Contacts of the strand formed by residues 154 - 163 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G SER 3.3 9.4 - - - -
26G GLU* 3.6 11.9 + - - -
33G ALA* 4.4 3.1 - - - -
81H ILE* 3.3 6.6 - - - +
82H SER 3.0 33.3 + - - -
89H ILE* 3.6 7.9 - - - +
148H HIS* 3.8 8.3 - - - -
150H VAL* 3.9 4.1 - - - +
153H LEU* 1.3 75.3 - - - +
155H CYS* 1.3 60.4 + - - -
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Residues in contact with CYS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G SER* 3.1 27.5 - - - -
25G SER 2.8 12.6 + - - -
33G ALA* 3.7 22.9 - - + +
34G PHE* 3.8 24.2 - - - -
37G ALA* 3.7 18.2 - - - +
79H TYR* 4.4 3.6 - - - -
80H ILE 3.2 10.1 - - - +
81H ILE* 3.8 16.8 - - + -
89H ILE* 4.1 2.9 - - - +
148H HIS* 4.3 2.3 - - - -
154H GLY* 1.3 74.8 - - - +
156H ALA* 1.3 72.1 + - - +
157H PHE* 4.4 0.4 - - - -
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLY 3.8 4.0 - - - -
24G SER* 4.3 2.0 - - - -
79H TYR* 3.1 6.9 - - - +
80H ILE* 2.9 45.8 + - + -
89H ILE* 3.8 27.0 - - + +
90H SER* 3.9 13.0 - - - -
91H ALA* 3.7 4.7 - - + +
146H VAL* 4.3 7.2 - - + +
148H HIS* 4.5 5.6 - - + +
155H CYS* 1.3 73.0 - - - +
157H PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G VAL* 4.6 0.7 - - + -
22G ALA* 3.1 5.4 - - - +
23G GLY 2.8 41.8 + - - +
34G PHE* 3.9 13.5 - + - -
37G ALA* 3.8 15.0 - - + -
38G LEU* 3.4 33.9 - - + -
41G ALA* 4.0 21.5 - - + -
43G ILE* 3.7 24.5 - - + -
48G LEU* 3.9 7.9 - - + -
77H TYR* 3.6 26.9 - + + -
78H GLY 3.5 10.1 - - - -
79H TYR* 4.1 5.4 - - + -
91H ALA* 3.7 3.5 - - - +
146H VAL* 3.5 2.5 - - - +
155H CYS* 4.4 1.1 - - - -
156H ALA* 1.3 76.3 - - - +
158H ALA* 1.3 63.8 + - - +
159H ALA* 3.5 26.7 - - + -
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Residues in contact with ALA 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G VAL 3.5 8.5 - - - +
22G ALA* 4.2 6.5 - - + -
77H TYR* 3.3 3.9 - - - +
78H GLY 2.9 33.7 + - - +
91H ALA* 3.6 7.0 - - + +
92H ALA* 3.5 43.5 - - - +
93H ILE* 3.9 8.4 - - + +
144H ILE 4.7 0.4 - - - +
157H PHE* 1.3 76.5 - - - +
159H ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER 4.3 0.2 - - - -
20G LEU* 3.4 4.2 - - - -
21G VAL* 2.8 44.7 + - + +
43G ILE* 4.3 0.7 - - + -
75H THR* 3.6 11.9 - - + -
76H ALA 3.2 11.9 - - - +
77H TYR* 3.5 11.7 - - + -
93H ILE* 3.7 12.1 - - - +
157H PHE* 3.5 20.4 - - + -
158H ALA* 1.3 76.1 - - - +
160H ALA* 1.3 60.7 + - - +
161H ALA 4.0 0.4 - - - -
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Residues in contact with ALA 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G VAL* 4.1 7.0 - - + -
19G SER 3.3 6.1 - - - -
20G LEU* 3.7 16.8 - - + -
74H PRO 4.1 0.2 - - - +
75H THR* 3.4 3.6 - - - -
76H ALA* 2.8 30.8 + - + +
93H ILE* 3.9 2.4 - - + +
107H ILE* 3.7 41.5 - - + -
159H ALA* 1.3 74.0 - - - +
161H ALA* 1.3 62.0 + - - +
162H LEU* 3.8 4.4 + - - +
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Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G THR 3.8 0.5 - - - +
18G VAL* 3.4 3.1 - - - -
19G SER* 2.8 37.9 + - - +
21G VAL* 5.4 2.0 - - + -
43G ILE* 5.0 12.6 - - + -
48G LEU* 6.0 0.2 - - + -
64H LEU* 4.4 20.9 - - + -
65H PRO* 6.1 0.2 - - - +
67H LEU* 5.5 0.7 - - + -
73H VAL* 4.0 18.2 - - + -
74H PRO 3.9 4.0 - - - -
75H THR* 4.2 9.9 - - + +
159H ALA 4.0 1.0 - - - -
160H ALA* 1.3 71.6 - - - +
162H LEU* 1.3 63.6 + - - +
163H TRP* 3.9 3.3 + - + +
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 3.8 24.5 - - + -
17G THR 3.3 2.7 - - - +
18G VAL* 3.4 31.2 - - + -
51G ILE* 3.6 25.1 - - + -
54H ILE 4.0 6.7 - - - +
56H PRO* 4.7 5.2 - - + -
73H VAL* 3.5 6.9 - - - +
74H PRO* 2.8 49.5 + - + +
107H ILE* 4.1 18.8 - - + -
160H ALA 4.6 2.2 - - - +
161H ALA* 1.3 72.6 - - - +
163H TRP* 1.3 64.0 + - - +
47K ASN* 3.9 19.1 - - - +
72L LEU* 4.4 2.0 - - + -
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Residues in contact with TRP 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 3.3 4.5 - - - +
16G ASN 3.0 23.4 + - - -
17G THR* 3.0 24.9 + - - +
65H PRO* 4.4 18.6 - - + -
66H LYS 5.3 1.4 + - - -
67H LEU* 3.4 29.0 - - + +
68H PRO* 4.4 13.9 - - + +
71H ALA* 3.8 25.8 - - + -
72H LEU 3.4 24.2 - - - -
73H VAL* 4.0 15.3 - - + -
74H PRO* 4.4 1.3 - - + -
161H ALA* 3.9 3.3 + - + +
162H LEU* 1.3 82.9 - - - +
164H TYR* 1.3 97.6 + + - +
11I TYR* 4.0 43.0 - + + -
14I LEU* 5.9 0.4 - - + -
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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