Contacts of the strand formed by residues 154 - 163 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER 3.3 9.4 - - - -
26A GLU* 3.7 11.3 + - - -
33A ALA* 4.3 3.8 - - - -
81B ILE* 3.3 5.5 - - - +
82B SER 3.0 32.9 + - - -
89B ILE* 3.5 8.1 - - - +
148B HIS* 3.7 9.2 - - - -
150B VAL* 3.9 3.5 - - - +
153B LEU* 1.3 75.4 - - - +
155B CYS* 1.3 61.1 + - - -
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Residues in contact with CYS 155 (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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24A SER* 3.1 9.1 - - - -
25A SER 2.9 29.0 + - - -
33A ALA* 3.7 23.3 - - + +
34A PHE* 3.8 30.3 - - - -
37A ALA* 3.9 10.7 - - - +
79B TYR* 4.4 4.3 - - - -
80B ILE 3.2 12.3 - - - +
81B ILE* 3.8 17.0 - - + -
89B ILE* 4.0 3.1 - - - +
148B HIS* 4.2 3.0 - - - -
154B GLY* 1.3 74.6 - - - +
156B ALA* 1.3 69.3 + - - +
157B PHE* 4.4 0.4 - - - -
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Residues in contact with ALA 156 (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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23A GLY 3.8 4.0 - - - -
24A SER* 4.2 2.2 - - - -
79B TYR* 3.1 6.9 - - - +
80B ILE* 3.0 45.4 + - + -
89B ILE* 3.8 27.3 - - + +
90B SER* 3.9 12.3 - - - -
91B ALA* 3.6 4.7 - - - +
146B VAL* 4.4 7.4 - - + +
148B HIS* 4.4 5.6 - - + +
155B CYS* 1.3 73.6 - - - +
157B PHE* 1.3 59.7 + - - +
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Residues in contact with PHE 157 (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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21A VAL* 4.6 0.9 - - + -
22A ALA* 3.2 2.8 - - - -
23A GLY 2.9 41.3 + - - +
34A PHE* 3.9 13.7 - + - -
37A ALA* 3.8 15.0 - - + -
38A LEU* 3.5 31.0 - - + -
41A ALA* 4.1 20.2 - - + -
43A ILE* 3.8 15.5 - - + -
48A LEU* 3.8 16.4 - - + -
77B TYR* 3.6 26.0 - + + -
78B GLY 3.6 10.1 - - - -
79B TYR* 4.0 4.7 - - + -
91B ALA* 3.8 3.1 - - - +
146B VAL* 3.3 4.8 - - - +
155B CYS* 4.4 1.1 - - - -
156B ALA* 1.3 76.9 - - - +
158B ALA* 1.3 63.1 + - - +
159B ALA* 3.5 29.6 - - + -
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Residues in contact with ALA 158 (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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21A VAL 3.5 8.5 - - - +
22A ALA* 4.1 7.2 - - + -
77B TYR* 3.2 3.9 - - - +
78B GLY 2.9 32.7 + - - +
91B ALA* 3.7 5.8 - - + +
92B ALA* 3.6 36.6 - - - +
93B ILE* 3.4 11.9 - - + +
144B ILE* 4.6 3.1 - - + +
157B PHE* 1.3 76.9 - - - +
159B ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 159 (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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20A LEU* 3.3 6.8 - - - +
21A VAL* 2.8 45.6 + - + +
43A ILE* 4.5 0.7 - - + -
75B THR* 3.6 12.1 - - + -
76B ALA 3.2 12.8 - - - +
77B TYR* 3.5 11.2 - - + -
93B ILE* 3.5 10.2 - - - +
157B PHE* 3.5 19.7 - - + -
158B ALA* 1.3 76.9 - - - +
160B ALA* 1.3 59.6 + - - +
161B ALA 4.0 0.7 - - - -
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Residues in contact with ALA 160 (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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18A VAL* 4.1 5.8 - - + -
19A SER 3.3 6.3 - - - -
20A LEU* 3.7 19.5 - - + -
75B THR* 3.4 3.4 - - - -
76B ALA* 2.8 32.3 + - + +
93B ILE* 4.0 2.0 - - + -
107B ILE* 3.8 38.6 - - + -
159B ALA* 1.3 73.0 - - - +
161B ALA* 1.3 60.8 + - - +
162B LEU* 3.6 5.4 - - - +
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Residues in contact with ALA 161 (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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17A THR 3.8 0.9 - - - +
18A VAL* 3.4 2.9 - - - -
19A SER* 2.8 42.6 + - - +
21A VAL* 5.4 2.2 - - + -
43A ILE* 5.0 11.9 - - + -
64B LEU* 4.3 20.9 - - + -
65B PRO* 6.4 0.2 - - + -
67B LEU* 5.4 1.1 - - + -
73B VAL* 4.0 18.2 - - + -
74B PRO 3.9 4.0 - - - -
75B THR* 4.1 10.1 - - + +
159B ALA 4.0 0.8 - - - -
160B ALA* 1.3 71.0 - - - +
162B LEU* 1.3 63.3 + - - +
163B TRP* 3.9 2.7 + - + +
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Residues in contact with LEU 162 (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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15A PRO* 3.8 28.7 - - + -
17A THR 3.3 4.3 - - - +
18A VAL* 4.1 17.9 - - + -
51A ILE* 4.0 17.0 - - + -
54B ILE 3.7 21.3 - - - +
56B PRO* 4.3 4.7 - - + -
73B VAL* 3.5 4.3 - - - +
74B PRO* 2.9 36.6 + - + +
107B ILE* 4.0 21.5 - - + -
160B ALA 3.6 18.2 - - - +
161B ALA* 1.3 72.8 - - - +
163B TRP* 1.3 66.4 + - - +
47C ASN* 3.8 14.8 - - - +
72D LEU* 4.7 4.7 - - + -
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Residues in contact with TRP 163 (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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15A PRO* 3.3 3.3 - - - +
16A ASN 2.9 25.1 + - - -
17A THR* 3.0 23.9 + - - +
65B PRO* 4.6 17.0 - - + -
66B LYS 5.1 2.2 + - - -
67B LEU* 3.5 30.2 - - + +
68B PRO* 4.3 15.4 - - + +
71B ALA* 3.9 23.1 - - + -
72B LEU 3.5 24.2 - - - -
73B VAL* 4.1 13.5 - - + -
74B PRO* 4.3 1.8 - - + -
161B ALA* 3.9 2.6 + - + +
162B LEU* 1.3 81.8 - - - +
164B TYR* 1.3 99.7 + + - +
11E TYR* 3.8 48.2 - + + -
14E LEU* 6.1 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