +
120B SER* 1.3 61.8 + - - +
121B CYS* 4.4 3.6 - - + -
219B PRO* 3.7 22.9 - - + -
231B TRP* 3.8 42.3 - + + -
234B LYS* 3.8 32.9 - - + -
237B MET* 4.5 4.0 - - + -
238B VAL* 3.7 30.3 - - + -
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 3.4 5.4 - - - +
64B SER* 2.8 63.1 + - - -
66B SER* 4.2 10.8 + - - -
89B GLN* 5.8 3.6 - - - +
118B LYS* 5.1 4.5 - - - -
119B PHE* 1.3 75.7 - - - +
121B CYS* 1.3 61.2 + - - +
122B SER* 4.0 0.9 + - - -
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Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B CYS* 2.0 50.7 - - - -
62B GLU 3.4 3.8 - - - -
119B PHE* 4.3 3.6 - - + -
120B SER* 1.3 71.4 - - - +
122B SER* 1.3 58.1 + - - +
123B GLY 3.4 20.2 - - - -
124B LYS* 4.3 6.4 - - + +
231B TRP* 3.7 33.8 - - + +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 2.7 41.0 + - - +
63B ALA* 4.4 2.4 + - - -
64B SER* 5.7 4.1 - - - -
120B SER 4.0 2.5 + - - -
121B CYS* 1.3 73.0 - - - +
123B GLY* 1.3 60.0 + - - +
124B LYS* 4.1 4.5 + - - +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.0 34.6 + - - -
62B GLU* 3.1 21.6 + - - +
121B CYS* 3.4 6.1 - - - -
122B SER* 1.3 81.7 + - - +
124B LYS* 1.3 59.9 + - - -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 4.4 17.3 - - + -
59B TYR 3.4 12.6 - - - +
60B CYS* 4.5 0.2 - - - +
61B ILE* 4.7 3.1 - - - -
121B CYS* 4.3 6.5 - - + +
122B SER 4.2 3.8 + - - +
123B GLY* 1.3 72.4 - - - +
125B ILE* 1.3 59.7 - - - +
126B THR* 4.2 5.2 + - - +
200B LYS 5.1 0.7 - - - +
201B MET* 5.7 1.2 - - - +
202B LYS 5.6 4.2 + - - -
231B TRP* 4.2 22.4 - - + -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG 4.4 0.2 - - - +
58B THR* 3.4 7.9 - - - +
59B TYR* 2.9 61.8 + - + +
61B ILE* 4.1 18.3 - - + +
124B LYS* 1.3 72.8 - - - +
126B THR* 1.3 60.3 + - - +
199B MET* 3.7 39.5 - - + -
200B LYS 3.4 16.8 - - - +
201B MET* 3.8 35.9 - - + +
213B PHE* 4.9 6.3 - - + -
216B LEU* 5.8 0.7 - - + -
218B LEU* 5.4 0.7 - - + -
260B MET* 3.9 13.7 - - + -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.8 19.5 - - + -
57B ARG 4.4 1.3 - - - -
58B THR* 4.5 10.8 - - + +
124B LYS* 4.2 5.7 + - - +
125B ILE* 1.3 73.8 - - - +
127B GLY* 1.3 58.1 - - - +
128B ASN* 3.5 20.0 - - - +
199B MET* 3.4 6.1 - - - +
200B LYS* 2.7 62.8 + - - +
213B PHE* 4.5 2.2 - - - -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.8 2.6 - - - +
56B LEU* 3.3 23.4 + - - +
57B ARG 3.3 18.1 + - - +
126B THR* 1.3 74.9 - - - +
128B ASN* 1.3 63.0 + - - -
197B ILE* 4.3 6.7 - - - -
198B LEU 3.6 5.8 - - - -
199B MET* 4.1 3.8 - - - -
213B PHE* 3.6 21.8 - - - -
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.8 40.5 + - + +
54B ALA 3.6 4.5 - - - +
55B LEU* 3.9 19.0 - - - +
126B THR* 3.5 21.9 - - - +
127B GLY* 1.3 75.3 + - - -
129B LEU* 1.3 59.7 + - - +
197B ILE* 3.7 5.0 - - - -
198B LEU* 2.8 53.4 + - + +
200B LYS* 5.2 6.8 - - - +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.4 21.0 - - - +
54B ALA* 2.8 31.4 + - + +
56B LEU* 4.7 16.3 - - + +
127B GLY 4.3 0.8 + - - -
128B ASN* 1.3 69.6 - - - +
130B VAL* 1.3 72.1 + - - +
131B GLN* 3.8 15.6 + - + +
193B PHE 5.4 2.2 - - - +
194B ASN* 5.7 2.0 - - - +
196B MET 4.8 3.1 - - - +
197B ILE* 3.8 25.1 - - + +
210B LYS* 4.2 22.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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