Contacts of the strand formed by residues 17 - 26 (chain C) in PDB entry 6D2P
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 SER 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C CYS 3.3 7.6 + - - -
16C SER* 1.3 73.9 - - - +
18C ASN* 1.3 63.8 + - - +
57C VAL* 5.5 0.3 - - - +
64C LEU* 3.8 37.0 - - - +
65C ASN* 3.6 17.9 + - - +
96C GLU* 3.8 5.5 - - - +
97C ILE* 3.0 35.7 + - - +
149C PHE* 5.4 0.5 - - - -
201C GOL 3.2 19.9 - - - -
202C GOL 4.3 5.8 - - - -
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Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER* 1.3 76.7 - - - +
19C ILE* 1.3 64.4 + - - +
20C THR* 3.1 5.7 + - + +
64C LEU* 3.8 1.0 - - - -
65C ASN* 3.0 39.4 + - - +
94C SER* 3.5 26.4 + - - -
95C VAL 3.4 3.4 - - - +
96C GLU* 3.3 38.6 - - - +
202C GOL 2.3 45.3 + - - +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER 4.0 0.4 - - - -
18C ASN* 1.3 68.0 - - - +
20C THR* 1.3 60.7 + - - +
21C GLY 3.6 21.8 - - - +
22C LEU* 5.4 0.4 - - + -
62C LEU* 3.8 23.8 - - + -
63C PHE 3.6 6.3 - - - +
64C LEU* 4.2 10.3 - - + -
91C LEU* 3.4 16.5 - - + +
94C SER* 3.3 6.1 - - - -
95C VAL* 2.9 41.8 + - + +
97C ILE* 3.8 18.2 - - + -
107C ILE* 3.7 31.4 - - + -
112C TRP* 4.0 23.6 - - + -
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASN* 3.5 13.9 - - + +
19C ILE* 1.3 74.1 - - - +
21C GLY* 1.3 56.5 + - - +
53C ILE* 4.5 1.4 + - - +
63C PHE* 2.8 17.7 + - - +
65C ASN* 4.1 3.6 - - - -
66C GLY* 2.7 52.2 + - - +
67C SER 3.4 11.9 + - - +
68C LEU* 3.7 27.2 - - + +
90C GLN* 4.0 1.9 - - - +
91C LEU* 3.1 23.6 + - - +
94C SER* 4.2 7.4 - - - -
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.4 13.9 - - - +
20C THR* 1.3 81.5 - - - +
22C LEU* 1.3 66.6 + - - +
53C ILE* 4.7 0.7 - - - -
62C LEU* 3.6 0.3 - - - -
63C PHE* 2.8 31.4 + - - +
89C VAL 3.1 13.7 - - - -
90C GLN* 4.4 0.4 - - - -
91C LEU* 3.8 12.5 - - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 5.4 0.7 - - + -
21C GLY* 1.3 76.1 - - - +
23C ILE* 1.3 62.3 + - - +
24C LEU* 3.6 35.4 - - + -
61C GLN 3.3 16.2 - - - +
62C LEU* 3.6 9.4 - - + -
63C PHE* 3.6 12.7 - - - -
88C CYS 4.0 0.2 - - - -
89C VAL* 2.8 55.2 + - + +
91C LEU* 5.5 2.9 - - + -
112C TRP* 3.5 36.3 - - + -
116C LEU* 5.1 1.6 - - + -
119C ILE* 4.1 16.6 - - + -
164C PHE* 4.5 9.0 - - + -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 1.3 78.0 - - - +
24C LEU* 1.3 71.0 + - - +
40C PRO* 3.9 2.9 - - - +
41C SER* 3.1 31.2 + - - +
47C ASP* 3.7 35.4 - - + +
48C ILE* 4.0 8.7 - - + +
51C CYS* 4.0 9.0 - - - -
60C THR 3.7 22.2 - - - +
61C GLN* 3.2 15.3 + - - +
63C PHE* 4.3 9.4 - - + -
86C SER* 3.6 26.2 - - - -
87C ILE 3.5 10.8 - - - +
164C PHE* 5.8 0.5 - - - -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.6 27.8 - - + -
23C ILE* 1.3 80.6 - - - +
25C THR* 1.3 63.5 + - - +
26C ARG 4.3 0.2 - - - -
38C PHE* 4.0 18.4 - - + -
39C ARG 3.2 22.9 - - - +
40C PRO 4.2 0.4 - - - -
41C SER* 3.9 2.9 - - - +
86C SER* 3.4 8.1 - - - -
87C ILE* 2.8 44.3 + - + +
89C VAL* 4.3 11.0 - - + -
119C ILE* 4.6 6.3 - - + -
123C LEU* 4.7 3.6 - - + -
134C PHE* 3.6 27.6 - - + -
164C PHE* 3.9 22.0 - - + -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 1.3 74.7 + - - +
26C ARG* 1.3 75.7 + - - +
27C GLN* 3.6 1.4 + - - -
38C PHE* 3.6 4.3 - - - -
39C ARG* 2.8 38.4 + - + +
40C PRO 4.3 2.2 - - - -
41C SER* 3.2 8.5 + - - -
42C GLY* 3.0 27.4 + - - +
43C GLY 4.7 0.2 + - - -
83C ASN 4.0 11.0 - - - +
85C LYS 5.4 1.7 - - - +
86C SER* 3.8 8.9 + - - +
50H TRP* 4.1 14.1 - - + -
58H THR 5.3 2.2 - - - +
59H ASN* 3.8 19.1 - - + +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU 4.3 0.2 - - - -
25C THR* 1.3 72.1 - - - +
27C GLN* 1.3 76.3 + - - +
28C GLY* 5.1 0.6 - - - -
29C GLY 5.8 1.2 + - - -
36C VAL* 3.7 28.5 - - + +
37C ILE 3.5 6.7 - - - +
38C PHE* 3.8 14.7 - - + -
80C TRP 3.6 10.6 + - - -
81C ARG* 3.3 20.4 + - - +
82C ASP 5.5 0.2 + - - -
83C ASN* 3.5 30.4 + - + +
85C LYS 5.5 2.0 + - - -
87C ILE* 4.5 10.0 - - + +
127C TYR* 3.2 39.5 + - - -
59H ASN* 3.0 18.5 + - - -
96L GLY* 2.9 39.5 + - - -
97L SER* 5.4 0.2 - - - -
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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