Contacts of the strand formed by residues 109 - 121 (chain B) in PDB entry 1K4R
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
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Residue Dist Surf HB Arom Phob DC
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75B PRO* 3.7 9.5 - - - +
98B ASP* 3.7 3.3 - - - -
99B ARG* 2.8 35.3 + - - +
107B LEU 3.8 3.2 + - - -
108B PHE* 1.3 74.2 - - - +
110B LYS* 1.3 65.3 + - - -
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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
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75B PRO* 3.4 21.1 - - - +
96B GLN* 3.9 46.0 + - + +
97B SER* 3.4 7.4 - - - +
98B ASP* 2.8 33.1 + - - +
109B GLY* 1.3 72.0 - - - -
111B GLY* 1.3 59.5 + - - +
7C GLU* 5.3 4.0 + - - -
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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
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73B ARG 3.3 15.5 - - - -
74B CYS 4.3 0.9 - - - -
75B PRO* 4.1 5.6 - - - -
96B GLN* 3.2 7.4 - - - -
97B SER* 2.8 38.6 + - - -
99B ARG* 4.0 9.8 - - - +
109B GLY 3.7 1.6 + - - -
110B LYS* 1.3 75.0 - - - +
112B SER* 1.3 64.6 + - - -
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Residues in contact with SER 112 (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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72B ALA* 3.2 3.5 - - - +
73B ARG* 2.8 34.4 + - - +
74B CYS 5.0 0.6 + - - -
78B GLY 3.7 14.7 + - - -
79B PRO* 3.9 4.3 - - - -
80B ALA* 2.7 33.7 + - - +
94B ARG* 3.5 13.0 + - - -
95B ASP 3.9 7.0 + - - -
96B GLN* 4.7 4.0 - - - +
97B SER* 5.2 0.2 + - - -
111B GLY* 1.3 72.6 - - - -
113B ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 113 (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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70B VAL* 3.9 14.1 - - + -
71B ALA 3.3 11.4 - - - +
72B ALA* 4.1 3.4 - - + -
80B ALA* 4.2 1.6 - - - -
94B ARG* 3.4 3.1 - - - +
95B ASP* 2.8 51.9 + - + +
96B GLN* 3.7 7.6 - - - +
97B SER* 4.0 8.3 - - - +
112B SER* 1.3 77.9 + - - +
114B VAL* 1.3 65.5 + - - +
247B PRO* 4.0 20.6 - - + -
249B ALA 3.8 20.6 - - - +
250B VAL* 3.8 6.5 - - - -
251B LYS 3.8 29.8 - - - +
252B MET* 4.3 8.7 - - + -
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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
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70B VAL* 3.3 3.7 - - - +
71B ALA* 2.9 52.8 + - + +
80B ALA 3.8 21.3 - - - +
81B THR 4.0 1.8 - - - +
82B LEU* 3.7 11.3 - - + +
85B GLU* 3.7 31.0 - - + +
92B CYS* 4.5 1.8 - - + -
93B LYS 3.3 13.9 - - - +
94B ARG* 3.8 18.4 - - + +
113B ILE* 1.3 75.8 - - - +
115B ALA* 1.3 67.3 + - - +
116B CYS* 4.4 4.5 - - - -
252B MET* 4.0 1.6 - - - -
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Residues in contact with ALA 115 (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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68B THR* 5.5 0.7 - - + -
69B LYS 3.2 9.6 - - - +
70B VAL* 3.9 15.7 - - + -
92B CYS* 3.1 3.5 - - - +
93B LYS 2.9 31.9 + - - -
114B VAL* 1.3 73.2 - - - +
116B CYS* 1.3 62.7 + - - +
244B PHE* 3.9 16.4 - - + -
252B MET* 3.2 31.3 - - + +
254B VAL* 5.0 3.4 - - + -
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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
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67B ASP 3.8 1.8 - - - +
68B THR* 3.4 6.0 - - - +
69B LYS* 2.8 32.8 + - + +
82B LEU* 3.8 19.7 - - + -
84B GLU* 3.8 27.4 - - + -
85B GLU* 4.0 10.8 - - - -
90B THR* 4.8 0.7 - - - -
91B VAL 3.2 6.1 - - - -
92B CYS* 2.0 45.5 - - - -
114B VAL* 4.4 0.7 - - - -
115B ALA* 1.3 74.3 - - - +
117B VAL* 1.3 63.6 + - - +
244B PHE* 4.9 1.8 - - - -
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Residues in contact with VAL 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 LEU* 4.4 23.8 - - + -
66B SER 3.8 7.4 - - - +
67B ASP 4.4 1.8 - - - -
68B THR* 3.3 34.3 - - + +
84B GLU* 6.3 0.4 - - - -
90B THR* 3.1 6.3 - - - -
91B VAL* 2.8 46.0 + - + +
116B CYS* 1.3 77.2 - - - +
118B LYS* 1.3 68.1 + - - +
119B ALA 3.6 0.2 + - - -
242B VAL* 4.5 2.0 - - + -
244B PHE* 4.4 5.8 - - + -
254B VAL* 3.8 30.1 - - + -
208C HIS* 4.7 0.9 - - + -
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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
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64B LYS 3.7 0.9 - - - +
65B LEU* 3.3 7.8 - - - +
66B SER* 2.9 47.6 + - - +
67B ASP* 3.0 38.1 + - + +
69B LYS* 6.3 1.3 - - - -
84B GLU* 5.5 8.3 - - + +
87B GLN* 5.8 2.7 - - - +
89B GLY 3.4 7.2 - - - +
90B THR* 3.9 19.7 - - + -
117B VAL* 1.3 74.3 - - - +
119B ALA* 1.3 58.3 + - - +
120B ALA* 5.7 0.2 - - - -
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Residues in contact with ALA 119 (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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63B ALA* 5.5 2.7 - - + -
64B LYS 3.8 2.7 - - - -
65B LEU* 3.9 15.7 - - + -
89B GLY* 2.9 24.3 + - - +
91B VAL* 3.9 15.5 - - + -
117B VAL 3.6 1.0 + - - +
118B LYS* 1.3 74.1 - - - +
120B ALA* 1.3 61.5 + - - +
234B ASN* 5.6 0.5 - - - +
235B TRP* 4.2 11.6 + - - +
238B ALA* 3.8 28.4 - - + +
242B VAL* 5.3 0.7 - - + -
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Residues in contact with ALA 120 (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* 4.4 1.4 - - - -
63B ALA* 3.4 9.7 - - - +
64B LYS* 2.9 40.4 + - + +
118B LYS 4.2 0.4 - - - -
119B ALA* 1.3 76.4 - - - +
121B CYS* 1.3 64.5 - - - +
235B TRP* 4.1 12.8 - - - +
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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 52.0 - - - -
62B HIS 3.7 2.0 - - - -
64B LYS* 4.1 9.8 - - - +
120B ALA* 1.3 79.2 - - - +
122B GLU* 1.3 72.4 + - - +
123B ALA* 3.6 1.7 + - - -
125B LYS 3.6 16.8 - - - -
126B LYS* 4.5 5.6 - - + -
235B TRP* 3.5 28.3 - - + +
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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