Contacts of the strand formed by residues 154 - 163 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25K SER 3.2 9.0 - - - -
26K GLU* 3.7 12.5 + - - -
33K ALA* 4.4 3.1 - - - -
81L ILE* 3.3 6.2 - - - +
82L SER 2.9 33.6 + - - -
89L ILE* 3.5 7.4 - - - +
148L HIS* 3.9 9.2 - - - -
150L VAL* 3.8 3.9 - - - +
153L LEU* 1.3 75.7 - - - +
155L CYS* 1.3 60.8 + - - -
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Residues in contact with CYS 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K SER* 3.0 28.2 - - - -
25K SER 2.8 12.4 + - - -
33K ALA* 3.7 26.9 - - + +
34K PHE* 3.8 24.2 - - - -
37K ALA* 3.8 16.6 - - - +
79L TYR* 4.5 2.7 - - - -
80L ILE 3.2 11.9 - - - +
81L ILE* 4.0 13.5 - - + -
89L ILE* 4.0 2.6 - - - +
148L HIS* 4.3 2.9 - - - +
154L GLY* 1.3 74.8 - - - +
156L ALA* 1.3 69.6 + - - +
157L PHE* 4.5 1.8 - - - -
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Residues in contact with ALA 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K GLY 3.8 3.8 - - - -
24K SER* 4.2 1.8 - - - -
79L TYR* 3.2 6.9 - - - +
80L ILE* 3.0 45.0 + - + +
89L ILE* 3.8 27.1 - - + +
90L SER* 3.9 12.6 - - - -
91L ALA* 3.7 4.2 - - + +
146L VAL* 4.3 7.9 - - + +
148L HIS* 4.5 5.6 - - + -
155L CYS* 1.3 72.9 - - - +
157L PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL* 4.5 1.3 - - + -
22K ALA* 3.2 2.6 - - - -
23K GLY 2.9 38.0 + - - +
34K PHE* 4.0 12.3 - + - -
37K ALA* 3.9 15.0 - - + -
38K LEU* 3.5 32.5 - - + -
41K ALA* 4.1 17.7 - - + -
43K ILE* 3.6 26.2 - - + -
48K LEU* 3.8 9.4 - - + -
77L TYR* 3.6 28.5 - + + -
78L GLY 3.5 11.0 - - - -
79L TYR* 4.1 4.5 - - + -
91L ALA* 3.8 3.7 - - - +
146L VAL* 3.3 5.3 - - - +
155L CYS* 4.5 2.0 - - - -
156L ALA* 1.3 75.8 - - - +
158L ALA* 1.3 63.4 + - - +
159L ALA* 3.5 23.8 - - + -
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Residues in contact with ALA 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL 3.4 8.7 - - - +
22K ALA* 4.2 6.7 - - + -
77L TYR* 3.2 4.4 - - - +
78L GLY 2.9 32.9 + - - +
91L ALA* 3.7 5.2 - - + +
92L ALA* 3.6 42.8 - - - +
93L ILE* 3.9 8.8 - - + +
144L ILE 4.6 0.9 - - - +
157L PHE* 1.3 77.5 - - - +
159L ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K SER 3.6 0.2 - - - +
20K LEU* 3.3 4.2 - - - -
21K VAL* 2.8 45.1 + - + +
43K ILE* 4.5 0.7 - - + -
75L THR* 3.5 12.6 - - + -
76L ALA 3.2 11.7 - - - +
77L TYR* 3.5 4.3 - - + -
93L ILE* 3.7 10.8 - - - +
157L PHE* 3.5 26.9 - - + -
158L ALA* 1.3 76.3 - - - +
160L ALA* 1.3 61.2 - - - +
161L ALA 4.0 0.7 - - - -
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Residues in contact with ALA 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K VAL* 3.9 12.8 - - + -
19K SER 3.3 6.5 - - - -
20K LEU* 3.7 18.8 - - + -
75L THR* 3.5 3.8 - - - -
76L ALA* 2.8 30.7 + - + +
93L ILE* 3.9 2.4 - - + +
107L ILE* 3.8 32.1 - - + -
159L ALA* 1.3 73.4 - - - +
161L ALA* 1.3 61.8 + - - +
162L LEU* 3.6 5.5 - - - +
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Residues in contact with ALA 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K THR 3.8 0.5 - - - +
18K VAL* 3.3 2.9 - - - -
19K SER* 2.8 42.3 + - - +
21K VAL* 5.3 4.7 - - + -
43K ILE* 5.1 9.2 - - + -
48K LEU* 5.9 0.2 - - + -
64L LEU* 4.6 19.1 - - + -
67L LEU* 5.6 1.8 - - + -
73L VAL* 3.9 18.4 - - + -
74L PRO 3.9 4.0 - - - -
75L THR* 4.1 9.9 - - + +
159L ALA 4.0 0.6 - - - -
160L ALA* 1.3 71.4 - - - +
162L LEU* 1.3 63.4 + - - +
163L TRP* 3.9 3.0 + - + +
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Residues in contact with LEU 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I ASN* 3.9 9.2 - - - +
72J LEU* 4.6 2.5 - - + -
15K PRO* 3.8 28.2 - - + +
17K THR 3.3 9.6 - - - +
18K VAL* 4.2 7.6 - - + -
51K ILE* 3.8 30.5 - - + -
54L ILE 3.9 17.0 - - - +
55L MET* 5.6 0.4 - - - -
56L PRO* 4.4 10.3 - - + -
73L VAL* 3.5 7.1 - - - +
74L PRO* 2.9 41.2 + - + +
107L ILE* 4.1 16.6 - - + -
160L ALA 3.6 15.9 - - - +
161L ALA* 1.3 72.8 - - - +
163L TRP* 1.3 63.9 + - - +
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Residues in contact with TRP 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 4.6 6.1 - + - -
14G LEU* 5.9 0.2 - - + -
9I HIS* 4.0 27.4 - + - -
11K TYR* 3.6 32.9 + + - -
15K PRO* 3.3 3.7 - - - +
16K ASN 2.9 25.3 + - - -
17K THR* 2.9 25.2 + - - +
65L PRO* 4.0 17.5 - - + -
66L LYS 5.4 1.4 + - - -
67L LEU* 3.4 30.2 - - + +
68L PRO* 4.3 14.1 - - + +
71L ALA* 3.9 24.0 - - + -
72L LEU 3.7 22.0 - - - -
73L VAL* 4.1 15.5 - - + -
74L PRO* 4.5 2.0 - - + -
161L ALA* 3.9 3.5 + - + +
162L LEU* 1.3 84.3 - - - +
164L TYR* 1.3 90.2 + + - +
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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