Contacts of the strand formed by residues 154 - 163 (chain D) in PDB entry 1N13
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 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C SER 3.3 9.6 - - - -
26C GLU* 3.8 11.9 + - - -
33C ALA* 4.4 3.4 - - - -
81D ILE* 3.2 5.9 - - - +
82D SER 2.9 34.6 + - - -
89D ILE* 3.5 8.1 - - - +
148D HIS* 3.9 8.3 - - - -
150D VAL* 3.9 3.5 - - - +
153D LEU* 1.3 75.4 - - - +
155D CYS* 1.3 60.3 + - - -
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Residues in contact with CYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C SER* 3.1 27.5 - - - -
25C SER 2.9 10.8 + - - -
33C ALA* 3.7 23.8 - - + +
34C PHE* 3.8 29.8 - - - -
37C ALA* 3.9 10.7 - - - +
79D TYR* 4.4 4.0 - - - -
80D ILE 3.2 9.9 - - - +
81D ILE* 3.9 16.4 - - + -
89D ILE* 4.0 2.7 - - - +
148D HIS* 4.4 2.1 - - - -
154D GLY* 1.3 75.4 - - - +
156D ALA* 1.3 71.7 + - - +
157D PHE* 4.4 0.7 - - - -
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY 3.8 3.8 - - - -
24C SER* 4.2 2.2 - - - -
79D TYR* 3.1 6.8 - - - +
80D ILE* 3.0 45.9 + - + -
89D ILE* 3.7 25.2 - - + +
90D SER* 3.9 12.8 - - - -
91D ALA* 3.7 4.5 - - - +
146D VAL* 4.4 7.0 - - + +
148D HIS* 4.5 4.9 - - + -
155D CYS* 1.3 74.2 - - - +
157D PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.6 0.7 - - + -
22C ALA* 3.2 2.8 - - - -
23C GLY 2.8 41.4 + - - +
34C PHE* 3.9 13.5 - + - -
37C ALA* 3.8 15.5 - - + -
38C LEU* 3.6 31.9 - - + -
41C ALA* 4.1 19.3 - - + -
43C ILE* 3.7 28.7 - - + -
48C LEU* 3.9 9.6 - - + -
77D TYR* 3.6 26.2 - + + -
78D GLY 3.5 13.5 - - - -
79D TYR* 4.1 4.7 - - + -
91D ALA* 3.7 4.1 - - - +
146D VAL* 3.4 5.3 - - - +
155D CYS* 4.4 1.3 - - - -
156D ALA* 1.3 76.9 - - - +
158D ALA* 1.3 59.9 + - - +
159D ALA* 3.5 25.6 - - + -
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL 3.4 8.7 - - - +
22C ALA* 4.0 7.6 - - + -
77D TYR* 3.3 4.1 - - - +
78D GLY 2.9 31.2 + - - +
91D ALA* 3.7 5.1 - - + +
92D ALA* 3.5 44.9 - - - +
93D ILE* 3.8 8.0 - - + +
144D ILE 4.6 0.7 - - - +
157D PHE* 1.3 76.7 - - - +
159D ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER 3.6 0.4 - - - +
20C LEU* 3.4 3.8 - - - -
21C VAL* 2.8 45.3 + - + +
43C ILE* 4.3 0.9 - - + -
75D THR* 3.6 12.1 - - + -
76D ALA 3.2 11.7 - - - +
77D TYR* 3.5 11.7 - - + -
93D ILE* 3.8 11.4 - - - +
157D PHE* 3.5 20.4 - - + -
158D ALA* 1.3 75.6 - - - +
160D ALA* 1.3 60.6 + - - +
161D ALA 4.0 0.4 - - - -
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.0 6.1 - - + -
19C SER 3.3 5.8 - - - -
20C LEU* 3.6 19.7 - - + -
75D THR* 3.4 3.6 - - - -
76D ALA* 2.8 30.9 + - + +
93D ILE* 3.8 1.5 - - + +
107D ILE* 3.6 39.5 - - + -
159D ALA* 1.3 73.6 - - - +
161D ALA* 1.3 61.1 + - - +
162D LEU* 3.7 5.8 - - - +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR 4.4 0.2 - - - -
18C VAL* 3.3 2.9 - - - -
19C SER* 2.8 41.3 + - - +
21C VAL* 5.5 2.0 - - + -
43C ILE* 4.9 12.3 - - + -
64D LEU* 4.5 18.8 - - + -
67D LEU* 5.5 1.6 - - + -
73D VAL* 3.8 19.5 - - + -
74D PRO 3.8 4.3 - - - -
75D THR* 4.2 9.0 - - + +
159D ALA 4.0 0.4 - - - -
160D ALA* 1.3 72.0 - - - +
162D LEU* 1.3 61.9 + - - +
163D TRP* 3.8 3.4 + - + +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.8 21.1 - - + -
17C THR 3.3 4.7 - - - +
18C VAL* 4.1 15.5 - - + -
51C ILE* 3.6 27.4 - - + -
54D ILE 3.8 20.0 - - - +
56D PRO* 4.3 10.3 - - + -
73D VAL* 3.5 3.8 - - - +
74D PRO* 2.9 43.2 + - + +
107D ILE* 4.1 17.0 - - + -
160D ALA 3.7 13.7 - - - +
161D ALA* 1.3 72.8 - - - +
163D TRP* 1.3 67.1 + - - +
47E ASN* 3.9 14.4 - - - +
72F LEU* 4.9 2.7 - - + -
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Residues in contact with TRP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.4 7.6 - + - -
11C TYR* 3.8 30.5 + + - -
15C PRO* 3.3 4.2 - - - +
16C ASN 2.9 24.9 + - - -
17C THR* 2.9 23.7 + - - +
65D PRO* 4.0 16.6 - - + -
66D LYS 5.3 1.7 + - - -
67D LEU* 3.5 30.6 - - + +
68D PRO* 4.2 16.7 - - + +
71D ALA* 3.7 24.0 - - + -
72D LEU 3.7 22.7 - - - -
73D VAL* 4.1 14.4 - - + -
74D PRO* 4.4 2.7 - - + -
161D ALA* 3.8 4.3 + - + +
162D LEU* 1.3 86.3 - - - +
164D TYR* 1.3 90.0 + + - +
9E HIS* 3.7 28.0 - + - -
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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